Starting phenix.real_space_refine
on Sun May 18 10:59:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hah_34589/05_2025/8hah_34589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hah_34589/05_2025/8hah_34589.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hah_34589/05_2025/8hah_34589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hah_34589/05_2025/8hah_34589.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hah_34589/05_2025/8hah_34589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hah_34589/05_2025/8hah_34589.cif"
  }
  resolution = 3.9
  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=   0.001
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     328      5.49       5
     S      47      5.16       5
     C    9780      2.51       5
     N    3123      2.21       5
     O    3818      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 113 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 17096
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 838
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 761
          Classifications: {'peptide': 97}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 3365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3365
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "J"
      Number of atoms: 3359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3359
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "K"
      Number of atoms: 4267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 4267
          Classifications: {'peptide': 517}
          Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 483}
          Chain breaks: 3
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N   ARG B  23 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  23 " occ=0.00
    residue:
      pdb=" N   LYS C  13 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS C  13 " occ=0.00
    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: 10.23, per 1000 atoms: 0.60
  Number of scatterers: 17096
  At special positions: 0
  Unit cell: (105.283, 164.142, 129.324, 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     328     15.00
     O    3818      8.00
     N    3123      7.00
     C    9780      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: 4.58
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2424

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      60.0% alpha, 6.5% beta
      157 base pairs and 272 stacking pairs defined.
    Time for finding SS restraints: 7.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 3.784A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.582A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.506A  pdb=" N   LEU A 100 " --> pdb=" O   CYS A  96 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.897A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 40
      removed outlier: 3.616A  pdb=" N   ARG B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 76
      removed outlier: 3.640A  pdb=" N   VAL B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 91
      removed outlier: 3.543A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 94
      No H-bonds generated for 'chain 'B' and resid 92 through 94'
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 4.680A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA C  53 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN C  68 " --> pdb=" O   GLU C  64 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA C  69 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.570A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.783A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.745A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 85
      removed outlier: 3.961A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY D  60 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 4.049A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 4.050A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
      removed outlier: 4.152A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLN E  55 " --> pdb=" O   ILE E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.623A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.977A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   TYR E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU E 100 " --> pdb=" O   CYS E  96 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL E 101 " --> pdb=" O   GLU E  97 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU E 105 " --> pdb=" O   VAL E 101 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.771A  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 50 through 76
      removed outlier: 3.698A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.654A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.906A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 57 through 83
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.741A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 4.221A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1055 through 1068
      Proline residue:  K1060  - end of helix
      removed outlier: 3.679A  pdb=" N   GLN K1068 " --> pdb=" O   ALA K1064 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1072 through 1077
      removed outlier: 4.305A  pdb=" N   GLN K1077 " --> pdb=" O   LEU K1073 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1080 through 1084
    Processing helix  chain 'K' and resid 1088 through 1093
    Processing helix  chain 'K' and resid 1098 through 1108
    Processing helix  chain 'K' and resid 1113 through 1132
      removed outlier: 3.944A  pdb=" N   TYR K1117 " --> pdb=" O   GLU K1113 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1136 through 1161
      removed outlier: 3.906A  pdb=" N   ASP K1154 " --> pdb=" O   GLU K1150 " (cutoff:3.500A)
      Proline residue:  K1155  - end of helix
    Processing helix  chain 'K' and resid 1256 through 1260
    Processing helix  chain 'K' and resid 1272 through 1279
    Processing helix  chain 'K' and resid 1289 through 1293
    Processing helix  chain 'K' and resid 1296 through 1314
    Processing helix  chain 'K' and resid 1336 through 1343
      removed outlier: 3.584A  pdb=" N   ARG K1342 " --> pdb=" O   GLY K1338 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1409 through 1429
    Processing helix  chain 'K' and resid 1459 through 1477
    Processing helix  chain 'K' and resid 1486 through 1494
    Processing helix  chain 'K' and resid 1497 through 1501
    Processing helix  chain 'K' and resid 1507 through 1517
      removed outlier: 3.965A  pdb=" N   ASN K1511 " --> pdb=" O   ASP K1507 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1579 through 1591
    Processing helix  chain 'K' and resid 1626 through 1637
      removed outlier: 3.871A  pdb=" N   PHE K1630 " --> pdb=" O   GLY K1626 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1643 through 1663
    Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 102
      removed outlier: 4.006A  pdb=" N   TYR F  98 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.394A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.455A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'K' and resid 1175 through 1176
      removed outlier: 3.632A  pdb=" N   LEU K1175 " --> pdb=" O   ILE K1185 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 1198 through 1201
    Processing sheet with id=AA7, first strand: chain 'K' and resid 1244 through 1246
    Processing sheet with id=AA8, first strand: chain 'K' and resid 1320 through 1334
      removed outlier: 4.135A  pdb=" N   GLU K1320 " --> pdb=" O   GLU K1365 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA K1359 " --> pdb=" O   VAL K1326 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA K1328 " --> pdb=" O   THR K1357 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR K1357 " --> pdb=" O   ALA K1328 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ASP K1330 " --> pdb=" O   TYR K1355 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TYR K1355 " --> pdb=" O   ASP K1330 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   THR K1332 " --> pdb=" O   PHE K1353 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   PHE K1353 " --> pdb=" O   THR K1332 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU K1360 " --> pdb=" O   MET K1376 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE K1374 " --> pdb=" O   ALA K1362 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   GLU K1364 " --> pdb=" O   CYS K1372 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   CYS K1372 " --> pdb=" O   GLU K1364 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE K1366 " --> pdb=" O   ASP K1370 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ASP K1370 " --> pdb=" O   ILE K1366 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   PHE K1373 " --> pdb=" O   SER K1400 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   SER K1400 " --> pdb=" O   PHE K1373 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   GLY K1375 " --> pdb=" O   LEU K1398 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   LEU K1398 " --> pdb=" O   GLY K1375 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   HIS K1377 " --> pdb=" O   SER K1396 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG K1392 " --> pdb=" O   TYR K1381 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   TRP K1436 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TYR K1397 " --> pdb=" O   TRP K1436 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP K1482 " --> pdb=" O   ARG K1599 " (cutoff:3.500A)

    534 hydrogen bonds defined for protein.
    1575 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      384 hydrogen bonds
      768 hydrogen bond angles
      0 basepair planarities
      157 basepair parallelities
      272 stacking parallelities
  Total time for adding SS restraints: 9.24

  Time building geometry restraints manager: 5.37 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: 3819
        1.34 -     1.46: 5326
        1.46 -     1.58: 8240
        1.58 -     1.70: 654
        1.70 -     1.82: 70
  Bond restraints: 18109
  Sorted by residual:
  bond pdb=" C3'  DA I 156 "
       pdb=" O3'  DA I 156 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.23e+00
  bond pdb=" CA  ILE H  54 "
       pdb=" CB  ILE H  54 "
    ideal  model  delta    sigma   weight residual
    1.533  1.551 -0.018 1.37e-02 5.33e+03 1.76e+00
  bond pdb=" CG  GLU C  61 "
       pdb=" CD  GLU C  61 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" C3'  DT I 109 "
       pdb=" C2'  DT I 109 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.22e-01
  bond pdb=" C3'  DG J 142 "
       pdb=" C2'  DG J 142 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.00e-02 2.50e+03 7.56e-01
  ... (remaining 18104 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 25361
        1.90 -     3.80: 466
        3.80 -     5.70: 32
        5.70 -     7.60: 5
        7.60 -     9.50: 2
  Bond angle restraints: 25866
  Sorted by residual:
  angle pdb=" CA  ARG K1055 "
        pdb=" CB  ARG K1055 "
        pdb=" CG  ARG K1055 "
      ideal   model   delta    sigma   weight residual
     114.10  121.67   -7.57 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" CB  MET A 120 "
        pdb=" CG  MET A 120 "
        pdb=" SD  MET A 120 "
      ideal   model   delta    sigma   weight residual
     112.70  122.20   -9.50 3.00e+00 1.11e-01 1.00e+01
  angle pdb=" C   TYR K1194 "
        pdb=" N   GLN K1195 "
        pdb=" CA  GLN K1195 "
      ideal   model   delta    sigma   weight residual
     121.54  126.89   -5.35 1.91e+00 2.74e-01 7.83e+00
  angle pdb=" N   GLU D  76 "
        pdb=" CA  GLU D  76 "
        pdb=" CB  GLU D  76 "
      ideal   model   delta    sigma   weight residual
     110.16  114.14   -3.98 1.48e+00 4.57e-01 7.23e+00
  angle pdb=" N   MET K1059 "
        pdb=" CA  MET K1059 "
        pdb=" C   MET K1059 "
      ideal   model   delta    sigma   weight residual
     109.81  115.43   -5.62 2.21e+00 2.05e-01 6.47e+00
  ... (remaining 25861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.93: 8413
       28.93 -    57.86: 1621
       57.86 -    86.80: 110
       86.80 -   115.73: 0
      115.73 -   144.66: 3
  Dihedral angle restraints: 10147
    sinusoidal: 6392
      harmonic: 3755
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" C4'  DT I 136 "
           pdb=" C3'  DT I 136 "
           pdb=" O3'  DT I 136 "
           pdb=" P    DT I 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.34  144.66     1      3.50e+01 8.16e-04 1.42e+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   77.47  142.53     1      3.50e+01 8.16e-04 1.41e+01
  ... (remaining 10144 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 2253
       0.035 -    0.070: 505
       0.070 -    0.104: 95
       0.104 -    0.139: 27
       0.139 -    0.174: 2
  Chirality restraints: 2882
  Sorted by residual:
  chirality pdb=" CA  ILE C  79 "
            pdb=" N   ILE C  79 "
            pdb=" C   ILE C  79 "
            pdb=" CB  ILE C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.56e-01
  chirality pdb=" CA  ILE K1598 "
            pdb=" N   ILE K1598 "
            pdb=" C   ILE K1598 "
            pdb=" CB  ILE K1598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  MET K1059 "
            pdb=" N   MET K1059 "
            pdb=" C   MET K1059 "
            pdb=" CB  MET K1059 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 2879 not shown)

  Planarity restraints: 2154
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 116 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.93e+00
        pdb=" C   LYS D 116 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   LYS D 116 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA D 117 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D 114 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   GLY D 114 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLY D 114 "    0.012 2.00e-02 2.50e+03
        pdb=" N   THR D 115 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 117 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   ALA D 117 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ALA D 117 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL D 118 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2151 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3584
        2.80 -     3.32: 15178
        3.32 -     3.85: 30584
        3.85 -     4.37: 34732
        4.37 -     4.90: 51853
  Nonbonded interactions: 135931
  Sorted by model distance:
  nonbonded pdb=" O   THR D 119 "
            pdb=" OG1 THR D 122 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   HIS B  75 "
            pdb=" NH1 ARG D  92 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NH1 ARG H  29 "
            pdb=" OP1  DG J 120 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   LYS D 116 "
            pdb=" OG1 THR D 119 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" NH1 ARG C  42 "
            pdb=" O   VAL C  43 "
     model   vdw
     2.327 3.120
  ... (remaining 135926 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' and resid 37 through 135)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 29 through 124)
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 12 through 169)
  selection = (chain 'J' and resid 12 through 169)
}

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:             2.410
  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:          0.770
  Check model and map are aligned:         0.140
  Set scattering table:                    0.160
  Process input model:                     47.170
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.070
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6151
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   0.045  18109  Z= 0.139
  Angle     :  0.550   9.504  25866  Z= 0.337
  Chirality :  0.032   0.174   2882
  Planarity :  0.003   0.039   2154
  Dihedral  : 24.017 144.661   7723
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.59 (0.24), residues: 1263
  helix:  1.62 (0.20), residues: 714
  sheet:  0.60 (0.67), residues: 66
  loop :  0.40 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1649 
 HIS   0.007   0.001   HIS D 109 
 PHE   0.008   0.001   PHE K1125 
 TYR   0.015   0.001   TYR C  57 
 ARG   0.017   0.000   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12255 (  918)
  hydrogen bonds       : angle       3.93359 ( 2343)
  covalent geometry    : bond        0.00274 (18109)
  covalent geometry    : angle       0.54983 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.7692 (tmm) cc_final: 0.7207 (tmm)
REVERT: K 1470 MET cc_start: 0.0448 (tmm) cc_final: 0.0027 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2799
  time to fit residues: 27.2178
Evaluate side-chains
  49 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 118 optimal weight:   50.0000
   chunk 65 optimal weight:    0.0070
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 63 optimal weight:   30.0000
   chunk 122 optimal weight:   30.0000
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 141 optimal weight:    1.9990
   overall best weight:    2.2004

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
D  49 HIS
F  25 ASN
** K1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1481 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.104162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.074954 restraints weight = 160411.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.075742 restraints weight = 116067.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.076565 restraints weight = 90450.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18109  Z= 0.160
  Angle     :  0.553   7.685  25866  Z= 0.320
  Chirality :  0.034   0.195   2882
  Planarity :  0.004   0.036   2154
  Dihedral  : 26.984 143.931   5102
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.86 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.86 (0.24), residues: 1263
  helix:  1.88 (0.20), residues: 720
  sheet:  0.58 (0.68), residues: 66
  loop :  0.44 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K1466 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.019   0.001   PHE K1090 
 TYR   0.018   0.002   TYR F  88 
 ARG   0.005   0.000   ARG K1055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05487 (  918)
  hydrogen bonds       : angle       3.11434 ( 2343)
  covalent geometry    : bond        0.00340 (18109)
  covalent geometry    : angle       0.55285 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.7893 (tmm) cc_final: 0.7395 (tmm)
REVERT: F   84 MET cc_start: 0.8187 (mmp) cc_final: 0.7472 (mmp)
REVERT: K 1470 MET cc_start: 0.1359 (tmm) cc_final: 0.1071 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 58
  average time/residue: 0.2507
  time to fit residues: 24.5238
Evaluate side-chains
  47 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 107 optimal weight:   50.0000
   chunk 99 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 111 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 148 optimal weight:   30.0000
   chunk 36 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
G  38 ASN
K1195 GLN
K1379 GLN
K1591 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.077619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.057240 restraints weight = 185391.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.057515 restraints weight = 124130.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.057766 restraints weight = 95463.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.6381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.118  18109  Z= 0.309
  Angle     :  0.790  13.418  25866  Z= 0.456
  Chirality :  0.042   0.256   2882
  Planarity :  0.007   0.079   2154
  Dihedral  : 28.608 149.053   5102
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 18.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  7.73 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.03 (0.23), residues: 1263
  helix:  1.12 (0.19), residues: 738
  sheet:  0.33 (0.71), residues: 67
  loop :  0.22 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K1129 
 HIS   0.009   0.002   HIS A 113 
 PHE   0.019   0.002   PHE A  67 
 TYR   0.034   0.003   TYR H  83 
 ARG   0.010   0.001   ARG E  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08713 (  918)
  hydrogen bonds       : angle       4.00937 ( 2343)
  covalent geometry    : bond        0.00645 (18109)
  covalent geometry    : angle       0.78972 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 1.703 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7671 (mtmm)
REVERT: D   68 ASP cc_start: 0.9157 (t0) cc_final: 0.8922 (t0)
REVERT: D   71 GLU cc_start: 0.8917 (pp20) cc_final: 0.8679 (pp20)
REVERT: E   90 MET cc_start: 0.8840 (ppp) cc_final: 0.8624 (ppp)
REVERT: E   94 GLU cc_start: 0.8576 (tp30) cc_final: 0.8187 (tp30)
REVERT: H   71 GLU cc_start: 0.9056 (tt0) cc_final: 0.8517 (tp30)
REVERT: K 1654 MET cc_start: 0.5950 (mmm) cc_final: 0.5696 (tpt)
  outliers start: 18
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2456
  time to fit residues: 29.3667
Evaluate side-chains
  44 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain K residue 1135 THR
Chi-restraints excluded: chain K residue 1613 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 131 optimal weight:    7.9990
   chunk 119 optimal weight:   30.0000
   chunk 118 optimal weight:    8.9990
   chunk 150 optimal weight:    9.9990
   chunk 139 optimal weight:    5.9990
   chunk 154 optimal weight:   20.0000
   chunk 146 optimal weight:   10.0000
   chunk 89 optimal weight:   50.0000
   chunk 107 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
H 109 HIS
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1661 GLN ** 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 = 0.3931 r_free = 0.3931 target = 0.069357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.048536 restraints weight = 188155.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.048934 restraints weight = 121647.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.049360 restraints weight = 92607.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.9209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093  18109  Z= 0.295
  Angle     :  0.776  12.877  25866  Z= 0.438
  Chirality :  0.042   0.240   2882
  Planarity :  0.005   0.048   2154
  Dihedral  : 29.504 148.315   5102
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  9.71 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  0.75 (0.23), residues: 1263
  helix:  1.01 (0.19), residues: 724
  sheet: -0.07 (0.68), residues: 76
  loop : -0.04 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K1436 
 HIS   0.005   0.001   HIS G  82 
 PHE   0.031   0.002   PHE G  25 
 TYR   0.050   0.003   TYR B  88 
 ARG   0.008   0.001   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07410 (  918)
  hydrogen bonds       : angle       3.94784 ( 2343)
  covalent geometry    : bond        0.00647 (18109)
  covalent geometry    : angle       0.77590 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 52
  time to evaluate  : 1.580 
Fit side-chains
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.9284 (mmm) cc_final: 0.8935 (mmm)
REVERT: E   94 GLU cc_start: 0.9127 (tp30) cc_final: 0.8791 (tp30)
REVERT: F   84 MET cc_start: 0.9384 (tpp) cc_final: 0.8811 (tpp)
REVERT: H   71 GLU cc_start: 0.9439 (tt0) cc_final: 0.8832 (tp30)
REVERT: K 1470 MET cc_start: 0.0634 (tmm) cc_final: 0.0356 (ttp)
  outliers start: 25
  outliers final: 13
  residues processed: 73
  average time/residue: 0.2753
  time to fit residues: 32.1322
Evaluate side-chains
  54 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue 1102 ILE
Chi-restraints excluded: chain K residue 1135 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 152 optimal weight:    0.2980
   chunk 110 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 143 optimal weight:    4.9990
   chunk 155 optimal weight:   40.0000
   chunk 22 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 93 optimal weight:    7.9990
   overall best weight:    2.4588

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1661 GLN ** 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 = 0.3935 r_free = 0.3935 target = 0.069718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.048591 restraints weight = 180633.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.049145 restraints weight = 119019.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.049348 restraints weight = 90834.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.9476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  18109  Z= 0.169
  Angle     :  0.610  10.528  25866  Z= 0.348
  Chirality :  0.036   0.241   2882
  Planarity :  0.004   0.040   2154
  Dihedral  : 29.347 150.743   5102
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.33 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.24 (0.23), residues: 1263
  helix:  1.42 (0.19), residues: 734
  sheet: -0.15 (0.66), residues: 76
  loop :  0.15 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K1649 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.012   0.001   PHE A  84 
 TYR   0.016   0.001   TYR K1194 
 ARG   0.011   0.000   ARG G  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05118 (  918)
  hydrogen bonds       : angle       3.40241 ( 2343)
  covalent geometry    : bond        0.00368 (18109)
  covalent geometry    : angle       0.61040 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.7534 (m-80) cc_final: 0.7264 (m-10)
REVERT: B   84 MET cc_start: 0.8380 (tmm) cc_final: 0.8163 (tmm)
REVERT: D   68 ASP cc_start: 0.9169 (t0) cc_final: 0.8651 (t0)
REVERT: D   71 GLU cc_start: 0.8853 (pp20) cc_final: 0.8616 (pp20)
REVERT: F   84 MET cc_start: 0.8904 (tpp) cc_final: 0.8646 (tpp)
REVERT: H   71 GLU cc_start: 0.9044 (tt0) cc_final: 0.8520 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 64
  average time/residue: 0.2541
  time to fit residues: 26.8767
Evaluate side-chains
  52 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue 1102 ILE
Chi-restraints excluded: chain K residue 1121 ILE
Chi-restraints excluded: chain K residue 1135 THR
Chi-restraints excluded: chain K residue 1612 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 115 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 88 optimal weight:   20.0000
   chunk 141 optimal weight:    0.0170
   chunk 144 optimal weight:   30.0000
   chunk 155 optimal weight:   50.0000
   chunk 117 optimal weight:   20.0000
   overall best weight:    6.0026

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1082 GLN
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1327 HIS
** K1451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1661 GLN ** 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 = 0.3716 r_free = 0.3716 target = 0.060563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.038818 restraints weight = 182370.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.039355 restraints weight = 115539.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.039512 restraints weight = 86085.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          1.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.141  18109  Z= 0.316
  Angle     :  0.772   9.905  25866  Z= 0.438
  Chirality :  0.042   0.252   2882
  Planarity :  0.006   0.072   2154
  Dihedral  : 29.905 146.069   5102
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 22.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.33 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  0.67 (0.23), residues: 1263
  helix:  1.00 (0.19), residues: 740
  sheet: -0.32 (0.66), residues: 75
  loop : -0.18 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1436 
 HIS   0.008   0.002   HIS K1659 
 PHE   0.020   0.002   PHE K1125 
 TYR   0.040   0.002   TYR B  88 
 ARG   0.015   0.001   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10356 (  918)
  hydrogen bonds       : angle       4.15061 ( 2343)
  covalent geometry    : bond        0.00692 (18109)
  covalent geometry    : angle       0.77193 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 42
  time to evaluate  : 1.584 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8831 (t0) cc_final: 0.8522 (p0)
REVERT: H   71 GLU cc_start: 0.9339 (tt0) cc_final: 0.8994 (tp30)
  outliers start: 29
  outliers final: 22
  residues processed: 69
  average time/residue: 0.2545
  time to fit residues: 28.8919
Evaluate side-chains
  61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 39
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue 1102 ILE
Chi-restraints excluded: chain K residue 1121 ILE
Chi-restraints excluded: chain K residue 1135 THR
Chi-restraints excluded: chain K residue 1446 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 155 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 150 optimal weight:   30.0000
   chunk 131 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.062528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.041544 restraints weight = 186276.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.041798 restraints weight = 119071.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.041993 restraints weight = 88675.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          1.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  18109  Z= 0.199
  Angle     :  0.659  12.153  25866  Z= 0.373
  Chirality :  0.038   0.218   2882
  Planarity :  0.004   0.040   2154
  Dihedral  : 29.975 152.862   5102
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.95 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  0.95 (0.23), residues: 1263
  helix:  1.23 (0.19), residues: 739
  sheet: -0.32 (0.68), residues: 70
  loop : -0.07 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K1649 
 HIS   0.004   0.001   HIS K1261 
 PHE   0.024   0.001   PHE K1090 
 TYR   0.026   0.002   TYR B  88 
 ARG   0.012   0.001   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05479 (  918)
  hydrogen bonds       : angle       3.66793 ( 2343)
  covalent geometry    : bond        0.00428 (18109)
  covalent geometry    : angle       0.65946 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 49
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 GLU cc_start: 0.9257 (tt0) cc_final: 0.8642 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 69
  average time/residue: 0.2443
  time to fit residues: 28.1351
Evaluate side-chains
  61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 1.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue 1121 ILE
Chi-restraints excluded: chain K residue 1135 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 149 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 105 optimal weight:   40.0000
   chunk 14 optimal weight:    0.9990
   chunk 128 optimal weight:    0.3980
   chunk 137 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 121 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    3.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.061723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.040729 restraints weight = 187669.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.041081 restraints weight = 118715.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.041455 restraints weight = 89723.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          1.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  18109  Z= 0.189
  Angle     :  0.663  18.591  25866  Z= 0.368
  Chirality :  0.037   0.319   2882
  Planarity :  0.004   0.038   2154
  Dihedral  : 29.743 155.088   5102
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.21 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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 (0.23), residues: 1263
  helix:  1.37 (0.19), residues: 734
  sheet: -0.24 (0.68), residues: 70
  loop : -0.06 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K1266 
 HIS   0.006   0.001   HIS C  82 
 PHE   0.022   0.001   PHE K1090 
 TYR   0.035   0.001   TYR B  88 
 ARG   0.005   0.000   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05827 (  918)
  hydrogen bonds       : angle       3.55215 ( 2343)
  covalent geometry    : bond        0.00415 (18109)
  covalent geometry    : angle       0.66310 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.6859 (tptp) cc_final: 0.6514 (tmtt)
REVERT: A  120 MET cc_start: 0.9363 (mmm) cc_final: 0.8978 (mmm)
REVERT: H   71 GLU cc_start: 0.9213 (tt0) cc_final: 0.8620 (tp30)
  outliers start: 22
  outliers final: 19
  residues processed: 69
  average time/residue: 0.2639
  time to fit residues: 29.2688
Evaluate side-chains
  64 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue 1121 ILE
Chi-restraints excluded: chain K residue 1446 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 105 optimal weight:   30.0000
   chunk 120 optimal weight:   40.0000
   chunk 151 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 153 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0010
   chunk 51 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 126 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.062882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.041718 restraints weight = 185678.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.042021 restraints weight = 114225.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.042407 restraints weight = 83321.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          1.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  18109  Z= 0.144
  Angle     :  0.627  14.266  25866  Z= 0.349
  Chirality :  0.036   0.308   2882
  Planarity :  0.004   0.035   2154
  Dihedral  : 29.681 157.580   5102
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.02 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.22 (0.23), residues: 1263
  helix:  1.47 (0.19), residues: 735
  sheet: -0.17 (0.67), residues: 70
  loop : -0.00 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K1649 
 HIS   0.005   0.001   HIS H 109 
 PHE   0.022   0.001   PHE K1090 
 TYR   0.037   0.001   TYR B  88 
 ARG   0.007   0.000   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 (  918)
  hydrogen bonds       : angle       3.37473 ( 2343)
  covalent geometry    : bond        0.00307 (18109)
  covalent geometry    : angle       0.62739 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.7127 (tptp) cc_final: 0.6767 (tmtt)
REVERT: A   52 ARG cc_start: 0.9222 (mtt180) cc_final: 0.8967 (mtm-85)
REVERT: A  120 MET cc_start: 0.9349 (mmm) cc_final: 0.8976 (mmm)
REVERT: F   25 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7887 (t0)
REVERT: H   71 GLU cc_start: 0.9237 (tt0) cc_final: 0.8622 (tp30)
  outliers start: 15
  outliers final: 12
  residues processed: 64
  average time/residue: 0.2526
  time to fit residues: 26.7531
Evaluate side-chains
  61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain K residue 1121 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 111 optimal weight:    7.9990
   chunk 136 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1661 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.076711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.048953 restraints weight = 177454.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.049637 restraints weight = 133004.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.050181 restraints weight = 111490.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          1.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  18109  Z= 0.226
  Angle     :  0.674  13.594  25866  Z= 0.375
  Chirality :  0.037   0.296   2882
  Planarity :  0.004   0.038   2154
  Dihedral  : 29.727 165.629   5102
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.39 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.20 (0.23), residues: 1263
  helix:  1.48 (0.19), residues: 736
  sheet: -0.40 (0.67), residues: 71
  loop : -0.01 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K1509 
 HIS   0.004   0.001   HIS H 109 
 PHE   0.021   0.002   PHE K1090 
 TYR   0.045   0.002   TYR B  88 
 ARG   0.005   0.001   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07861 (  918)
  hydrogen bonds       : angle       3.59693 ( 2343)
  covalent geometry    : bond        0.00493 (18109)
  covalent geometry    : angle       0.67379 (25866)

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

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

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2526 Ramachandran restraints generated.
    1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 1.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   94 GLU cc_start: 0.9437 (tp30) cc_final: 0.9199 (tp30)
REVERT: H   71 GLU cc_start: 0.9266 (tt0) cc_final: 0.8962 (tp30)
  outliers start: 21
  outliers final: 18
  residues processed: 65
  average time/residue: 0.2774
  time to fit residues: 29.3859
Evaluate side-chains
  61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 1.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain K residue 1121 ILE
Chi-restraints excluded: chain K residue 1135 THR
Chi-restraints excluded: chain K residue 1446 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 145 optimal weight:   20.0000
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 133 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 122 optimal weight:    0.2980
   chunk 132 optimal weight:    7.9990
   chunk 146 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.062751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.039762 restraints weight = 173313.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.040649 restraints weight = 101979.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.041307 restraints weight = 74051.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          1.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18109  Z= 0.144
  Angle     :  0.631  13.558  25866  Z= 0.350
  Chirality :  0.036   0.303   2882
  Planarity :  0.004   0.036   2154
  Dihedral  : 29.719 161.502   5102
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.93 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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 (0.24), residues: 1263
  helix:  1.54 (0.19), residues: 736
  sheet: -0.27 (0.68), residues: 68
  loop :  0.06 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K1129 
 HIS   0.005   0.001   HIS H 109 
 PHE   0.020   0.001   PHE K1090 
 TYR   0.040   0.001   TYR B  88 
 ARG   0.006   0.000   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 (  918)
  hydrogen bonds       : angle       3.41174 ( 2343)
  covalent geometry    : bond        0.00307 (18109)
  covalent geometry    : angle       0.63080 (25866)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7309.98 seconds
wall clock time: 127 minutes 27.13 seconds (7647.13 seconds total)