Starting phenix.real_space_refine
on Tue Dec 31 17:35:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hak_34594/12_2024/8hak_34594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hak_34594/12_2024/8hak_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_34594/12_2024/8hak_34594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hak_34594/12_2024/8hak_34594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hak_34594/12_2024/8hak_34594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hak_34594/12_2024/8hak_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.03, per 1000 atoms: 0.55
  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 1.6 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: 7.36
  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: 7.76

  Time building geometry restraints manager: 4.41 seconds

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

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

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

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

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.570
  Check model and map are aligned:         0.130
  Set scattering table:                    0.150
  Process input model:                     43.370
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.760
-------------------------------------------------------------------------------
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= 0.189
  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 

*********************** 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  : 1.449 
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: 0.2799
  time to fit residues: 77.1998
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  : 1.496 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  17266  Z= 0.324
  Angle     :  0.657   8.016  24572  Z= 0.381
  Chirality :  0.039   0.154   2738
  Planarity :  0.005   0.062   2114
  Dihedral  : 28.816 171.778   4715
  Min Nonbonded Distance : 2.445

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

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

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

*********************** 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  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8747 (m-10) cc_final: 0.8405 (m-10)
REVERT: A  106 ASP cc_start: 0.9152 (m-30) cc_final: 0.8920 (m-30)
REVERT: C   38 ASN cc_start: 0.8367 (t0) cc_final: 0.7672 (t0)
REVERT: D   68 ASP cc_start: 0.9041 (m-30) cc_final: 0.8820 (m-30)
REVERT: D   86 ARG cc_start: 0.9056 (mmp80) cc_final: 0.8781 (mmp80)
REVERT: D  121 TYR cc_start: 0.8518 (t80) cc_final: 0.8159 (t80)
REVERT: E   97 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8630 (mm-30)
REVERT: E  120 MET cc_start: 0.8677 (tpt) cc_final: 0.8455 (mmm)
REVERT: F   62 LEU cc_start: 0.9733 (mt) cc_final: 0.9491 (mp)
REVERT: F   70 VAL cc_start: 0.9714 (m) cc_final: 0.9474 (m)
REVERT: F   74 GLU cc_start: 0.9224 (pp20) cc_final: 0.8736 (pp20)
REVERT: F   93 GLN cc_start: 0.8860 (tt0) cc_final: 0.8323 (tm-30)
REVERT: G   38 ASN cc_start: 0.8919 (m-40) cc_final: 0.8124 (t0)
REVERT: G   64 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8920 (mm-30)
REVERT: G   68 ASN cc_start: 0.8983 (m-40) cc_final: 0.8664 (t0)
REVERT: G   72 ASP cc_start: 0.9193 (m-30) cc_final: 0.8706 (m-30)
REVERT: G   74 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9156 (tptp)
REVERT: G   99 ARG cc_start: 0.7721 (tpt90) cc_final: 0.7162 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2814
  time to fit residues: 67.8373
Evaluate side-chains
  114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 115 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 139 optimal weight:    0.6980
   chunk 150 optimal weight:   20.0000
   chunk 123 optimal weight:   10.0000
   chunk 138 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   overall best weight:    3.0786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  17266  Z= 0.269
  Angle     :  0.615   7.828  24572  Z= 0.359
  Chirality :  0.037   0.153   2738
  Planarity :  0.005   0.068   2114
  Dihedral  : 29.354 179.796   4715
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.70 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.22), residues: 1256
  helix:  1.42 (0.18), residues: 762
  sheet:  0.24 (0.72), residues: 55
  loop : -0.26 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP N1509 
 HIS   0.007   0.001   HIS G  31 
 PHE   0.020   0.002   PHE N1595 
 TYR   0.014   0.002   TYR G  57 
 ARG   0.007   0.001   ARG D  92 

*********************** 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
  159 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9163 (m-30) cc_final: 0.8935 (m-30)
REVERT: B   74 GLU cc_start: 0.9286 (pp20) cc_final: 0.8982 (pp20)
REVERT: B   84 MET cc_start: 0.8644 (tpt) cc_final: 0.8343 (tpp)
REVERT: C   56 GLU cc_start: 0.9186 (pm20) cc_final: 0.8871 (pm20)
REVERT: D   62 MET cc_start: 0.9595 (mmm) cc_final: 0.9325 (mmm)
REVERT: D   65 PHE cc_start: 0.9763 (t80) cc_final: 0.9370 (t80)
REVERT: D   68 ASP cc_start: 0.9024 (m-30) cc_final: 0.8636 (m-30)
REVERT: D   86 ARG cc_start: 0.9085 (mmp80) cc_final: 0.8765 (mmp80)
REVERT: D  121 TYR cc_start: 0.9020 (t80) cc_final: 0.8790 (t80)
REVERT: E   97 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8793 (mm-30)
REVERT: E  110 CYS cc_start: 0.9734 (m) cc_final: 0.9149 (t)
REVERT: F   62 LEU cc_start: 0.9741 (mt) cc_final: 0.9507 (mp)
REVERT: F   74 GLU cc_start: 0.9220 (pp20) cc_final: 0.8669 (pp20)
REVERT: F   84 MET cc_start: 0.8962 (tpp) cc_final: 0.8758 (tpp)
REVERT: F   88 TYR cc_start: 0.8619 (m-10) cc_final: 0.7963 (m-10)
REVERT: F   93 GLN cc_start: 0.8830 (tt0) cc_final: 0.8411 (tm-30)
REVERT: G   74 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9226 (mmmm)
REVERT: G   99 ARG cc_start: 0.7846 (tpt90) cc_final: 0.7497 (mmm160)
REVERT: G  100 VAL cc_start: 0.8893 (t) cc_final: 0.8689 (t)
REVERT: N 1349 MET cc_start: 0.1160 (tpt) cc_final: 0.0942 (tpt)
REVERT: N 1624 MET cc_start: -0.1047 (mmm) cc_final: -0.1333 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2874
  time to fit residues: 68.1972
Evaluate side-chains
  110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 137 optimal weight:    0.0270
   chunk 104 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 66 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   chunk 139 optimal weight:    1.9990
   chunk 147 optimal weight:    1.9990
   chunk 132 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 123 optimal weight:    7.9990
   overall best weight:    0.9642

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
C  68 ASN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E  93 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  17266  Z= 0.179
  Angle     :  0.567   8.887  24572  Z= 0.329
  Chirality :  0.035   0.145   2738
  Planarity :  0.004   0.066   2114
  Dihedral  : 29.283 178.358   4715
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.71 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.23), residues: 1256
  helix:  1.68 (0.18), residues: 758
  sheet:  0.23 (0.70), residues: 55
  loop : -0.19 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N1115 
 HIS   0.004   0.001   HIS N1377 
 PHE   0.016   0.001   PHE E  67 
 TYR   0.011   0.001   TYR F  98 
 ARG   0.008   0.000   ARG D  99 

*********************** 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
  169 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 1.461 
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   84 PHE cc_start: 0.8604 (m-10) cc_final: 0.8260 (m-80)
REVERT: A  106 ASP cc_start: 0.9119 (m-30) cc_final: 0.8878 (m-30)
REVERT: B   74 GLU cc_start: 0.9395 (pp20) cc_final: 0.9037 (pp20)
REVERT: B   84 MET cc_start: 0.8535 (tpt) cc_final: 0.8267 (tpp)
REVERT: D   62 MET cc_start: 0.9580 (mmm) cc_final: 0.9228 (mmm)
REVERT: D   65 PHE cc_start: 0.9770 (t80) cc_final: 0.9483 (t80)
REVERT: D   80 LEU cc_start: 0.9689 (mm) cc_final: 0.9321 (mm)
REVERT: D   86 ARG cc_start: 0.8986 (mmp80) cc_final: 0.8627 (mmp80)
REVERT: D  121 TYR cc_start: 0.8871 (t80) cc_final: 0.8517 (t80)
REVERT: E   90 MET cc_start: 0.8976 (mmp) cc_final: 0.8681 (mmm)
REVERT: E   97 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8726 (mm-30)
REVERT: E  120 MET cc_start: 0.8858 (tpt) cc_final: 0.8575 (mmm)
REVERT: F   59 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8677 (ptpp)
REVERT: F   62 LEU cc_start: 0.9745 (mt) cc_final: 0.9490 (mt)
REVERT: F   63 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8528 (mp0)
REVERT: F   74 GLU cc_start: 0.9162 (pp20) cc_final: 0.8636 (pp20)
REVERT: F   84 MET cc_start: 0.8825 (tpp) cc_final: 0.8548 (tpp)
REVERT: F   87 VAL cc_start: 0.9468 (t) cc_final: 0.9266 (t)
REVERT: F   88 TYR cc_start: 0.8485 (m-10) cc_final: 0.7761 (m-10)
REVERT: F   93 GLN cc_start: 0.8842 (tt0) cc_final: 0.8395 (tm-30)
REVERT: G   38 ASN cc_start: 0.8979 (m-40) cc_final: 0.8714 (p0)
REVERT: G   39 TYR cc_start: 0.9194 (m-80) cc_final: 0.8724 (m-80)
REVERT: G   74 LYS cc_start: 0.9437 (mmmm) cc_final: 0.9192 (mmmm)
REVERT: G   99 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7401 (mmm160)
REVERT: H   93 GLU cc_start: 0.9524 (pm20) cc_final: 0.9294 (pm20)
REVERT: N 1349 MET cc_start: 0.1102 (tpt) cc_final: 0.0823 (tpt)
REVERT: N 1624 MET cc_start: -0.1113 (mmm) cc_final: -0.1384 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 169
  average time/residue: 0.3071
  time to fit residues: 76.2574
Evaluate side-chains
  116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 2 optimal weight:    0.2980
   chunk 110 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 126 optimal weight:   40.0000
   chunk 102 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 75 optimal weight:    7.9990
   chunk 132 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    2.8384

-------------------------------------------------------------------------------
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**
** 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
N1261 HIS
N1591 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  17266  Z= 0.265
  Angle     :  0.608   9.655  24572  Z= 0.353
  Chirality :  0.036   0.154   2738
  Planarity :  0.005   0.070   2114
  Dihedral  : 29.448 178.219   4715
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.07 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.23), residues: 1256
  helix:  1.57 (0.18), residues: 763
  sheet:  0.24 (0.70), residues: 55
  loop : -0.22 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP N1436 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.018   0.001   PHE H  65 
 TYR   0.032   0.002   TYR N1394 
 ARG   0.005   0.000   ARG A 134 

*********************** 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
  154 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9098 (tt0) cc_final: 0.8564 (tt0)
REVERT: B   74 GLU cc_start: 0.9377 (pp20) cc_final: 0.8986 (pp20)
REVERT: B   84 MET cc_start: 0.8694 (tpt) cc_final: 0.8312 (tpp)
REVERT: D   68 ASP cc_start: 0.9118 (m-30) cc_final: 0.8819 (m-30)
REVERT: D  121 TYR cc_start: 0.8973 (t80) cc_final: 0.8504 (t80)
REVERT: E   90 MET cc_start: 0.8987 (mmp) cc_final: 0.8752 (mmm)
REVERT: E   97 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8726 (mm-30)
REVERT: E  120 MET cc_start: 0.8939 (tpt) cc_final: 0.8647 (mmm)
REVERT: F   62 LEU cc_start: 0.9744 (mt) cc_final: 0.9502 (mt)
REVERT: F   63 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8473 (mp0)
REVERT: F   70 VAL cc_start: 0.9698 (m) cc_final: 0.9441 (m)
REVERT: F   74 GLU cc_start: 0.9216 (pp20) cc_final: 0.8705 (pp20)
REVERT: F   84 MET cc_start: 0.8791 (tpp) cc_final: 0.8421 (tpp)
REVERT: F   87 VAL cc_start: 0.9443 (t) cc_final: 0.9240 (t)
REVERT: F   88 TYR cc_start: 0.8520 (m-10) cc_final: 0.7770 (m-10)
REVERT: F   93 GLN cc_start: 0.8886 (tt0) cc_final: 0.8501 (tm-30)
REVERT: G   38 ASN cc_start: 0.9035 (m-40) cc_final: 0.8714 (p0)
REVERT: G   39 TYR cc_start: 0.9181 (m-80) cc_final: 0.8745 (m-80)
REVERT: G   64 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9130 (mm-30)
REVERT: G   68 ASN cc_start: 0.8941 (m-40) cc_final: 0.8705 (m-40)
REVERT: G   74 LYS cc_start: 0.9415 (mmmm) cc_final: 0.9203 (mmmm)
REVERT: G   99 ARG cc_start: 0.7637 (tpt90) cc_final: 0.7366 (mmm160)
REVERT: H   68 ASP cc_start: 0.9173 (t0) cc_final: 0.8932 (t0)
REVERT: N 1349 MET cc_start: 0.2218 (tpt) cc_final: 0.1409 (tpt)
REVERT: N 1624 MET cc_start: -0.0793 (mmm) cc_final: -0.1121 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.3115
  time to fit residues: 70.5087
Evaluate side-chains
  108 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 133 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 86 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 148 optimal weight:    7.9990
   chunk 122 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 142 optimal weight:   10.0000
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17266  Z= 0.184
  Angle     :  0.573   9.013  24572  Z= 0.330
  Chirality :  0.035   0.143   2738
  Planarity :  0.004   0.070   2114
  Dihedral  : 29.391 179.388   4715
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.80 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.38 (0.23), residues: 1256
  helix:  1.65 (0.18), residues: 759
  sheet:  0.31 (0.71), residues: 55
  loop : -0.21 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N1436 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.015   0.001   TYR G  57 
 ARG   0.004   0.000   ARG D  99 

*********************** 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
  166 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 1.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9005 (tt0) cc_final: 0.8441 (tt0)
REVERT: A  120 MET cc_start: 0.8072 (mpp) cc_final: 0.7818 (mpp)
REVERT: B   44 LYS cc_start: 0.8568 (pptt) cc_final: 0.8282 (pptt)
REVERT: B   74 GLU cc_start: 0.9380 (pp20) cc_final: 0.9038 (pp20)
REVERT: B   84 MET cc_start: 0.8576 (tpt) cc_final: 0.8223 (tpp)
REVERT: C   56 GLU cc_start: 0.9279 (pm20) cc_final: 0.8861 (pm20)
REVERT: D   67 ASN cc_start: 0.9214 (m-40) cc_final: 0.8710 (m-40)
REVERT: D   68 ASP cc_start: 0.9150 (m-30) cc_final: 0.8775 (m-30)
REVERT: D   80 LEU cc_start: 0.9701 (mm) cc_final: 0.9286 (mm)
REVERT: D   86 ARG cc_start: 0.9118 (mmp80) cc_final: 0.8736 (mmp80)
REVERT: E   97 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8697 (mm-30)
REVERT: E  120 MET cc_start: 0.8957 (tpt) cc_final: 0.8622 (mmm)
REVERT: F   62 LEU cc_start: 0.9746 (mt) cc_final: 0.9491 (mp)
REVERT: F   63 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8594 (mp0)
REVERT: F   70 VAL cc_start: 0.9689 (m) cc_final: 0.9419 (m)
REVERT: F   74 GLU cc_start: 0.9181 (pp20) cc_final: 0.8652 (pp20)
REVERT: F   84 MET cc_start: 0.8639 (tpp) cc_final: 0.8284 (tpp)
REVERT: F   88 TYR cc_start: 0.8513 (m-10) cc_final: 0.7758 (m-10)
REVERT: F   93 GLN cc_start: 0.8925 (tt0) cc_final: 0.8596 (tm-30)
REVERT: G   38 ASN cc_start: 0.9039 (m-40) cc_final: 0.8647 (p0)
REVERT: G   39 TYR cc_start: 0.9179 (m-80) cc_final: 0.8702 (m-80)
REVERT: G   64 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: G   74 LYS cc_start: 0.9389 (mmmm) cc_final: 0.9160 (mmmm)
REVERT: G   99 ARG cc_start: 0.7718 (tpt90) cc_final: 0.7432 (mmm160)
REVERT: N 1349 MET cc_start: 0.1928 (tpt) cc_final: 0.1014 (tpt)
REVERT: N 1624 MET cc_start: -0.0853 (mmm) cc_final: -0.1160 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 165
  average time/residue: 0.3001
  time to fit residues: 73.6984
Evaluate side-chains
  117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 108 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 147 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
D 109 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086  17266  Z= 0.338
  Angle     :  0.665  11.644  24572  Z= 0.381
  Chirality :  0.039   0.169   2738
  Planarity :  0.005   0.071   2114
  Dihedral  : 29.787 178.645   4715
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.06 (0.23), residues: 1256
  helix:  1.38 (0.18), residues: 763
  sheet:  0.01 (0.72), residues: 55
  loop : -0.31 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N1436 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.014   0.002   PHE D  70 
 TYR   0.014   0.002   TYR G  39 
 ARG   0.006   0.001   ARG G  42 

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

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9135 (mm-30)
REVERT: A   94 GLU cc_start: 0.9024 (tt0) cc_final: 0.8734 (tt0)
REVERT: A  106 ASP cc_start: 0.9196 (m-30) cc_final: 0.8990 (m-30)
REVERT: B   74 GLU cc_start: 0.9426 (pp20) cc_final: 0.9009 (pp20)
REVERT: B   84 MET cc_start: 0.8765 (tpt) cc_final: 0.8417 (tpp)
REVERT: C   56 GLU cc_start: 0.9234 (pm20) cc_final: 0.9014 (pm20)
REVERT: D   68 ASP cc_start: 0.9120 (m-30) cc_final: 0.8715 (m-30)
REVERT: D   86 ARG cc_start: 0.9294 (mmp80) cc_final: 0.8717 (mmp80)
REVERT: D  121 TYR cc_start: 0.9165 (t80) cc_final: 0.8922 (t80)
REVERT: E   90 MET cc_start: 0.9109 (mmp) cc_final: 0.8772 (mmm)
REVERT: E   97 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8841 (mm-30)
REVERT: E  110 CYS cc_start: 0.9725 (m) cc_final: 0.9204 (t)
REVERT: E  120 MET cc_start: 0.8951 (tpt) cc_final: 0.8650 (mmm)
REVERT: F   84 MET cc_start: 0.8607 (tpp) cc_final: 0.8137 (tpp)
REVERT: F   87 VAL cc_start: 0.9421 (t) cc_final: 0.9207 (t)
REVERT: F   88 TYR cc_start: 0.8568 (m-10) cc_final: 0.7770 (m-10)
REVERT: F   93 GLN cc_start: 0.8936 (tt0) cc_final: 0.8641 (tm-30)
REVERT: G   36 LYS cc_start: 0.8513 (mppt) cc_final: 0.8295 (mmtm)
REVERT: G   38 ASN cc_start: 0.9155 (m-40) cc_final: 0.8761 (p0)
REVERT: G   39 TYR cc_start: 0.9239 (m-80) cc_final: 0.8741 (m-80)
REVERT: G   90 ASP cc_start: 0.9418 (t0) cc_final: 0.9141 (t0)
REVERT: N 1349 MET cc_start: 0.3121 (tpt) cc_final: 0.2483 (tpt)
REVERT: N 1624 MET cc_start: -0.0555 (mmm) cc_final: -0.0871 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.3020
  time to fit residues: 63.8300
Evaluate side-chains
  94 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 115 optimal weight:    7.9990
   chunk 134 optimal weight:   20.0000
   chunk 141 optimal weight:    9.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.5430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  17266  Z= 0.255
  Angle     :  0.639  12.237  24572  Z= 0.366
  Chirality :  0.037   0.168   2738
  Planarity :  0.005   0.072   2114
  Dihedral  : 29.966 178.052   4715
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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:  1.38 (0.18), residues: 769
  sheet: -0.09 (0.73), residues: 55
  loop : -0.35 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N1509 
 HIS   0.005   0.001   HIS E 113 
 PHE   0.027   0.002   PHE E 104 
 TYR   0.013   0.002   TYR G  57 
 ARG   0.013   0.000   ARG B  95 

*********************** 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
  145 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.475 
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   50 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9165 (mm-30)
REVERT: A   94 GLU cc_start: 0.9022 (tt0) cc_final: 0.8736 (tt0)
REVERT: B   74 GLU cc_start: 0.9412 (pp20) cc_final: 0.9020 (pp20)
REVERT: B   84 MET cc_start: 0.8720 (tpt) cc_final: 0.8279 (tpp)
REVERT: C   56 GLU cc_start: 0.9369 (pm20) cc_final: 0.8969 (pm20)
REVERT: D   68 ASP cc_start: 0.9111 (m-30) cc_final: 0.8675 (m-30)
REVERT: D  121 TYR cc_start: 0.9145 (t80) cc_final: 0.8897 (t80)
REVERT: E   90 MET cc_start: 0.9105 (mmp) cc_final: 0.8779 (mmm)
REVERT: E   93 GLN cc_start: 0.9238 (tt0) cc_final: 0.9033 (tp40)
REVERT: E   97 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8842 (mm-30)
REVERT: E  110 CYS cc_start: 0.9713 (m) cc_final: 0.9225 (t)
REVERT: E  120 MET cc_start: 0.8873 (tpt) cc_final: 0.8557 (mmm)
REVERT: F   63 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8663 (mt-10)
REVERT: F   70 VAL cc_start: 0.9716 (m) cc_final: 0.9475 (m)
REVERT: F   74 GLU cc_start: 0.9215 (pp20) cc_final: 0.8684 (pp20)
REVERT: F   84 MET cc_start: 0.8611 (tpp) cc_final: 0.8143 (tpp)
REVERT: F   87 VAL cc_start: 0.9392 (t) cc_final: 0.9172 (t)
REVERT: F   88 TYR cc_start: 0.8548 (m-10) cc_final: 0.7708 (m-10)
REVERT: F   93 GLN cc_start: 0.9037 (tt0) cc_final: 0.8654 (tm-30)
REVERT: G   38 ASN cc_start: 0.9114 (m-40) cc_final: 0.8752 (p0)
REVERT: G   39 TYR cc_start: 0.9234 (m-80) cc_final: 0.8718 (m-80)
REVERT: G   64 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8814 (mm-30)
REVERT: G   89 ASN cc_start: 0.9608 (m-40) cc_final: 0.9404 (m110)
REVERT: H   62 MET cc_start: 0.9460 (tpp) cc_final: 0.9191 (tpt)
REVERT: H   68 ASP cc_start: 0.9387 (t0) cc_final: 0.9094 (t0)
REVERT: N 1349 MET cc_start: 0.3393 (tpt) cc_final: 0.2648 (tpt)
REVERT: N 1624 MET cc_start: -0.0498 (mmm) cc_final: -0.0823 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.3076
  time to fit residues: 66.0653
Evaluate side-chains
  105 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 128 optimal weight:    0.5980
   chunk 137 optimal weight:    8.9990
   chunk 141 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 124 optimal weight:   10.0000
   chunk 129 optimal weight:    5.9990
   chunk 136 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    4.9188

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1173 GLN
** N1389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.6118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.079  17266  Z= 0.382
  Angle     :  0.705  11.995  24572  Z= 0.403
  Chirality :  0.041   0.241   2738
  Planarity :  0.006   0.074   2114
  Dihedral  : 30.323 178.307   4715
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 18.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.81 (0.22), residues: 1256
  helix:  1.19 (0.18), residues: 769
  sheet: -0.50 (0.67), residues: 59
  loop : -0.37 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N1436 
 HIS   0.010   0.002   HIS F  18 
 PHE   0.023   0.002   PHE E 104 
 TYR   0.020   0.002   TYR G  57 
 ARG   0.006   0.001   ARG C  81 

*********************** 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
  134 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9169 (mm-30)
REVERT: A   94 GLU cc_start: 0.9016 (tt0) cc_final: 0.8640 (pt0)
REVERT: B   63 GLU cc_start: 0.9147 (pm20) cc_final: 0.8876 (pm20)
REVERT: B   74 GLU cc_start: 0.9458 (pp20) cc_final: 0.9065 (pp20)
REVERT: B   84 MET cc_start: 0.8734 (tpt) cc_final: 0.8290 (tpp)
REVERT: C   56 GLU cc_start: 0.9304 (pm20) cc_final: 0.8950 (pm20)
REVERT: D   68 ASP cc_start: 0.9137 (m-30) cc_final: 0.8690 (m-30)
REVERT: E   90 MET cc_start: 0.9113 (mmp) cc_final: 0.8767 (mmm)
REVERT: E   97 GLU cc_start: 0.9377 (mt-10) cc_final: 0.8836 (mm-30)
REVERT: E  110 CYS cc_start: 0.9710 (m) cc_final: 0.9231 (t)
REVERT: E  120 MET cc_start: 0.8829 (tpt) cc_final: 0.8620 (mmm)
REVERT: F   70 VAL cc_start: 0.9727 (m) cc_final: 0.9497 (m)
REVERT: F   74 GLU cc_start: 0.9274 (pp20) cc_final: 0.8698 (pp20)
REVERT: F   84 MET cc_start: 0.8585 (tpp) cc_final: 0.8174 (tpp)
REVERT: F   87 VAL cc_start: 0.9436 (t) cc_final: 0.9212 (t)
REVERT: F   93 GLN cc_start: 0.9094 (tt0) cc_final: 0.8724 (tm-30)
REVERT: G   38 ASN cc_start: 0.9180 (m-40) cc_final: 0.8764 (p0)
REVERT: G   39 TYR cc_start: 0.9231 (m-80) cc_final: 0.8812 (m-80)
REVERT: G   64 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8734 (mm-30)
REVERT: G   90 ASP cc_start: 0.9346 (t0) cc_final: 0.9129 (t70)
REVERT: N 1349 MET cc_start: 0.3920 (tpt) cc_final: 0.3269 (tpt)
REVERT: N 1624 MET cc_start: -0.0119 (mmm) cc_final: -0.0365 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.3076
  time to fit residues: 61.4946
Evaluate side-chains
  91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 145 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 152 optimal weight:   30.0000
   chunk 140 optimal weight:    5.9990
   chunk 121 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N1659 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.6365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  17266  Z= 0.281
  Angle     :  0.671  11.609  24572  Z= 0.381
  Chirality :  0.039   0.198   2738
  Planarity :  0.005   0.072   2114
  Dihedral  : 30.473 174.470   4715
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.22), residues: 1256
  helix:  1.14 (0.18), residues: 769
  sheet: -0.48 (0.69), residues: 59
  loop : -0.35 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP N1509 
 HIS   0.006   0.001   HIS E 113 
 PHE   0.024   0.002   PHE D  65 
 TYR   0.017   0.002   TYR F  88 
 ARG   0.007   0.001   ARG F  67 

********************** 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
  135 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.482 
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: 0.9540 (mm-30) cc_final: 0.9219 (mm-30)
REVERT: B   63 GLU cc_start: 0.9077 (pm20) cc_final: 0.8806 (pm20)
REVERT: B   74 GLU cc_start: 0.9416 (pp20) cc_final: 0.9012 (pp20)
REVERT: B   84 MET cc_start: 0.8596 (tpt) cc_final: 0.8085 (tpp)
REVERT: C   56 GLU cc_start: 0.9280 (pm20) cc_final: 0.8931 (pm20)
REVERT: C  112 GLN cc_start: 0.9030 (mp10) cc_final: 0.8699 (mp10)
REVERT: D   68 ASP cc_start: 0.9177 (m-30) cc_final: 0.8791 (m-30)
REVERT: E   97 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8802 (mm-30)
REVERT: E  110 CYS cc_start: 0.9715 (m) cc_final: 0.9217 (t)
REVERT: E  120 MET cc_start: 0.8967 (tpt) cc_final: 0.8656 (mmm)
REVERT: F   70 VAL cc_start: 0.9710 (m) cc_final: 0.9478 (m)
REVERT: F   74 GLU cc_start: 0.9216 (pp20) cc_final: 0.8660 (pp20)
REVERT: F   84 MET cc_start: 0.8544 (tpp) cc_final: 0.8083 (tpp)
REVERT: F   87 VAL cc_start: 0.9388 (t) cc_final: 0.9159 (t)
REVERT: F   88 TYR cc_start: 0.8554 (m-10) cc_final: 0.8293 (m-10)
REVERT: F   93 GLN cc_start: 0.8921 (tt0) cc_final: 0.8610 (tm-30)
REVERT: G   38 ASN cc_start: 0.9126 (m-40) cc_final: 0.8755 (p0)
REVERT: G   39 TYR cc_start: 0.9201 (m-80) cc_final: 0.8372 (m-80)
REVERT: G   64 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8778 (mm-30)
REVERT: N 1349 MET cc_start: 0.3322 (tpt) cc_final: 0.2643 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.3084
  time to fit residues: 62.0525
Evaluate side-chains
  99 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 121 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  84 ASN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1638 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.056539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.034618 restraints weight = 141444.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.035574 restraints weight = 74938.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.036148 restraints weight = 51141.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.6371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  17266  Z= 0.208
  Angle     :  0.641  11.348  24572  Z= 0.362
  Chirality :  0.037   0.187   2738
  Planarity :  0.005   0.069   2114
  Dihedral  : 30.238 176.262   4715
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  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:  0.89 (0.23), residues: 1256
  helix:  1.24 (0.18), residues: 769
  sheet: -0.45 (0.70), residues: 59
  loop : -0.32 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N1436 
 HIS   0.005   0.001   HIS N1638 
 PHE   0.021   0.001   PHE C  25 
 TYR   0.014   0.002   TYR D  83 
 ARG   0.005   0.000   ARG A 116 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2635.01 seconds
wall clock time: 49 minutes 31.42 seconds (2971.42 seconds total)