Starting phenix.real_space_refine
on Sat Jun 14 15:47:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hak_34594/06_2025/8hak_34594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hak_34594/06_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_34594/06_2025/8hak_34594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hak_34594/06_2025/8hak_34594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hak_34594/06_2025/8hak_34594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hak_34594/06_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-5710/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: 9.44, per 1000 atoms: 0.58
  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: 4.09
  Conformation dependent library (CDL) restraints added in 1.3 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: 6.07
  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: 7.40

  Time building geometry restraints manager: 4.88 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:             0.940
  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:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     42.400
  Find NCS groups from input model:        0.400
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.560
-------------------------------------------------------------------------------
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  : 1.451 
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: 0.2595
  time to fit residues: 71.4321
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  : 1.457 
-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.066334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.044414 restraints weight = 155743.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.045646 restraints weight = 80230.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.046420 restraints weight = 53425.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2358

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= 0.261
  Angle     :  0.656   8.026  24572  Z= 0.380
  Chirality :  0.039   0.146   2738
  Planarity :  0.005   0.063   2114
  Dihedral  : 28.806 171.752   4715
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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        0.07549 (  831)
  hydrogen bonds       : angle       3.91022 ( 2214)
  covalent geometry    : bond        0.00571 (17266)
  covalent geometry    : angle       0.65566 (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  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8723 (m-10) cc_final: 0.8370 (m-10)
REVERT: A  106 ASP cc_start: 0.9199 (m-30) cc_final: 0.8962 (m-30)
REVERT: C   38 ASN cc_start: 0.8357 (t0) cc_final: 0.7675 (t0)
REVERT: D   68 ASP cc_start: 0.9069 (m-30) cc_final: 0.8856 (m-30)
REVERT: D   86 ARG cc_start: 0.8993 (mmp80) cc_final: 0.8724 (mmp80)
REVERT: D  121 TYR cc_start: 0.8408 (t80) cc_final: 0.8081 (t80)
REVERT: E   97 GLU cc_start: 0.9431 (mt-10) cc_final: 0.8629 (mm-30)
REVERT: E  120 MET cc_start: 0.8682 (tpt) cc_final: 0.8438 (mmm)
REVERT: F   62 LEU cc_start: 0.9721 (mt) cc_final: 0.9506 (mp)
REVERT: F   70 VAL cc_start: 0.9724 (m) cc_final: 0.9459 (m)
REVERT: F   74 GLU cc_start: 0.9186 (pp20) cc_final: 0.8712 (pp20)
REVERT: F   93 GLN cc_start: 0.8838 (tt0) cc_final: 0.8336 (tm-30)
REVERT: G   38 ASN cc_start: 0.8935 (m-40) cc_final: 0.8129 (t0)
REVERT: G   68 ASN cc_start: 0.8986 (m-40) cc_final: 0.8673 (t0)
REVERT: G   72 ASP cc_start: 0.9190 (m-30) cc_final: 0.8695 (m-30)
REVERT: G   74 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9172 (tptp)
REVERT: G   99 ARG cc_start: 0.7684 (tpt90) cc_final: 0.7135 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2784
  time to fit residues: 67.1833
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  : 1.323 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 124 optimal weight:    0.1980
   chunk 138 optimal weight:   30.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E  93 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.068056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.046076 restraints weight = 151857.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.047370 restraints weight = 77012.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.048195 restraints weight = 50836.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  17266  Z= 0.139
  Angle     :  0.563   7.169  24572  Z= 0.327
  Chirality :  0.035   0.161   2738
  Planarity :  0.004   0.065   2114
  Dihedral  : 28.870 178.446   4715
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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:  1.29 (0.23), residues: 1256
  helix:  1.55 (0.18), residues: 761
  sheet:  0.38 (0.72), residues: 55
  loop : -0.22 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N1509 
 HIS   0.004   0.001   HIS D 109 
 PHE   0.019   0.001   PHE E  67 
 TYR   0.014   0.001   TYR F  98 
 ARG   0.003   0.000   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04172 (  831)
  hydrogen bonds       : angle       3.53768 ( 2214)
  covalent geometry    : bond        0.00297 (17266)
  covalent geometry    : angle       0.56265 (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
  171 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8308 (m-10) cc_final: 0.7945 (m-10)
REVERT: B   74 GLU cc_start: 0.9284 (pp20) cc_final: 0.9061 (pp20)
REVERT: B   84 MET cc_start: 0.8588 (tpt) cc_final: 0.8317 (tpp)
REVERT: B   97 LEU cc_start: 0.9103 (tp) cc_final: 0.8866 (tp)
REVERT: C   56 GLU cc_start: 0.9162 (pm20) cc_final: 0.8917 (pm20)
REVERT: D   68 ASP cc_start: 0.9090 (m-30) cc_final: 0.8781 (m-30)
REVERT: D   86 ARG cc_start: 0.9005 (mmp80) cc_final: 0.8681 (mmp80)
REVERT: D  121 TYR cc_start: 0.8296 (t80) cc_final: 0.8093 (t80)
REVERT: E   90 MET cc_start: 0.9097 (mmp) cc_final: 0.8833 (mmm)
REVERT: E   97 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8633 (mm-30)
REVERT: E  120 MET cc_start: 0.8657 (tpt) cc_final: 0.8424 (mmm)
REVERT: F   59 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8878 (ptpp)
REVERT: F   63 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8395 (mp0)
REVERT: F   74 GLU cc_start: 0.9118 (pp20) cc_final: 0.8577 (pp20)
REVERT: F   93 GLN cc_start: 0.8833 (tt0) cc_final: 0.8342 (tm-30)
REVERT: G   38 ASN cc_start: 0.8925 (m-40) cc_final: 0.8659 (p0)
REVERT: G   64 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8984 (mm-30)
REVERT: G   68 ASN cc_start: 0.8923 (m-40) cc_final: 0.8551 (t0)
REVERT: G   72 ASP cc_start: 0.9141 (m-30) cc_final: 0.8573 (m-30)
REVERT: G   74 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9137 (tptp)
REVERT: N 1349 MET cc_start: 0.2358 (tpt) cc_final: 0.1637 (tpt)
REVERT: N 1624 MET cc_start: -0.1353 (mmm) cc_final: -0.1580 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2677
  time to fit residues: 69.4003
Evaluate side-chains
  119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 119 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 137 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.064516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.042315 restraints weight = 153414.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.043494 restraints weight = 79457.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.044195 restraints weight = 53348.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3263

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= 0.196
  Angle     :  0.588   8.946  24572  Z= 0.344
  Chirality :  0.036   0.145   2738
  Planarity :  0.005   0.067   2114
  Dihedral  : 29.096 177.418   4715
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.98 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.23), residues: 1256
  helix:  1.69 (0.18), residues: 767
  sheet:  0.43 (0.68), residues: 60
  loop : -0.17 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP N1436 
 HIS   0.006   0.001   HIS N1377 
 PHE   0.017   0.001   PHE E  67 
 TYR   0.027   0.002   TYR N1394 
 ARG   0.027   0.001   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06247 (  831)
  hydrogen bonds       : angle       3.54644 ( 2214)
  covalent geometry    : bond        0.00428 (17266)
  covalent geometry    : angle       0.58763 (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
  159 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9183 (m-30) cc_final: 0.8981 (m-30)
REVERT: B   68 ASP cc_start: 0.9284 (m-30) cc_final: 0.8821 (m-30)
REVERT: B   74 GLU cc_start: 0.9291 (pp20) cc_final: 0.8960 (pp20)
REVERT: B   84 MET cc_start: 0.8665 (tpt) cc_final: 0.8332 (tpp)
REVERT: D   62 MET cc_start: 0.9583 (mmm) cc_final: 0.9293 (mmm)
REVERT: D   65 PHE cc_start: 0.9754 (t80) cc_final: 0.9361 (t80)
REVERT: D   68 ASP cc_start: 0.9039 (m-30) cc_final: 0.8776 (m-30)
REVERT: D   86 ARG cc_start: 0.8971 (mmp80) cc_final: 0.8676 (mmp80)
REVERT: D  121 TYR cc_start: 0.8830 (t80) cc_final: 0.8625 (t80)
REVERT: E   90 MET cc_start: 0.9089 (mmp) cc_final: 0.8865 (mmm)
REVERT: E   97 GLU cc_start: 0.9425 (mt-10) cc_final: 0.8732 (mm-30)
REVERT: F   62 LEU cc_start: 0.9723 (mt) cc_final: 0.9503 (mt)
REVERT: F   63 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8501 (mp0)
REVERT: F   70 VAL cc_start: 0.9718 (m) cc_final: 0.9422 (m)
REVERT: F   74 GLU cc_start: 0.9191 (pp20) cc_final: 0.8683 (pp20)
REVERT: F   93 GLN cc_start: 0.8859 (tt0) cc_final: 0.8349 (tm-30)
REVERT: G   38 ASN cc_start: 0.9175 (m-40) cc_final: 0.8726 (p0)
REVERT: G   39 TYR cc_start: 0.9080 (m-80) cc_final: 0.8811 (m-80)
REVERT: G   64 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8901 (mm-30)
REVERT: G   74 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9179 (mmmm)
REVERT: G   99 ARG cc_start: 0.7786 (tpt90) cc_final: 0.7381 (mmm160)
REVERT: H   71 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9120 (pt0)
REVERT: N 1349 MET cc_start: 0.4627 (tpt) cc_final: 0.4117 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2641
  time to fit residues: 63.7779
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  : 1.357 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 147 optimal weight:    9.9990
   chunk 137 optimal weight:   50.0000
   chunk 66 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   chunk 142 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 111 optimal weight:    4.9990
   chunk 124 optimal weight:    9.9990
   chunk 122 optimal weight:    0.8980
   chunk 130 optimal weight:    9.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
G 110 ASN
N1236 ASN
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 = 0.3563 r_free = 0.3563 target = 0.061034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.039082 restraints weight = 158999.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.040123 restraints weight = 81497.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.040746 restraints weight = 54435.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  17266  Z= 0.266
  Angle     :  0.675   9.356  24572  Z= 0.388
  Chirality :  0.039   0.177   2738
  Planarity :  0.006   0.070   2114
  Dihedral  : 29.812 178.536   4715
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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:  1.11 (0.22), residues: 1256
  helix:  1.38 (0.18), residues: 758
  sheet:  0.15 (0.70), residues: 55
  loop : -0.19 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP N1115 
 HIS   0.006   0.002   HIS B  75 
 PHE   0.026   0.002   PHE H  65 
 TYR   0.017   0.002   TYR G  39 
 ARG   0.007   0.001   ARG G  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06990 (  831)
  hydrogen bonds       : angle       3.98288 ( 2214)
  covalent geometry    : bond        0.00576 (17266)
  covalent geometry    : angle       0.67454 (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
  146 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9230 (m-30) cc_final: 0.8818 (m-30)
REVERT: B   74 GLU cc_start: 0.9312 (pp20) cc_final: 0.8985 (pp20)
REVERT: B   84 MET cc_start: 0.8655 (tpt) cc_final: 0.8394 (tpp)
REVERT: D   68 ASP cc_start: 0.9167 (m-30) cc_final: 0.8876 (m-30)
REVERT: D   79 ARG cc_start: 0.9133 (ptm160) cc_final: 0.8792 (ptm160)
REVERT: E   90 MET cc_start: 0.9187 (mmp) cc_final: 0.8908 (mmm)
REVERT: E   97 GLU cc_start: 0.9441 (mt-10) cc_final: 0.8778 (mm-30)
REVERT: E  110 CYS cc_start: 0.9728 (m) cc_final: 0.9126 (t)
REVERT: E  120 MET cc_start: 0.9033 (tpt) cc_final: 0.8732 (mmm)
REVERT: F   84 MET cc_start: 0.8880 (tpp) cc_final: 0.8631 (tpp)
REVERT: F   88 TYR cc_start: 0.8567 (m-10) cc_final: 0.7824 (m-10)
REVERT: F   93 GLN cc_start: 0.8836 (tt0) cc_final: 0.8586 (tm-30)
REVERT: G   38 ASN cc_start: 0.9295 (m-40) cc_final: 0.8804 (p0)
REVERT: G   39 TYR cc_start: 0.9224 (m-80) cc_final: 0.8846 (m-80)
REVERT: G   74 LYS cc_start: 0.9418 (mmmm) cc_final: 0.9206 (mmmm)
REVERT: H   68 ASP cc_start: 0.9456 (t0) cc_final: 0.9213 (t0)
REVERT: H   71 GLU cc_start: 0.9324 (tm-30) cc_final: 0.9094 (tm-30)
REVERT: H   83 TYR cc_start: 0.8855 (m-10) cc_final: 0.8624 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.3109
  time to fit residues: 66.6130
Evaluate side-chains
  100 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 92 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 120 optimal weight:    8.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
C  68 ASN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.061850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.039796 restraints weight = 155661.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.040833 restraints weight = 79038.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.041395 restraints weight = 52835.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  17266  Z= 0.182
  Angle     :  0.606   9.623  24572  Z= 0.348
  Chirality :  0.036   0.166   2738
  Planarity :  0.005   0.071   2114
  Dihedral  : 29.754 179.383   4715
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.89 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.33 (0.23), residues: 1256
  helix:  1.60 (0.18), residues: 760
  sheet:  0.29 (0.73), residues: 55
  loop : -0.21 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP N1436 
 HIS   0.006   0.001   HIS E 113 
 PHE   0.029   0.001   PHE E 104 
 TYR   0.020   0.001   TYR N1394 
 ARG   0.010   0.000   ARG N1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05067 (  831)
  hydrogen bonds       : angle       3.66676 ( 2214)
  covalent geometry    : bond        0.00399 (17266)
  covalent geometry    : angle       0.60640 (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
  147 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 CYS cc_start: 0.8920 (t) cc_final: 0.8629 (t)
REVERT: B   74 GLU cc_start: 0.9321 (pp20) cc_final: 0.8918 (pp20)
REVERT: B   84 MET cc_start: 0.8681 (tpt) cc_final: 0.8358 (tpp)
REVERT: D   68 ASP cc_start: 0.9239 (m-30) cc_final: 0.8848 (m-30)
REVERT: E   97 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8818 (mm-30)
REVERT: E  110 CYS cc_start: 0.9707 (m) cc_final: 0.9173 (t)
REVERT: E  120 MET cc_start: 0.8895 (tpt) cc_final: 0.8652 (mmm)
REVERT: F   63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8566 (mp0)
REVERT: F   70 VAL cc_start: 0.9733 (m) cc_final: 0.9473 (m)
REVERT: F   74 GLU cc_start: 0.9159 (pp20) cc_final: 0.8620 (pp20)
REVERT: F   84 MET cc_start: 0.8614 (tpp) cc_final: 0.8319 (tpp)
REVERT: F   87 VAL cc_start: 0.9482 (t) cc_final: 0.9249 (t)
REVERT: F   88 TYR cc_start: 0.8496 (m-10) cc_final: 0.7674 (m-10)
REVERT: F   93 GLN cc_start: 0.8863 (tt0) cc_final: 0.8573 (tm-30)
REVERT: G   38 ASN cc_start: 0.9234 (m-40) cc_final: 0.8760 (p0)
REVERT: G   39 TYR cc_start: 0.9203 (m-80) cc_final: 0.8430 (m-80)
REVERT: G   74 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9201 (mmmm)
REVERT: G   90 ASP cc_start: 0.9424 (t0) cc_final: 0.9201 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 145
  average time/residue: 0.3147
  time to fit residues: 69.8030
Evaluate side-chains
  101 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 143 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0870
   chunk 107 optimal weight:   20.0000
   chunk 112 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
** E  55 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.060105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.038177 restraints weight = 158335.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.039163 restraints weight = 81897.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.039823 restraints weight = 54998.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  17266  Z= 0.244
  Angle     :  0.654  11.260  24572  Z= 0.373
  Chirality :  0.038   0.158   2738
  Planarity :  0.005   0.066   2114
  Dihedral  : 29.946 179.451   4715
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.08 %
    Favored  : 98.83 %
  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:  1.18 (0.23), residues: 1256
  helix:  1.48 (0.18), residues: 760
  sheet:  0.01 (0.72), residues: 55
  loop : -0.25 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N1436 
 HIS   0.006   0.001   HIS D 109 
 PHE   0.015   0.002   PHE A  67 
 TYR   0.012   0.002   TYR C  50 
 ARG   0.005   0.001   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06741 (  831)
  hydrogen bonds       : angle       3.91547 ( 2214)
  covalent geometry    : bond        0.00532 (17266)
  covalent geometry    : angle       0.65445 (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
  140 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.413 
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: B   63 GLU cc_start: 0.9226 (pm20) cc_final: 0.8874 (pm20)
REVERT: B   68 ASP cc_start: 0.9032 (m-30) cc_final: 0.8679 (t70)
REVERT: B   74 GLU cc_start: 0.9362 (pp20) cc_final: 0.8991 (pp20)
REVERT: B   84 MET cc_start: 0.8632 (tpt) cc_final: 0.8275 (tpp)
REVERT: C   56 GLU cc_start: 0.9188 (pm20) cc_final: 0.8956 (pm20)
REVERT: D   68 ASP cc_start: 0.9219 (m-30) cc_final: 0.8892 (m-30)
REVERT: E   90 MET cc_start: 0.9128 (mmp) cc_final: 0.8814 (mmm)
REVERT: E   97 GLU cc_start: 0.9383 (mt-10) cc_final: 0.8895 (mm-30)
REVERT: E  110 CYS cc_start: 0.9711 (m) cc_final: 0.9214 (t)
REVERT: E  120 MET cc_start: 0.8864 (tpt) cc_final: 0.8620 (mmm)
REVERT: F   70 VAL cc_start: 0.9751 (m) cc_final: 0.9493 (m)
REVERT: F   74 GLU cc_start: 0.9191 (pp20) cc_final: 0.8667 (pp20)
REVERT: F   84 MET cc_start: 0.8560 (tpp) cc_final: 0.8284 (tpp)
REVERT: F   87 VAL cc_start: 0.9530 (t) cc_final: 0.9297 (t)
REVERT: F   93 GLN cc_start: 0.8857 (tt0) cc_final: 0.8606 (tm-30)
REVERT: G   38 ASN cc_start: 0.9236 (m-40) cc_final: 0.8768 (p0)
REVERT: G   39 TYR cc_start: 0.9263 (m-80) cc_final: 0.8395 (m-80)
REVERT: G   64 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8752 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 140
  average time/residue: 0.2878
  time to fit residues: 60.2696
Evaluate side-chains
  100 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 134 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 150 optimal weight:   40.0000
   chunk 13 optimal weight:    0.6980
   chunk 99 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 142 optimal weight:    7.9990
   overall best weight:    1.1386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.062170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.040069 restraints weight = 153654.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.041098 restraints weight = 77960.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.041771 restraints weight = 52144.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.5340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17266  Z= 0.151
  Angle     :  0.608  10.601  24572  Z= 0.348
  Chirality :  0.036   0.185   2738
  Planarity :  0.004   0.073   2114
  Dihedral  : 29.810 178.239   4715
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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:  1.28 (0.23), residues: 1256
  helix:  1.56 (0.18), residues: 760
  sheet:  0.06 (0.73), residues: 55
  loop : -0.20 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N1436 
 HIS   0.008   0.001   HIS N1255 
 PHE   0.017   0.001   PHE E  67 
 TYR   0.011   0.001   TYR G  57 
 ARG   0.006   0.000   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  831)
  hydrogen bonds       : angle       3.63607 ( 2214)
  covalent geometry    : bond        0.00327 (17266)
  covalent geometry    : angle       0.60831 (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
  155 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.457 
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  105 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9069 (mm-30)
REVERT: B   68 ASP cc_start: 0.8950 (m-30) cc_final: 0.8576 (t0)
REVERT: B   74 GLU cc_start: 0.9342 (pp20) cc_final: 0.8995 (pp20)
REVERT: B   84 MET cc_start: 0.8549 (tpt) cc_final: 0.8091 (tpp)
REVERT: C   56 GLU cc_start: 0.9174 (pm20) cc_final: 0.8936 (pm20)
REVERT: D   68 ASP cc_start: 0.9173 (m-30) cc_final: 0.8871 (m-30)
REVERT: E   90 MET cc_start: 0.9127 (mmp) cc_final: 0.8790 (mmm)
REVERT: E   97 GLU cc_start: 0.9429 (mt-10) cc_final: 0.8861 (mm-30)
REVERT: E  110 CYS cc_start: 0.9682 (m) cc_final: 0.9123 (t)
REVERT: E  120 MET cc_start: 0.8810 (tpt) cc_final: 0.8501 (mmm)
REVERT: F   62 LEU cc_start: 0.9743 (mt) cc_final: 0.9543 (mp)
REVERT: F   70 VAL cc_start: 0.9727 (m) cc_final: 0.9454 (m)
REVERT: F   74 GLU cc_start: 0.9146 (pp20) cc_final: 0.8624 (pp20)
REVERT: F   84 MET cc_start: 0.8457 (tpp) cc_final: 0.8185 (tpp)
REVERT: F   88 TYR cc_start: 0.8279 (m-10) cc_final: 0.7994 (m-10)
REVERT: F   93 GLN cc_start: 0.8978 (tt0) cc_final: 0.8581 (tm-30)
REVERT: G   38 ASN cc_start: 0.9181 (m-40) cc_final: 0.8704 (p0)
REVERT: G   39 TYR cc_start: 0.9223 (m-80) cc_final: 0.8423 (m-80)
REVERT: G   99 ARG cc_start: 0.7647 (tpt90) cc_final: 0.7353 (mmm160)
REVERT: H   79 ARG cc_start: 0.9406 (tpp80) cc_final: 0.9167 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.3164
  time to fit residues: 71.8605
Evaluate side-chains
  109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.5980
   chunk 142 optimal weight:    0.3980
   chunk 79 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 101 optimal weight:    7.9990
   chunk 132 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** F  25 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.063000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.040457 restraints weight = 151647.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.041532 restraints weight = 77348.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.042290 restraints weight = 51695.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17266  Z= 0.145
  Angle     :  0.604  10.395  24572  Z= 0.344
  Chirality :  0.036   0.189   2738
  Planarity :  0.004   0.072   2114
  Dihedral  : 29.588 179.618   4715
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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:  1.26 (0.23), residues: 1256
  helix:  1.50 (0.18), residues: 764
  sheet:  0.07 (0.74), residues: 55
  loop : -0.15 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N1436 
 HIS   0.004   0.001   HIS N1255 
 PHE   0.016   0.001   PHE E  67 
 TYR   0.010   0.001   TYR N1117 
 ARG   0.006   0.000   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  831)
  hydrogen bonds       : angle       3.59820 ( 2214)
  covalent geometry    : bond        0.00311 (17266)
  covalent geometry    : angle       0.60441 (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
  153 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8773 (tt0) cc_final: 0.8527 (tt0)
REVERT: A   94 GLU cc_start: 0.9130 (tt0) cc_final: 0.8121 (pt0)
REVERT: A  105 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9098 (mm-30)
REVERT: B   68 ASP cc_start: 0.8904 (m-30) cc_final: 0.8566 (t0)
REVERT: B   74 GLU cc_start: 0.9323 (pp20) cc_final: 0.8959 (pp20)
REVERT: B   84 MET cc_start: 0.8556 (tpt) cc_final: 0.8260 (tpp)
REVERT: C   56 GLU cc_start: 0.9153 (pm20) cc_final: 0.8908 (pm20)
REVERT: D   67 ASN cc_start: 0.9233 (m-40) cc_final: 0.8967 (m110)
REVERT: D   68 ASP cc_start: 0.9184 (m-30) cc_final: 0.8830 (m-30)
REVERT: D   79 ARG cc_start: 0.9010 (ptm160) cc_final: 0.8314 (ttp-110)
REVERT: E   90 MET cc_start: 0.9138 (mmp) cc_final: 0.8810 (mmm)
REVERT: E   97 GLU cc_start: 0.9450 (mt-10) cc_final: 0.8846 (mm-30)
REVERT: E  120 MET cc_start: 0.8785 (tpt) cc_final: 0.8466 (mmm)
REVERT: F   62 LEU cc_start: 0.9742 (mt) cc_final: 0.9529 (mp)
REVERT: F   63 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8748 (mt-10)
REVERT: F   70 VAL cc_start: 0.9713 (m) cc_final: 0.9413 (m)
REVERT: F   74 GLU cc_start: 0.9114 (pp20) cc_final: 0.8588 (pp20)
REVERT: F   84 MET cc_start: 0.8487 (tpp) cc_final: 0.8177 (tpp)
REVERT: F   88 TYR cc_start: 0.8394 (m-10) cc_final: 0.8140 (m-10)
REVERT: F   93 GLN cc_start: 0.8922 (tt0) cc_final: 0.8524 (tm-30)
REVERT: G   38 ASN cc_start: 0.9150 (m-40) cc_final: 0.8713 (p0)
REVERT: G   39 TYR cc_start: 0.9176 (m-80) cc_final: 0.8297 (m-80)
REVERT: G   64 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: G   99 ARG cc_start: 0.7735 (tpt90) cc_final: 0.7376 (mmm160)
REVERT: H   41 VAL cc_start: 0.9446 (t) cc_final: 0.9205 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2971
  time to fit residues: 66.9856
Evaluate side-chains
  113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 113 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 102 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 119 optimal weight:    0.2980
   chunk 90 optimal weight:    7.9990
   chunk 141 optimal weight:   10.0000
   chunk 106 optimal weight:    7.9990
   chunk 151 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   overall best weight:    2.5784

-------------------------------------------------------------------------------
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**
N1173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.060891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.038660 restraints weight = 156071.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.039723 restraints weight = 80838.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.040408 restraints weight = 53903.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.5784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17266  Z= 0.202
  Angle     :  0.620  10.316  24572  Z= 0.355
  Chirality :  0.037   0.186   2738
  Planarity :  0.005   0.075   2114
  Dihedral  : 29.743 179.783   4715
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  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:  1.21 (0.23), residues: 1256
  helix:  1.47 (0.18), residues: 764
  sheet: -0.11 (0.70), residues: 59
  loop : -0.16 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N1436 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.014   0.001   PHE E  67 
 TYR   0.017   0.001   TYR D 121 
 ARG   0.006   0.000   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05589 (  831)
  hydrogen bonds       : angle       3.83082 ( 2214)
  covalent geometry    : bond        0.00440 (17266)
  covalent geometry    : angle       0.61983 (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
  147 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.545 
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: 0.9508 (mm-30) cc_final: 0.9163 (mm-30)
REVERT: A   94 GLU cc_start: 0.9065 (tt0) cc_final: 0.8097 (pt0)
REVERT: A  105 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9075 (mm-30)
REVERT: A  110 CYS cc_start: 0.9168 (t) cc_final: 0.8961 (t)
REVERT: B   68 ASP cc_start: 0.9011 (m-30) cc_final: 0.8653 (t0)
REVERT: B   74 GLU cc_start: 0.9337 (pp20) cc_final: 0.8931 (pp20)
REVERT: B   84 MET cc_start: 0.8578 (tpt) cc_final: 0.8252 (tpp)
REVERT: D   68 ASP cc_start: 0.9179 (m-30) cc_final: 0.8823 (m-30)
REVERT: D   79 ARG cc_start: 0.8995 (ptm160) cc_final: 0.8429 (ttp-110)
REVERT: D  121 TYR cc_start: 0.9019 (t80) cc_final: 0.8709 (t80)
REVERT: E   90 MET cc_start: 0.9153 (mmp) cc_final: 0.8820 (mmm)
REVERT: E   97 GLU cc_start: 0.9445 (mt-10) cc_final: 0.8825 (mm-30)
REVERT: E  110 CYS cc_start: 0.9689 (m) cc_final: 0.9160 (t)
REVERT: E  120 MET cc_start: 0.8849 (tpt) cc_final: 0.8540 (mmm)
REVERT: F   63 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8771 (mt-10)
REVERT: F   70 VAL cc_start: 0.9731 (m) cc_final: 0.9455 (m)
REVERT: F   74 GLU cc_start: 0.9178 (pp20) cc_final: 0.8652 (pp20)
REVERT: F   84 MET cc_start: 0.8471 (tpp) cc_final: 0.8231 (tpp)
REVERT: F   88 TYR cc_start: 0.8345 (m-10) cc_final: 0.8002 (m-10)
REVERT: F   93 GLN cc_start: 0.8918 (tt0) cc_final: 0.8558 (tm-30)
REVERT: G   38 ASN cc_start: 0.9175 (m-40) cc_final: 0.8719 (p0)
REVERT: G   39 TYR cc_start: 0.9262 (m-80) cc_final: 0.8457 (m-80)
REVERT: G   64 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8426 (mm-30)
REVERT: G   99 ARG cc_start: 0.7602 (tpt90) cc_final: 0.7326 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.3023
  time to fit residues: 65.8417
Evaluate side-chains
  106 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 86 optimal weight:    7.9990
   chunk 135 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 131 optimal weight:    4.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1659 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.055735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.034086 restraints weight = 141040.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.035074 restraints weight = 74290.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.035653 restraints weight = 50515.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.6334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17266  Z= 0.225
  Angle     :  0.655  10.990  24572  Z= 0.374
  Chirality :  0.037   0.184   2738
  Planarity :  0.005   0.074   2114
  Dihedral  : 30.098 175.674   4715
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  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:  1.05 (0.23), residues: 1256
  helix:  1.34 (0.18), residues: 769
  sheet: -0.29 (0.69), residues: 59
  loop : -0.21 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N1436 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.014   0.002   PHE A  67 
 TYR   0.018   0.002   TYR G  50 
 ARG   0.008   0.001   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06061 (  831)
  hydrogen bonds       : angle       3.98312 ( 2214)
  covalent geometry    : bond        0.00490 (17266)
  covalent geometry    : angle       0.65511 (24572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5914.61 seconds
wall clock time: 102 minutes 54.63 seconds (6174.63 seconds total)