Starting phenix.real_space_refine
on Sat May 17 23:55:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hak_34594/05_2025/8hak_34594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hak_34594/05_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_34594/05_2025/8hak_34594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hak_34594/05_2025/8hak_34594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hak_34594/05_2025/8hak_34594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hak_34594/05_2025/8hak_34594.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ARG:plan': 1, 'ALY:plan-2': 2, 'ALY:plan-1': 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: 8.68, per 1000 atoms: 0.53
  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: 3.72
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 6.85
  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: 7.70

  Time building geometry restraints manager: 4.40 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:             1.340
  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:             0.020
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     41.170
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.080
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.630
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.033   0.002   TRP N1129 
 HIS   0.005   0.001   HIS D 109 
 PHE   0.047   0.002   PHE E  67 
 TYR   0.022   0.001   TYR C  50 
 ARG   0.008   0.000   ARG D  99 

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

*********************** 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  : 1.310 
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: 0.2537
  time to fit residues: 70.2967
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  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:   40.0000
   chunk 115 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 138 optimal weight:   40.0000
   overall best weight:    3.3786

-------------------------------------------------------------------------------
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
** N1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN
N1255 HIS
N1379 GLN
** N1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.066254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.044419 restraints weight = 155498.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.045660 restraints weight = 80892.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.046473 restraints weight = 54339.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  17266  Z= 0.262
  Angle     :  0.657   8.016  24572  Z= 0.381
  Chirality :  0.039   0.154   2738
  Planarity :  0.005   0.062   2114
  Dihedral  : 28.816 171.778   4715
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.42 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.22), residues: 1256
  helix:  1.40 (0.18), residues: 757
  sheet:  0.51 (0.74), residues: 55
  loop : -0.36 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP N1122 
 HIS   0.006   0.002   HIS E 113 
 PHE   0.030   0.002   PHE E  67 
 TYR   0.017   0.002   TYR F  98 
 ARG   0.006   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07526 (  831)
  hydrogen bonds       : angle       3.91231 ( 2214)
  covalent geometry    : bond        0.00572 (17266)
  covalent geometry    : angle       0.65686 (24572)

*********************** 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
  161 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8725 (m-10) cc_final: 0.8370 (m-10)
REVERT: A  106 ASP cc_start: 0.9198 (m-30) cc_final: 0.8959 (m-30)
REVERT: C   38 ASN cc_start: 0.8358 (t0) cc_final: 0.7674 (t0)
REVERT: D   68 ASP cc_start: 0.9039 (m-30) cc_final: 0.8822 (m-30)
REVERT: D   86 ARG cc_start: 0.8995 (mmp80) cc_final: 0.8728 (mmp80)
REVERT: D  121 TYR cc_start: 0.8428 (t80) cc_final: 0.8096 (t80)
REVERT: E   97 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8717 (mm-30)
REVERT: E  120 MET cc_start: 0.8679 (tpt) cc_final: 0.8461 (mmm)
REVERT: F   62 LEU cc_start: 0.9720 (mt) cc_final: 0.9503 (mp)
REVERT: F   70 VAL cc_start: 0.9738 (m) cc_final: 0.9478 (m)
REVERT: F   74 GLU cc_start: 0.9176 (pp20) cc_final: 0.8709 (pp20)
REVERT: F   93 GLN cc_start: 0.8842 (tt0) cc_final: 0.8336 (tm-30)
REVERT: G   38 ASN cc_start: 0.8934 (m-40) cc_final: 0.8127 (t0)
REVERT: G   68 ASN cc_start: 0.8987 (m-40) cc_final: 0.8665 (t0)
REVERT: G   72 ASP cc_start: 0.9190 (m-30) cc_final: 0.8694 (m-30)
REVERT: G   74 LYS cc_start: 0.9375 (mmmm) cc_final: 0.9145 (tptp)
REVERT: G   99 ARG cc_start: 0.7688 (tpt90) cc_final: 0.7140 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2719
  time to fit residues: 65.8930
Evaluate side-chains
  114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 99 optimal weight:    6.9990
   chunk 124 optimal weight:    0.6980
   chunk 138 optimal weight:   30.0000
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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**
N1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.066875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.048529 restraints weight = 131132.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.050025 restraints weight = 61491.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.050858 restraints weight = 36947.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  17266  Z= 0.157
  Angle     :  0.569   7.560  24572  Z= 0.332
  Chirality :  0.035   0.158   2738
  Planarity :  0.004   0.066   2114
  Dihedral  : 28.963 178.998   4715
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.23), residues: 1256
  helix:  1.59 (0.18), residues: 758
  sheet:  0.48 (0.68), residues: 60
  loop : -0.28 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP N1509 
 HIS   0.003   0.001   HIS D  49 
 PHE   0.019   0.001   PHE E  67 
 TYR   0.013   0.001   TYR F  98 
 ARG   0.002   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  831)
  hydrogen bonds       : angle       3.60421 ( 2214)
  covalent geometry    : bond        0.00342 (17266)
  covalent geometry    : angle       0.56927 (24572)

*********************** 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
  168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.641 
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: E   97 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8679 (mm-30)
REVERT: F   74 GLU cc_start: 0.8973 (pp20) cc_final: 0.8674 (pp20)
REVERT: G   38 ASN cc_start: 0.8525 (m-40) cc_final: 0.8211 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2751
  time to fit residues: 71.2555
Evaluate side-chains
  108 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 110 optimal weight:   20.0000
   chunk 119 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 137 optimal weight:    0.2980
   chunk 41 optimal weight:    7.9990
   overall best weight:    4.6588

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.059698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.037987 restraints weight = 159431.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.039002 restraints weight = 82644.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.039656 restraints weight = 55592.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.089  17266  Z= 0.332
  Angle     :  0.726   9.805  24572  Z= 0.418
  Chirality :  0.042   0.161   2738
  Planarity :  0.006   0.070   2114
  Dihedral  : 29.870 178.484   4715
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.22), residues: 1256
  helix:  1.13 (0.18), residues: 764
  sheet: -0.02 (0.69), residues: 59
  loop : -0.30 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP N1115 
 HIS   0.008   0.002   HIS B  75 
 PHE   0.021   0.002   PHE D  70 
 TYR   0.019   0.002   TYR G  39 
 ARG   0.028   0.001   ARG G  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09871 (  831)
  hydrogen bonds       : angle       4.21831 ( 2214)
  covalent geometry    : bond        0.00723 (17266)
  covalent geometry    : angle       0.72601 (24572)

*********************** 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
  155 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 1.444 
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   50 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9137 (mm-30)
REVERT: A  106 ASP cc_start: 0.9282 (m-30) cc_final: 0.8842 (m-30)
REVERT: A  120 MET cc_start: 0.8082 (mpp) cc_final: 0.7859 (mpp)
REVERT: B   74 GLU cc_start: 0.9294 (pp20) cc_final: 0.8983 (pp20)
REVERT: B   84 MET cc_start: 0.8775 (tpt) cc_final: 0.8466 (tpp)
REVERT: C   56 GLU cc_start: 0.9332 (pm20) cc_final: 0.9011 (pm20)
REVERT: C  112 GLN cc_start: 0.8976 (mp10) cc_final: 0.8757 (mp10)
REVERT: D   65 PHE cc_start: 0.9719 (t80) cc_final: 0.9407 (t80)
REVERT: D  121 TYR cc_start: 0.9141 (t80) cc_final: 0.8892 (t80)
REVERT: E   90 MET cc_start: 0.9072 (mmp) cc_final: 0.8650 (mmp)
REVERT: E   97 GLU cc_start: 0.9415 (mt-10) cc_final: 0.8793 (mm-30)
REVERT: E  110 CYS cc_start: 0.9648 (m) cc_final: 0.9122 (t)
REVERT: E  120 MET cc_start: 0.9037 (tpt) cc_final: 0.8814 (mmm)
REVERT: F   62 LEU cc_start: 0.9721 (mt) cc_final: 0.9473 (mt)
REVERT: F   88 TYR cc_start: 0.8817 (m-10) cc_final: 0.6351 (m-10)
REVERT: F   93 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8799 (tm-30)
REVERT: G   38 ASN cc_start: 0.9122 (m-40) cc_final: 0.8775 (p0)
REVERT: G   64 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9060 (mm-30)
REVERT: G   90 ASP cc_start: 0.9414 (t0) cc_final: 0.9212 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 155
  average time/residue: 0.2883
  time to fit residues: 66.0537
Evaluate side-chains
  107 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 147 optimal weight:    8.9990
   chunk 137 optimal weight:    0.0970
   chunk 66 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 142 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 111 optimal weight:    7.9990
   chunk 124 optimal weight:    9.9990
   chunk 122 optimal weight:   10.0000
   chunk 130 optimal weight:    0.5980
   overall best weight:    3.3384

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** 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 = 0.3551 r_free = 0.3551 target = 0.060480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.038637 restraints weight = 158436.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.039665 restraints weight = 82419.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.040308 restraints weight = 55331.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4942

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= 0.235
  Angle     :  0.642   9.940  24572  Z= 0.372
  Chirality :  0.038   0.160   2738
  Planarity :  0.005   0.071   2114
  Dihedral  : 30.048 179.474   4715
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.43 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.22), residues: 1256
  helix:  1.24 (0.18), residues: 767
  sheet: -0.03 (0.69), residues: 55
  loop : -0.28 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP N1115 
 HIS   0.007   0.001   HIS E 113 
 PHE   0.027   0.002   PHE E 104 
 TYR   0.019   0.002   TYR C  50 
 ARG   0.013   0.001   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06353 (  831)
  hydrogen bonds       : angle       3.96903 ( 2214)
  covalent geometry    : bond        0.00514 (17266)
  covalent geometry    : angle       0.64175 (24572)

*********************** 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
  142 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9582 (mm-30) cc_final: 0.9168 (mm-30)
REVERT: A   94 GLU cc_start: 0.9145 (tt0) cc_final: 0.8924 (tt0)
REVERT: A  110 CYS cc_start: 0.8821 (t) cc_final: 0.8529 (t)
REVERT: B   74 GLU cc_start: 0.9339 (pp20) cc_final: 0.9076 (pp20)
REVERT: B   84 MET cc_start: 0.8615 (tpt) cc_final: 0.8297 (tpp)
REVERT: C   68 ASN cc_start: 0.9213 (m-40) cc_final: 0.8974 (t0)
REVERT: C   72 ASP cc_start: 0.9183 (m-30) cc_final: 0.8701 (m-30)
REVERT: C   99 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8117 (mmm-85)
REVERT: D   37 TYR cc_start: 0.9332 (m-80) cc_final: 0.8951 (m-80)
REVERT: D   62 MET cc_start: 0.9640 (mmm) cc_final: 0.9388 (mmm)
REVERT: D   65 PHE cc_start: 0.9743 (t80) cc_final: 0.9365 (t80)
REVERT: D   68 ASP cc_start: 0.9103 (m-30) cc_final: 0.8811 (m-30)
REVERT: D  121 TYR cc_start: 0.9030 (t80) cc_final: 0.8820 (t80)
REVERT: E   90 MET cc_start: 0.9186 (mmp) cc_final: 0.8585 (mmp)
REVERT: E   97 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8776 (mm-30)
REVERT: E  110 CYS cc_start: 0.9674 (m) cc_final: 0.9111 (t)
REVERT: E  120 MET cc_start: 0.8872 (tpt) cc_final: 0.8630 (mmm)
REVERT: F   70 VAL cc_start: 0.9749 (m) cc_final: 0.9490 (m)
REVERT: F   74 GLU cc_start: 0.9186 (pp20) cc_final: 0.8648 (pp20)
REVERT: F   84 MET cc_start: 0.8887 (tpt) cc_final: 0.8686 (tpp)
REVERT: F   93 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8382 (tm-30)
REVERT: G   38 ASN cc_start: 0.9103 (m-40) cc_final: 0.8715 (p0)
REVERT: G   39 TYR cc_start: 0.9201 (m-80) cc_final: 0.8754 (m-80)
REVERT: G   74 LYS cc_start: 0.9580 (tptm) cc_final: 0.9368 (mmmm)
  outliers start: 2
  outliers final: 1
  residues processed: 141
  average time/residue: 0.3075
  time to fit residues: 63.3737
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  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 101 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 120 optimal weight:   20.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
E  93 GLN
** F  25 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.061465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.039353 restraints weight = 155865.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.040394 restraints weight = 79801.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.041107 restraints weight = 53124.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.5031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  17266  Z= 0.172
  Angle     :  0.611  10.200  24572  Z= 0.350
  Chirality :  0.036   0.145   2738
  Planarity :  0.005   0.064   2114
  Dihedral  : 29.917 179.870   4715
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.80 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1256
  helix:  1.45 (0.18), residues: 765
  sheet: -0.10 (0.71), residues: 55
  loop : -0.29 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP N1436 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.022   0.002   TYR N1394 
 ARG   0.008   0.000   ARG N1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04818 (  831)
  hydrogen bonds       : angle       3.70937 ( 2214)
  covalent geometry    : bond        0.00372 (17266)
  covalent geometry    : angle       0.61058 (24572)

*********************** 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
  164 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9163 (mm-30)
REVERT: A   94 GLU cc_start: 0.9185 (tt0) cc_final: 0.8913 (tt0)
REVERT: A  105 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9089 (mm-30)
REVERT: A  110 CYS cc_start: 0.8909 (t) cc_final: 0.8637 (t)
REVERT: B   74 GLU cc_start: 0.9370 (pp20) cc_final: 0.9029 (pp20)
REVERT: B   84 MET cc_start: 0.8552 (tpt) cc_final: 0.8243 (tpp)
REVERT: C   56 GLU cc_start: 0.9309 (pm20) cc_final: 0.8972 (pm20)
REVERT: C   68 ASN cc_start: 0.9200 (m-40) cc_final: 0.8765 (t0)
REVERT: C   72 ASP cc_start: 0.9171 (m-30) cc_final: 0.8320 (m-30)
REVERT: C   90 ASP cc_start: 0.9421 (t0) cc_final: 0.9216 (t0)
REVERT: C   99 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8122 (mmm-85)
REVERT: D   62 MET cc_start: 0.9602 (mmm) cc_final: 0.9339 (mmm)
REVERT: D   65 PHE cc_start: 0.9753 (t80) cc_final: 0.9484 (t80)
REVERT: D   68 ASP cc_start: 0.9145 (m-30) cc_final: 0.8860 (m-30)
REVERT: E   97 GLU cc_start: 0.9412 (mt-10) cc_final: 0.8827 (mm-30)
REVERT: E  110 CYS cc_start: 0.9692 (m) cc_final: 0.9167 (t)
REVERT: E  120 MET cc_start: 0.8846 (tpt) cc_final: 0.8535 (mmm)
REVERT: F   63 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8562 (mp0)
REVERT: F   70 VAL cc_start: 0.9741 (m) cc_final: 0.9470 (m)
REVERT: F   74 GLU cc_start: 0.9163 (pp20) cc_final: 0.8630 (pp20)
REVERT: F   84 MET cc_start: 0.8876 (tpt) cc_final: 0.8606 (tpp)
REVERT: F   93 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: G   38 ASN cc_start: 0.8972 (m-40) cc_final: 0.8761 (p0)
REVERT: G   39 TYR cc_start: 0.9143 (m-80) cc_final: 0.8407 (m-80)
REVERT: H   86 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8108 (tpp-160)
REVERT: H   89 ILE cc_start: 0.9424 (mt) cc_final: 0.9183 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.3080
  time to fit residues: 72.3557
Evaluate side-chains
  112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 143 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   chunk 112 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
D 109 HIS
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1173 GLN
** N1389 ASN ** 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 = 0.3478 r_free = 0.3478 target = 0.054911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.033333 restraints weight = 145066.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.034278 restraints weight = 77610.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.034816 restraints weight = 53211.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.5744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  17266  Z= 0.270
  Angle     :  0.675  12.147  24572  Z= 0.386
  Chirality :  0.038   0.169   2738
  Planarity :  0.005   0.061   2114
  Dihedral  : 30.104 179.783   4715
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.22), residues: 1256
  helix:  1.19 (0.18), residues: 765
  sheet: -0.20 (0.70), residues: 55
  loop : -0.34 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP N1436 
 HIS   0.006   0.001   HIS E 113 
 PHE   0.018   0.002   PHE E  67 
 TYR   0.016   0.002   TYR G  39 
 ARG   0.006   0.001   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07872 (  831)
  hydrogen bonds       : angle       4.09634 ( 2214)
  covalent geometry    : bond        0.00588 (17266)
  covalent geometry    : angle       0.67532 (24572)

*********************** 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
  143 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9153 (tt0) cc_final: 0.8502 (pt0)
REVERT: A  110 CYS cc_start: 0.9041 (t) cc_final: 0.8740 (t)
REVERT: B   63 GLU cc_start: 0.9284 (pm20) cc_final: 0.8924 (pm20)
REVERT: B   74 GLU cc_start: 0.9344 (pp20) cc_final: 0.9090 (pp20)
REVERT: B   84 MET cc_start: 0.8653 (tpt) cc_final: 0.8391 (tpp)
REVERT: C   90 ASP cc_start: 0.9357 (t0) cc_final: 0.9152 (t0)
REVERT: D   37 TYR cc_start: 0.9288 (m-80) cc_final: 0.8743 (m-80)
REVERT: D   68 ASP cc_start: 0.9139 (m-30) cc_final: 0.8763 (m-30)
REVERT: D   80 LEU cc_start: 0.9626 (mm) cc_final: 0.9033 (mm)
REVERT: D   86 ARG cc_start: 0.9218 (mmp80) cc_final: 0.8626 (mmp80)
REVERT: E   90 MET cc_start: 0.8946 (mmp) cc_final: 0.8386 (mmm)
REVERT: E   97 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8801 (mm-30)
REVERT: E  110 CYS cc_start: 0.9682 (m) cc_final: 0.9156 (t)
REVERT: E  120 MET cc_start: 0.8797 (tpt) cc_final: 0.8580 (mmm)
REVERT: F   70 VAL cc_start: 0.9739 (m) cc_final: 0.9485 (m)
REVERT: F   74 GLU cc_start: 0.9210 (pp20) cc_final: 0.8677 (pp20)
REVERT: F   87 VAL cc_start: 0.9475 (t) cc_final: 0.9269 (t)
REVERT: F   93 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: G   38 ASN cc_start: 0.9110 (m-40) cc_final: 0.8787 (p0)
REVERT: G   39 TYR cc_start: 0.9270 (m-80) cc_final: 0.8454 (m-80)
REVERT: G   64 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8957 (mm-30)
REVERT: H   86 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8161 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.3080
  time to fit residues: 64.0449
Evaluate side-chains
  96 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 134 optimal weight:    9.9990
   chunk 81 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 150 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0970
   chunk 72 optimal weight:    5.9990
   chunk 142 optimal weight:    0.9980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 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 = 0.3547 r_free = 0.3547 target = 0.060685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.038883 restraints weight = 154919.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.039960 restraints weight = 80124.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.040636 restraints weight = 53798.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  17266  Z= 0.176
  Angle     :  0.633  12.030  24572  Z= 0.360
  Chirality :  0.037   0.162   2738
  Planarity :  0.005   0.061   2114
  Dihedral  : 30.083 177.701   4715
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.23), residues: 1256
  helix:  1.27 (0.18), residues: 768
  sheet: -0.24 (0.71), residues: 55
  loop : -0.32 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP N1436 
 HIS   0.004   0.001   HIS N1638 
 PHE   0.014   0.001   PHE A  67 
 TYR   0.039   0.002   TYR F  88 
 ARG   0.007   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  831)
  hydrogen bonds       : angle       3.85626 ( 2214)
  covalent geometry    : bond        0.00382 (17266)
  covalent geometry    : angle       0.63290 (24572)

*********************** 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
  153 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9605 (mm-30) cc_final: 0.9234 (mm-30)
REVERT: A  105 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9060 (mm-30)
REVERT: A  110 CYS cc_start: 0.8978 (t) cc_final: 0.8693 (t)
REVERT: B   74 GLU cc_start: 0.9306 (pp20) cc_final: 0.9037 (pp20)
REVERT: B   84 MET cc_start: 0.8478 (tpt) cc_final: 0.8161 (tpp)
REVERT: C   56 GLU cc_start: 0.9329 (pm20) cc_final: 0.8985 (pm20)
REVERT: C   68 ASN cc_start: 0.9512 (t0) cc_final: 0.8918 (t0)
REVERT: C   72 ASP cc_start: 0.8958 (m-30) cc_final: 0.8388 (m-30)
REVERT: C   99 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8106 (mmm-85)
REVERT: C  112 GLN cc_start: 0.9105 (mp10) cc_final: 0.8894 (mp10)
REVERT: D   37 TYR cc_start: 0.9336 (m-80) cc_final: 0.9128 (m-80)
REVERT: D   68 ASP cc_start: 0.9129 (m-30) cc_final: 0.8787 (m-30)
REVERT: D   80 LEU cc_start: 0.9679 (mm) cc_final: 0.9134 (mm)
REVERT: D   99 ARG cc_start: 0.9384 (ttm110) cc_final: 0.8926 (ttm110)
REVERT: E   90 MET cc_start: 0.9130 (mmp) cc_final: 0.8828 (mmm)
REVERT: E   97 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8819 (mm-30)
REVERT: E  110 CYS cc_start: 0.9680 (m) cc_final: 0.9137 (t)
REVERT: E  120 MET cc_start: 0.8807 (tpt) cc_final: 0.8546 (mmm)
REVERT: F   63 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8576 (mp0)
REVERT: F   70 VAL cc_start: 0.9726 (m) cc_final: 0.9447 (m)
REVERT: F   74 GLU cc_start: 0.9172 (pp20) cc_final: 0.8627 (pp20)
REVERT: F   87 VAL cc_start: 0.9406 (t) cc_final: 0.9118 (t)
REVERT: F   88 TYR cc_start: 0.8493 (m-80) cc_final: 0.8243 (m-80)
REVERT: F   93 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: G   38 ASN cc_start: 0.9048 (m-40) cc_final: 0.8747 (p0)
REVERT: G   39 TYR cc_start: 0.9250 (m-80) cc_final: 0.8506 (m-80)
REVERT: G   64 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9039 (mm-30)
REVERT: G   90 ASP cc_start: 0.9472 (t0) cc_final: 0.9192 (t0)
REVERT: H   41 VAL cc_start: 0.9465 (t) cc_final: 0.9202 (t)
REVERT: H   86 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8149 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.3107
  time to fit residues: 68.2262
Evaluate side-chains
  115 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:   20.0000
   chunk 142 optimal weight:    0.5980
   chunk 79 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 132 optimal weight:    0.0270
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    2.1244

-------------------------------------------------------------------------------
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 ** 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 = 0.060216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.038489 restraints weight = 156554.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.039566 restraints weight = 81137.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.040177 restraints weight = 54692.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.5964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17266  Z= 0.189
  Angle     :  0.625  10.755  24572  Z= 0.359
  Chirality :  0.037   0.167   2738
  Planarity :  0.005   0.077   2114
  Dihedral  : 29.980 178.822   4715
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.22), residues: 1256
  helix:  1.22 (0.18), residues: 770
  sheet: -0.39 (0.69), residues: 55
  loop : -0.35 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP N1436 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.021   0.002   PHE H  65 
 TYR   0.034   0.002   TYR F  88 
 ARG   0.007   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05423 (  831)
  hydrogen bonds       : angle       3.88424 ( 2214)
  covalent geometry    : bond        0.00411 (17266)
  covalent geometry    : angle       0.62493 (24572)

*********************** 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
  147 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9212 (mm-30)
REVERT: A  105 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9027 (mm-30)
REVERT: A  110 CYS cc_start: 0.8996 (t) cc_final: 0.8733 (t)
REVERT: B   74 GLU cc_start: 0.9285 (pp20) cc_final: 0.9021 (pp20)
REVERT: B   84 MET cc_start: 0.8321 (tpt) cc_final: 0.8084 (tpp)
REVERT: C   68 ASN cc_start: 0.9199 (t0) cc_final: 0.8882 (t0)
REVERT: C   72 ASP cc_start: 0.8549 (m-30) cc_final: 0.8239 (m-30)
REVERT: C  112 GLN cc_start: 0.9152 (mp10) cc_final: 0.8947 (mp10)
REVERT: D   62 MET cc_start: 0.9401 (mmp) cc_final: 0.9139 (mmp)
REVERT: D   68 ASP cc_start: 0.9046 (m-30) cc_final: 0.8674 (m-30)
REVERT: D   80 LEU cc_start: 0.9664 (mm) cc_final: 0.9316 (mm)
REVERT: D   99 ARG cc_start: 0.9357 (ttm110) cc_final: 0.8911 (ttm110)
REVERT: E   90 MET cc_start: 0.9139 (mmp) cc_final: 0.8821 (mmm)
REVERT: E   97 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8801 (mm-30)
REVERT: E  110 CYS cc_start: 0.9674 (m) cc_final: 0.9136 (t)
REVERT: E  120 MET cc_start: 0.8762 (tpt) cc_final: 0.8509 (mmm)
REVERT: F   70 VAL cc_start: 0.9747 (m) cc_final: 0.9474 (m)
REVERT: F   74 GLU cc_start: 0.9156 (pp20) cc_final: 0.8629 (pp20)
REVERT: F   87 VAL cc_start: 0.9468 (t) cc_final: 0.9202 (t)
REVERT: F   88 TYR cc_start: 0.8441 (m-80) cc_final: 0.8106 (m-80)
REVERT: F   93 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: G   38 ASN cc_start: 0.9026 (m-40) cc_final: 0.8783 (p0)
REVERT: G   39 TYR cc_start: 0.8802 (m-80) cc_final: 0.8462 (m-80)
REVERT: G   64 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8883 (mm-30)
REVERT: G   74 LYS cc_start: 0.9580 (mmtm) cc_final: 0.9323 (mmmt)
REVERT: H   86 ARG cc_start: 0.8339 (tpp80) cc_final: 0.8139 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2977
  time to fit residues: 63.9714
Evaluate side-chains
  103 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 119 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 141 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0000
   chunk 151 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.9992

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.061582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.039605 restraints weight = 156771.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.040690 restraints weight = 80037.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.041344 restraints weight = 53549.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.5935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17266  Z= 0.155
  Angle     :  0.627  10.806  24572  Z= 0.355
  Chirality :  0.036   0.172   2738
  Planarity :  0.004   0.061   2114
  Dihedral  : 29.827 177.554   4715
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.22), residues: 1256
  helix:  1.15 (0.18), residues: 769
  sheet: -0.39 (0.70), residues: 55
  loop : -0.28 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP N1436 
 HIS   0.004   0.001   HIS N1638 
 PHE   0.021   0.001   PHE G  25 
 TYR   0.027   0.001   TYR F  88 
 ARG   0.004   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  831)
  hydrogen bonds       : angle       3.81279 ( 2214)
  covalent geometry    : bond        0.00335 (17266)
  covalent geometry    : angle       0.62727 (24572)

********************** 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
  151 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9223 (mm-30)
REVERT: A   94 GLU cc_start: 0.8946 (pt0) cc_final: 0.8596 (pt0)
REVERT: A  105 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9051 (mm-30)
REVERT: A  110 CYS cc_start: 0.9008 (t) cc_final: 0.8732 (t)
REVERT: B   63 GLU cc_start: 0.9258 (pm20) cc_final: 0.8960 (pm20)
REVERT: B   74 GLU cc_start: 0.9322 (pp20) cc_final: 0.9017 (pp20)
REVERT: C   56 GLU cc_start: 0.9258 (pm20) cc_final: 0.9041 (pm20)
REVERT: C   68 ASN cc_start: 0.9060 (t0) cc_final: 0.8771 (t0)
REVERT: D   37 TYR cc_start: 0.9327 (m-80) cc_final: 0.9120 (m-80)
REVERT: D   62 MET cc_start: 0.9388 (mmp) cc_final: 0.9122 (mmp)
REVERT: D   68 ASP cc_start: 0.9153 (m-30) cc_final: 0.8846 (m-30)
REVERT: D   99 ARG cc_start: 0.9358 (ttm110) cc_final: 0.8913 (ttm110)
REVERT: E   90 MET cc_start: 0.9157 (mmp) cc_final: 0.8798 (mmm)
REVERT: E   97 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8820 (mm-30)
REVERT: E  120 MET cc_start: 0.8774 (tpt) cc_final: 0.8498 (mmm)
REVERT: F   63 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8758 (mt-10)
REVERT: F   70 VAL cc_start: 0.9709 (m) cc_final: 0.9426 (m)
REVERT: F   74 GLU cc_start: 0.9123 (pp20) cc_final: 0.8613 (pp20)
REVERT: F   87 VAL cc_start: 0.9438 (t) cc_final: 0.9144 (t)
REVERT: F   88 TYR cc_start: 0.8479 (m-80) cc_final: 0.8018 (m-80)
REVERT: F   93 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: G   38 ASN cc_start: 0.8957 (m-40) cc_final: 0.8718 (p0)
REVERT: G   39 TYR cc_start: 0.8640 (m-80) cc_final: 0.8300 (m-80)
REVERT: G   64 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8913 (mm-30)
REVERT: G   74 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9340 (mmmt)
REVERT: H   41 VAL cc_start: 0.9384 (t) cc_final: 0.8828 (t)
REVERT: H   62 MET cc_start: 0.9367 (tpp) cc_final: 0.8933 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2907
  time to fit residues: 64.2303
Evaluate side-chains
  112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 86 optimal weight:    8.9990
   chunk 135 optimal weight:   30.0000
   chunk 43 optimal weight:    8.9990
   chunk 131 optimal weight:    7.9990
   chunk 105 optimal weight:    0.7980
   overall best weight:    2.3182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.056417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.034459 restraints weight = 144881.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.035393 restraints weight = 77007.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.035980 restraints weight = 53030.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  17266  Z= 0.195
  Angle     :  0.632  10.212  24572  Z= 0.361
  Chirality :  0.037   0.178   2738
  Planarity :  0.005   0.076   2114
  Dihedral  : 29.851 178.652   4715
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.23), residues: 1256
  helix:  1.20 (0.18), residues: 770
  sheet: -0.49 (0.66), residues: 59
  loop : -0.31 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP N1436 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.015   0.001   PHE G  25 
 TYR   0.028   0.002   TYR F  88 
 ARG   0.005   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05603 (  831)
  hydrogen bonds       : angle       3.91842 ( 2214)
  covalent geometry    : bond        0.00426 (17266)
  covalent geometry    : angle       0.63222 (24572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5534.79 seconds
wall clock time: 97 minutes 30.07 seconds (5850.07 seconds total)