Starting phenix.real_space_refine
on Sun Aug 24 04:13:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hah_34589/08_2025/8hah_34589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hah_34589/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hah_34589/08_2025/8hah_34589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hah_34589/08_2025/8hah_34589.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hah_34589/08_2025/8hah_34589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hah_34589/08_2025/8hah_34589.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.10, per 1000 atoms: 0.18
  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: 1.23
  Conformation dependent library (CDL) restraints added in 408.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 1.93
  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: 3.90

  Time building geometry restraints manager: 1.68 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:             2.280
  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:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.910
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.910
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (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
 ARG   0.017   0.000   ARG H  79 
 TYR   0.015   0.001   TYR C  57 
 PHE   0.008   0.001   PHE K1125 
 TRP   0.007   0.001   TRP K1649 
 HIS   0.007   0.001   HIS D 109 

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

*********************** 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  : 0.527 
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: 0.1040
  time to fit residues: 10.2955
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  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:   30.0000
   overall best weight:    3.9786

-------------------------------------------------------------------------------
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**
C 112 GLN
F  25 ASN
K1195 GLN
K1255 HIS
K1379 GLN
** K1451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1481 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.083429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.063089 restraints weight = 196995.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.064118 restraints weight = 124350.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.064868 restraints weight = 90708.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.065218 restraints weight = 75040.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.066063 restraints weight = 65567.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  18109  Z= 0.270
  Angle     :  0.769   8.697  25866  Z= 0.435
  Chirality :  0.043   0.200   2882
  Planarity :  0.006   0.112   2154
  Dihedral  : 27.965 146.363   5102
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  6.65 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.23), residues: 1263
  helix:  1.10 (0.19), residues: 724
  sheet:  0.52 (0.74), residues: 58
  loop :  0.18 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG K1324 
 TYR   0.030   0.003   TYR F  88 
 PHE   0.037   0.002   PHE K1090 
 TRP   0.009   0.001   TRP K1129 
 HIS   0.012   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 (18109)
  covalent geometry    : angle       0.76858 (25866)
  hydrogen bonds       : bond        0.09774 (  918)
  hydrogen bonds       : angle       3.92091 ( 2343)

*********************** 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
  69 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7031 (mtmm)
REVERT: D   68 ASP cc_start: 0.9079 (t0) cc_final: 0.8741 (t0)
REVERT: D   71 GLU cc_start: 0.8863 (pp20) cc_final: 0.8636 (pp20)
REVERT: H   59 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8108 (tpt)
REVERT: H   71 GLU cc_start: 0.9030 (tt0) cc_final: 0.8517 (tp30)
REVERT: K 1652 MET cc_start: 0.5583 (ppp) cc_final: 0.5282 (ppp)
  outliers start: 10
  outliers final: 5
  residues processed: 66
  average time/residue: 0.1059
  time to fit residues: 11.1619
Evaluate side-chains
  46 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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 E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain K residue 1059 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 140 optimal weight:   40.0000
   chunk 126 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 95 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 145 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.079306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.057571 restraints weight = 186202.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.058695 restraints weight = 112982.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.059555 restraints weight = 82725.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.059981 restraints weight = 67530.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.060754 restraints weight = 59681.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  18109  Z= 0.205
  Angle     :  0.625   7.688  25866  Z= 0.362
  Chirality :  0.037   0.175   2882
  Planarity :  0.004   0.061   2154
  Dihedral  : 28.586 145.813   5102
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.26 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.23), residues: 1263
  helix:  1.53 (0.19), residues: 730
  sheet:  0.59 (0.69), residues: 71
  loop :  0.24 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  99 
 TYR   0.026   0.002   TYR F  88 
 PHE   0.013   0.001   PHE F 100 
 TRP   0.004   0.001   TRP K1122 
 HIS   0.006   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (18109)
  covalent geometry    : angle       0.62536 (25866)
  hydrogen bonds       : bond        0.05312 (  918)
  hydrogen bonds       : angle       3.38100 ( 2343)

*********************** 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
  58 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.390 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8831 (tmm) cc_final: 0.8459 (tmm)
REVERT: B   88 TYR cc_start: 0.8774 (m-80) cc_final: 0.8548 (m-80)
REVERT: D   71 GLU cc_start: 0.9058 (pp20) cc_final: 0.8844 (pp20)
REVERT: F   84 MET cc_start: 0.9303 (tpp) cc_final: 0.8974 (tpp)
REVERT: H   71 GLU cc_start: 0.9488 (tt0) cc_final: 0.8970 (tp30)
REVERT: K 1652 MET cc_start: 0.5837 (ppp) cc_final: 0.5561 (ppp)
  outliers start: 11
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0935
  time to fit residues: 8.9048
Evaluate side-chains
  45 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain K residue 1102 ILE
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 51 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 87 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 132 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 103 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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**
E  39 HIS
K1591 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.070132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.047208 restraints weight = 182450.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.048174 restraints weight = 116802.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.048954 restraints weight = 88457.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.049615 restraints weight = 72849.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.049901 restraints weight = 63760.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.8468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094  18109  Z= 0.280
  Angle     :  0.725   8.776  25866  Z= 0.416
  Chirality :  0.040   0.244   2882
  Planarity :  0.006   0.057   2154
  Dihedral  : 28.920 143.641   5102
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 18.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  9.62 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.23), residues: 1263
  helix:  1.24 (0.19), residues: 729
  sheet: -0.05 (0.66), residues: 77
  loop :  0.08 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  99 
 TYR   0.047   0.002   TYR F  88 
 PHE   0.019   0.002   PHE K1090 
 TRP   0.007   0.001   TRP K1649 
 HIS   0.009   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 (18109)
  covalent geometry    : angle       0.72490 (25866)
  hydrogen bonds       : bond        0.08461 (  918)
  hydrogen bonds       : angle       3.78983 ( 2343)

*********************** 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
  78 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 0.360 
Fit side-chains
REVERT: F   84 MET cc_start: 0.9198 (tpp) cc_final: 0.8993 (tpp)
REVERT: G   25 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7699 (m-10)
REVERT: H   71 GLU cc_start: 0.9505 (tt0) cc_final: 0.9029 (tp30)
  outliers start: 27
  outliers final: 13
  residues processed: 72
  average time/residue: 0.1030
  time to fit residues: 12.0495
Evaluate side-chains
  49 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   54 ILE
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 E residue  118 THR
Chi-restraints excluded: chain G residue   25 PHE
Chi-restraints excluded: chain H residue   59 MET
Chi-restraints excluded: chain K residue 1102 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0050
   chunk 36 optimal weight:   10.0000
   chunk 108 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 130 optimal weight:   50.0000
   chunk 12 optimal weight:    5.9990
   chunk 136 optimal weight:    8.9990
   chunk 129 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C  89 ASN
K1489 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.070826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.047847 restraints weight = 178719.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.048927 restraints weight = 110546.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.049535 restraints weight = 82254.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.050042 restraints weight = 68303.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.050632 restraints weight = 59864.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.8691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  18109  Z= 0.157
  Angle     :  0.574   9.061  25866  Z= 0.331
  Chirality :  0.035   0.276   2882
  Planarity :  0.003   0.051   2154
  Dihedral  : 29.033 145.967   5102
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.06 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.24), residues: 1263
  helix:  1.59 (0.19), residues: 734
  sheet:  0.07 (0.66), residues: 77
  loop :  0.26 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  39 
 TYR   0.033   0.001   TYR F  88 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.005   0.001   TRP K1649 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (18109)
  covalent geometry    : angle       0.57418 (25866)
  hydrogen bonds       : bond        0.04339 (  918)
  hydrogen bonds       : angle       3.26596 ( 2343)

*********************** 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
  63 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 GLU cc_start: 0.9280 (tt0) cc_final: 0.9038 (tp30)
  outliers start: 18
  outliers final: 11
  residues processed: 60
  average time/residue: 0.1106
  time to fit residues: 10.8907
Evaluate side-chains
  47 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   85 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 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 88 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 144 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
** K1199 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 = 0.3940 r_free = 0.3940 target = 0.069941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.049004 restraints weight = 183842.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.049459 restraints weight = 115089.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.049661 restraints weight = 85708.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.050501 restraints weight = 74184.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.050605 restraints weight = 66076.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.9467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  18109  Z= 0.170
  Angle     :  0.581   9.566  25866  Z= 0.335
  Chirality :  0.035   0.243   2882
  Planarity :  0.004   0.036   2154
  Dihedral  : 28.805 143.571   5102
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.51 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.24), residues: 1263
  helix:  1.71 (0.19), residues: 737
  sheet:  0.35 (0.69), residues: 71
  loop :  0.23 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  72 
 TYR   0.036   0.001   TYR F  88 
 PHE   0.015   0.001   PHE G  25 
 TRP   0.006   0.001   TRP K1649 
 HIS   0.007   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (18109)
  covalent geometry    : angle       0.58083 (25866)
  hydrogen bonds       : bond        0.05082 (  918)
  hydrogen bonds       : angle       3.16533 ( 2343)

*********************** 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
  65 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 42
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 GLU cc_start: 0.9405 (tt0) cc_final: 0.8769 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 62
  average time/residue: 0.0957
  time to fit residues: 9.9158
Evaluate side-chains
  56 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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   85 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   61 LEU
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 F residue   85 ASP
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue 1102 ILE
Chi-restraints excluded: chain K residue 1121 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 146 optimal weight:   30.0000
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 122 optimal weight:    0.0070
   chunk 33 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 73 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 112 optimal weight:    9.9990
   overall best weight:    4.4006

-------------------------------------------------------------------------------
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  93 GLN
C  73 ASN
** K1451 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 = 0.3829 r_free = 0.3829 target = 0.064323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.043207 restraints weight = 188040.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.043630 restraints weight = 118083.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.044075 restraints weight = 87557.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.044290 restraints weight = 73693.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.044274 restraints weight = 62944.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          1.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  18109  Z= 0.245
  Angle     :  0.686  10.928  25866  Z= 0.388
  Chirality :  0.039   0.238   2882
  Planarity :  0.006   0.082   2154
  Dihedral  : 29.591 148.870   5102
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.23 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.23), residues: 1263
  helix:  1.20 (0.19), residues: 744
  sheet: -0.18 (0.68), residues: 73
  loop :  0.11 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  55 
 TYR   0.023   0.002   TYR B  51 
 PHE   0.017   0.002   PHE K1125 
 TRP   0.007   0.001   TRP K1649 
 HIS   0.009   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (18109)
  covalent geometry    : angle       0.68598 (25866)
  hydrogen bonds       : bond        0.07086 (  918)
  hydrogen bonds       : angle       3.81832 ( 2343)

*********************** 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
  61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 40
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 GLU cc_start: 0.9381 (tt0) cc_final: 0.8777 (tp30)
  outliers start: 21
  outliers final: 15
  residues processed: 56
  average time/residue: 0.0946
  time to fit residues: 9.4879
Evaluate side-chains
  52 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
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 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 1446 TYR
Chi-restraints excluded: chain K residue 1624 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0370
   chunk 57 optimal weight:    1.9990
   chunk 150 optimal weight:    0.0040
   chunk 101 optimal weight:    9.9990
   chunk 147 optimal weight:   10.0000
   chunk 111 optimal weight:    6.9990
   chunk 88 optimal weight:   20.0000
   chunk 148 optimal weight:   10.0000
   overall best weight:    2.6076

-------------------------------------------------------------------------------
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 108 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1199 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 = 0.3776 r_free = 0.3776 target = 0.063326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.039967 restraints weight = 180137.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.040508 restraints weight = 115853.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.040991 restraints weight = 84498.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.041422 restraints weight = 70929.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.041752 restraints weight = 62581.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          1.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  18109  Z= 0.168
  Angle     :  0.609  11.969  25866  Z= 0.343
  Chirality :  0.036   0.278   2882
  Planarity :  0.004   0.042   2154
  Dihedral  : 29.449 149.641   5102
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.95 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.23), residues: 1263
  helix:  1.46 (0.19), residues: 739
  sheet: -0.12 (0.68), residues: 71
  loop :  0.14 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  99 
 TYR   0.034   0.001   TYR F  88 
 PHE   0.011   0.001   PHE K1504 
 TRP   0.007   0.001   TRP K1649 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (18109)
  covalent geometry    : angle       0.60903 (25866)
  hydrogen bonds       : bond        0.04958 (  918)
  hydrogen bonds       : angle       3.44163 ( 2343)

*********************** 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
  64 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   71 GLU cc_start: 0.9276 (tt0) cc_final: 0.9022 (tp30)
  outliers start: 22
  outliers final: 17
  residues processed: 61
  average time/residue: 0.0996
  time to fit residues: 10.4932
Evaluate side-chains
  57 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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 C residue   62 ILE
Chi-restraints excluded: chain C residue   85 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   61 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   89 VAL
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 49 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 147 optimal weight:    0.0370
   chunk 29 optimal weight:    0.8980
   chunk 150 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 132 optimal weight:   30.0000
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 107 optimal weight:    7.9990
   overall best weight:    1.9662

-------------------------------------------------------------------------------
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**
** 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 = 0.3840 r_free = 0.3840 target = 0.064725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.043600 restraints weight = 185174.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.043962 restraints weight = 112872.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.044151 restraints weight = 83388.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.044816 restraints weight = 71712.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.044889 restraints weight = 63397.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          1.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  18109  Z= 0.154
  Angle     :  0.602  11.378  25866  Z= 0.338
  Chirality :  0.036   0.300   2882
  Planarity :  0.003   0.036   2154
  Dihedral  : 29.336 150.377   5102
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.22 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.23), residues: 1263
  helix:  1.57 (0.19), residues: 735
  sheet: -0.18 (0.67), residues: 71
  loop :  0.16 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  42 
 TYR   0.031   0.001   TYR F  88 
 PHE   0.012   0.001   PHE K1504 
 TRP   0.006   0.001   TRP K1649 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (18109)
  covalent geometry    : angle       0.60173 (25866)
  hydrogen bonds       : bond        0.04519 (  918)
  hydrogen bonds       : angle       3.34820 ( 2343)

*********************** 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
  60 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.7141 (tptp) cc_final: 0.6719 (tmtt)
REVERT: E   50 GLU cc_start: 0.9265 (pm20) cc_final: 0.8963 (pm20)
REVERT: H   71 GLU cc_start: 0.9417 (tt0) cc_final: 0.8785 (tp30)
  outliers start: 18
  outliers final: 17
  residues processed: 58
  average time/residue: 0.0917
  time to fit residues: 8.7997
Evaluate side-chains
  58 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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 C residue   62 ILE
Chi-restraints excluded: chain C residue   85 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  117 VAL
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 1445 ASP
Chi-restraints excluded: chain K residue 1446 TYR
Chi-restraints excluded: chain K residue 1624 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 105 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0670
   chunk 102 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 21 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 137 optimal weight:   50.0000
   chunk 47 optimal weight:    0.9980
   overall best weight:    2.3522

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1389 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.063800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.043040 restraints weight = 187084.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.043776 restraints weight = 113833.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.044210 restraints weight = 84389.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.044363 restraints weight = 69136.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.044655 restraints weight = 62342.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          1.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  18109  Z= 0.164
  Angle     :  0.615  12.587  25866  Z= 0.342
  Chirality :  0.036   0.287   2882
  Planarity :  0.004   0.036   2154
  Dihedral  : 29.282 154.707   5102
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.31 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.23), residues: 1263
  helix:  1.60 (0.19), residues: 735
  sheet: -0.18 (0.68), residues: 69
  loop :  0.13 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  42 
 TYR   0.031   0.001   TYR F  88 
 PHE   0.013   0.001   PHE A 104 
 TRP   0.005   0.001   TRP K1649 
 HIS   0.006   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (18109)
  covalent geometry    : angle       0.61458 (25866)
  hydrogen bonds       : bond        0.04834 (  918)
  hydrogen bonds       : angle       3.34970 ( 2343)

********************** 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
  61 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.6770 (tptp) cc_final: 0.6336 (tmtt)
REVERT: H   71 GLU cc_start: 0.9045 (tt0) cc_final: 0.8541 (tp30)
  outliers start: 20
  outliers final: 17
  residues processed: 57
  average time/residue: 0.0997
  time to fit residues: 9.7085
Evaluate side-chains
  56 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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   58 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   85 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  117 VAL
Chi-restraints excluded: chain E residue  118 THR
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 1445 ASP
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 110 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 154 optimal weight:    0.0970
   chunk 42 optimal weight:    6.9990
   chunk 147 optimal weight:    8.9990
   chunk 121 optimal weight:    5.9990
   chunk 146 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    5.4186

-------------------------------------------------------------------------------
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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
C  73 ASN
** K1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1327 HIS
** K1451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.058138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.038420 restraints weight = 198945.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.037763 restraints weight = 125960.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.038155 restraints weight = 90570.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.038508 restraints weight = 73631.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.038745 restraints weight = 64437.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          1.4094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  18109  Z= 0.282
  Angle     :  0.739  11.059  25866  Z= 0.412
  Chirality :  0.042   0.315   2882
  Planarity :  0.006   0.069   2154
  Dihedral  : 30.129 178.695   5102
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 20.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.40 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.23), residues: 1263
  helix:  1.14 (0.19), residues: 744
  sheet: -0.44 (0.71), residues: 59
  loop : -0.13 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E  49 
 TYR   0.035   0.002   TYR F  88 
 PHE   0.023   0.002   PHE K1504 
 TRP   0.008   0.001   TRP K1436 
 HIS   0.008   0.002   HIS K1659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00611 (18109)
  covalent geometry    : angle       0.73940 (25866)
  hydrogen bonds       : bond        0.08929 (  918)
  hydrogen bonds       : angle       4.02845 ( 2343)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4092.74 seconds
wall clock time: 70 minutes 35.86 seconds (4235.86 seconds total)