Starting phenix.real_space_refine
on Fri Jun  5 01:13:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21wa_68034/06_2026/21wa_68034.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21wa_68034/06_2026/21wa_68034.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/21wa_68034/06_2026/21wa_68034.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21wa_68034/06_2026/21wa_68034.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/21wa_68034/06_2026/21wa_68034.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21wa_68034/06_2026/21wa_68034.map"
  }
  resolution = 3.7
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     P     276      5.49       5
     Mg      1      5.21       5
     S      38      5.16       5
     Be      1      3.05       5
     C    9673      2.51       5
     N    3092      2.21       5
     O    3617      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16701
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 825
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "G"
      Number of atoms: 858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 858
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 5, 'TRANS': 106}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 4936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 4936
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 19, 'TRANS': 583}
          Chain breaks: 5
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "X"
      Number of atoms: 2791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 2791
          Classifications: {'DNA': 137}
          Link IDs: {'rna3p': 136}
    Chain: "Y"
      Number of atoms: 2826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 2826
          Classifications: {'DNA': 137}
          Link IDs: {'rna3p': 136}
    Chain: "I"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.24, per 1000 atoms: 0.25
  Number of scatterers: 16701
  At special positions: 0
  Unit cell: (106.7, 121, 156.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      38     16.00
     P     276     15.00
     Mg      1     11.99
     F       3      9.00
     O    3617      8.00
     N    3092      7.00
     C    9673      6.00
     Be      1      4.00
    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: 1.48
  Conformation dependent library (CDL) restraints added in 605.4 milliseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 10 sheets defined
      62.7% alpha, 4.6% beta
      98 base pairs and 230 stacking pairs defined.
    Time for finding SS restraints: 2.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.970A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 76
    Processing helix  chain 'A' and resid 85 through 112
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.818A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.931A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.492A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.596A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
      removed outlier: 3.534A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 105 through 123
      removed outlier: 3.617A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.673A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.871A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.689A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.820A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.907A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR F  88 " --> pdb=" O   MET F  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.677A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.662A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.940A  pdb=" N   ALA H  97 " --> pdb=" O   GLU H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.519A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 548 through 573
      removed outlier: 3.521A  pdb=" N   TYR I 552 " --> pdb=" O   LYS I 548 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN I 555 " --> pdb=" O   ALA I 551 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLN I 556 " --> pdb=" O   TYR I 552 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP I 558 " --> pdb=" O   LEU I 554 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   VAL I 561 " --> pdb=" O   THR I 557 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ALA I 562 " --> pdb=" O   ASP I 558 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 732 through 736
      removed outlier: 3.785A  pdb=" N   HIS I 736 " --> pdb=" O   TYR I 732 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 732 through 736'
    Processing helix  chain 'I' and resid 755 through 771
    Processing helix  chain 'I' and resid 786 through 799
    Processing helix  chain 'I' and resid 811 through 825
      removed outlier: 4.667A  pdb=" N   SER I 816 " --> pdb=" O   LEU I 812 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ASN I 817 " --> pdb=" O   SER I 813 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA I 819 " --> pdb=" O   LEU I 815 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 837 through 843
    Processing helix  chain 'I' and resid 844 through 851
    Processing helix  chain 'I' and resid 859 through 866
      removed outlier: 3.662A  pdb=" N   ILE I 863 " --> pdb=" O   THR I 859 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE I 864 " --> pdb=" O   TYR I 860 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 866 through 871
    Processing helix  chain 'I' and resid 882 through 888
      removed outlier: 3.799A  pdb=" N   ARG I 885 " --> pdb=" O   GLU I 882 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASN I 888 " --> pdb=" O   ARG I 885 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 891 through 899
    Processing helix  chain 'I' and resid 918 through 929
    Processing helix  chain 'I' and resid 960 through 972
      removed outlier: 3.990A  pdb=" N   LEU I 972 " --> pdb=" O   LEU I 968 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 980 through 985
      removed outlier: 3.634A  pdb=" N   VAL I 984 " --> pdb=" O   LEU I 980 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1001 through 1015
      removed outlier: 4.006A  pdb=" N   ARG I1009 " --> pdb=" O   ARG I1005 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   HIS I1010 " --> pdb=" O   VAL I1006 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1037 through 1048
      removed outlier: 3.503A  pdb=" N   GLN I1041 " --> pdb=" O   ASN I1037 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1049 through 1053
      removed outlier: 3.829A  pdb=" N   PHE I1052 " --> pdb=" O   PRO I1049 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLN I1053 " --> pdb=" O   TYR I1050 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 1049 through 1053'
    Processing helix  chain 'I' and resid 1054 through 1063
    Processing helix  chain 'I' and resid 1073 through 1079
      removed outlier: 4.255A  pdb=" N   SER I1079 " --> pdb=" O   LEU I1075 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1079 through 1095
      Proline residue:  I1090  - end of helix
      removed outlier: 3.576A  pdb=" N   THR I1095 " --> pdb=" O   LYS I1091 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1105 through 1120
      removed outlier: 3.665A  pdb=" N   MET I1109 " --> pdb=" O   MET I1105 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ASP I1114 " --> pdb=" O   THR I1110 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   TYR I1115 " --> pdb=" O   ILE I1111 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1133 through 1144
      removed outlier: 4.391A  pdb=" N   MET I1137 " --> pdb=" O   GLU I1133 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1179 through 1188
      removed outlier: 3.851A  pdb=" N   ASP I1183 " --> pdb=" O   ASN I1179 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1189 through 1191
      No H-bonds generated for 'chain 'I' and resid 1189 through 1191'
    Processing helix  chain 'I' and resid 1209 through 1227
      removed outlier: 4.265A  pdb=" N   LYS I1213 " --> pdb=" O   SER I1209 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL I1224 " --> pdb=" O   TYR I1220 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LYS I1227 " --> pdb=" O   ASN I1223 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1241 through 1255
      removed outlier: 3.615A  pdb=" N   ALA I1245 " --> pdb=" O   HIS I1241 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA I1249 " --> pdb=" O   ALA I1245 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ILE I1250 " --> pdb=" O   PHE I1246 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU I1251 " --> pdb=" O   LEU I1247 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLU I1252 " --> pdb=" O   GLN I1248 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU I1255 " --> pdb=" O   LEU I1251 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1300 through 1307
      removed outlier: 4.187A  pdb=" N   GLN I1304 " --> pdb=" O   GLU I1300 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1309 through 1317
      removed outlier: 3.580A  pdb=" N   PHE I1316 " --> pdb=" O   GLU I1312 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   MET I1317 " --> pdb=" O   PHE I1313 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1319 through 1330
      removed outlier: 3.771A  pdb=" N   ASN I1330 " --> pdb=" O   GLU I1326 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.816A  pdb=" N   THR B  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.376A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.887A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.695A  pdb=" N   THR F  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.459A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA8, first strand: chain 'I' and resid 776 through 777
      removed outlier: 6.561A  pdb=" N   MET I 878 " --> pdb=" O   LEU I 907 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   LEU I 909 " --> pdb=" O   MET I 878 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL I 880 " --> pdb=" O   LEU I 909 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU I 807 " --> pdb=" O   ILE I 879 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ILE I 808 " --> pdb=" O   THR I 858 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL I 832 " --> pdb=" O   LEU I 857 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 992 through 998
      removed outlier: 6.986A  pdb=" N   VAL I1171 " --> pdb=" O   LEU I1202 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   LEU I1204 " --> pdb=" O   VAL I1171 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   ILE I1173 " --> pdb=" O   LEU I1204 " (cutoff:3.500A)
      removed outlier: 8.853A  pdb=" N   THR I1206 " --> pdb=" O   ILE I1173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL I1099 " --> pdb=" O   PHE I1152 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LEU I1154 " --> pdb=" O   VAL I1099 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU I1101 " --> pdb=" O   LEU I1154 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU I1124 " --> pdb=" O   LEU I1153 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   SER I1155 " --> pdb=" O   LEU I1124 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   LEU I1126 " --> pdb=" O   SER I1155 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 1016 through 1018

    559 hydrogen bonds defined for protein.
    1659 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      253 hydrogen bonds
      494 hydrogen bond angles
      0 basepair planarities
      98 basepair parallelities
      230 stacking parallelities
  Total time for adding SS restraints: 4.25

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3628
        1.33 -     1.45: 4838
        1.45 -     1.57: 8476
        1.57 -     1.69: 549
        1.69 -     1.81: 68
  Bond restraints: 17559
  Sorted by residual:
  bond pdb=" C3'  DT Y  15 "
       pdb=" O3'  DT Y  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.84e+00
  bond pdb=" C3'  DG Y  94 "
       pdb=" O3'  DG Y  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" N   LYS C  74 "
       pdb=" CA  LYS C  74 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.21e+00
  bond pdb=" C4  ADP I1802 "
       pdb=" C5  ADP I1802 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.04e+00
  bond pdb=" C3'  DC Y 126 "
       pdb=" O3'  DC Y 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 1.02e+00
  ... (remaining 17554 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 24126
        1.40 -     2.81: 654
        2.81 -     4.21: 57
        4.21 -     5.62: 23
        5.62 -     7.02: 6
  Bond angle restraints: 24866
  Sorted by residual:
  angle pdb=" N   ILE A 112 "
        pdb=" CA  ILE A 112 "
        pdb=" C   ILE A 112 "
      ideal   model   delta    sigma   weight residual
     112.83  107.33    5.50 9.90e-01 1.02e+00 3.09e+01
  angle pdb=" N   GLY I1072 "
        pdb=" CA  GLY I1072 "
        pdb=" C   GLY I1072 "
      ideal   model   delta    sigma   weight residual
     111.56  115.07   -3.51 1.01e+00 9.80e-01 1.21e+01
  angle pdb=" N   PHE F 100 "
        pdb=" CA  PHE F 100 "
        pdb=" C   PHE F 100 "
      ideal   model   delta    sigma   weight residual
     114.56  111.21    3.35 1.27e+00 6.20e-01 6.97e+00
  angle pdb=" CA  ILE C  79 "
        pdb=" C   ILE C  79 "
        pdb=" N   PRO C  80 "
      ideal   model   delta    sigma   weight residual
     117.33  119.99   -2.66 1.01e+00 9.80e-01 6.96e+00
  angle pdb=" C   LEU I1063 "
        pdb=" N   GLY I1064 "
        pdb=" CA  GLY I1064 "
      ideal   model   delta    sigma   weight residual
     123.30  120.63    2.67 1.06e+00 8.90e-01 6.37e+00
  ... (remaining 24861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.34: 8548
       34.34 -    68.68: 1306
       68.68 -   103.01: 46
      103.01 -   137.35: 0
      137.35 -   171.69: 3
  Dihedral angle restraints: 9903
    sinusoidal: 5902
      harmonic: 4001
  Sorted by residual:
  dihedral pdb=" O2A ADP I1802 "
           pdb=" O3A ADP I1802 "
           pdb=" PA  ADP I1802 "
           pdb=" PB  ADP I1802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -159.53   99.54     1      2.00e+01 2.50e-03 2.80e+01
  dihedral pdb=" C4'  DT Y  15 "
           pdb=" C3'  DT Y  15 "
           pdb=" O3'  DT Y  15 "
           pdb=" P    DC Y  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   48.31  171.69     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG Y  94 "
           pdb=" C3'  DG Y  94 "
           pdb=" O3'  DG Y  94 "
           pdb=" P    DG Y  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.08  161.92     1      3.50e+01 8.16e-04 1.53e+01
  ... (remaining 9900 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1777
       0.027 -    0.054: 714
       0.054 -    0.082: 201
       0.082 -    0.109: 85
       0.109 -    0.136: 32
  Chirality restraints: 2809
  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    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  ILE F  46 "
            pdb=" N   ILE F  46 "
            pdb=" C   ILE F  46 "
            pdb=" CB  ILE F  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CA  ILE I 808 "
            pdb=" N   ILE I 808 "
            pdb=" C   ILE I 808 "
            pdb=" CB  ILE I 808 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 2806 not shown)

  Planarity restraints: 2196
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA Y  91 "   -0.025 2.00e-02 2.50e+03   1.17e-02 3.73e+00
        pdb=" N9   DA Y  91 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA Y  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DA Y  91 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA Y  91 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DA Y  91 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA Y  91 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA Y  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA Y  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA Y  91 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA Y  91 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY I 804 "   -0.027 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO I 805 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO I 805 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO I 805 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA X 131 "    0.023 2.00e-02 2.50e+03   9.66e-03 2.57e+00
        pdb=" N9   DA X 131 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DA X 131 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DA X 131 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA X 131 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA X 131 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA X 131 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA X 131 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DA X 131 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA X 131 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA X 131 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 2193 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 199
        2.64 -     3.20: 14515
        3.20 -     3.77: 28208
        3.77 -     4.33: 37525
        4.33 -     4.90: 56843
  Nonbonded interactions: 137290
  Sorted by model distance:
  nonbonded pdb=" O2   DC X 143 "
            pdb=" N2   DG Y   5 "
     model   vdw
     2.069 2.496
  nonbonded pdb=" N2   DG X 148 "
            pdb=" O2   DC Y   0 "
     model   vdw
     2.075 2.496
  nonbonded pdb=" O2   DC X  95 "
            pdb=" N2   DG Y  53 "
     model   vdw
     2.077 2.496
  nonbonded pdb=" OD2 ASP I 881 "
            pdb="MG    MG I1801 "
     model   vdw
     2.152 2.170
  nonbonded pdb=" OE1 GLN I1104 "
            pdb=" OG1 THR I1156 "
     model   vdw
     2.214 3.040
  ... (remaining 137285 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and (resid 22 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
  selection = (chain 'F' and resid 22 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 117)
}
ncs_group {
  reference = (chain 'D' and resid 31 through 124)
  selection = chain 'H'
}

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=1.00 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:             4.450
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     19.800
  Find NCS groups from input model:        0.160
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
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   0.041  17559  Z= 0.154
  Angle     :  0.562   7.019  24866  Z= 0.332
  Chirality :  0.035   0.136   2809
  Planarity :  0.004   0.041   2196
  Dihedral  : 24.504 171.690   7315
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.51 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.14 (0.23), residues: 1346
  helix:  1.16 (0.19), residues: 788
  sheet: -0.11 (0.69), residues: 64
  loop : -1.66 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I 966 
 TYR   0.020   0.001   TYR I 560 
 PHE   0.012   0.001   PHE I1152 
 TRP   0.012   0.001   TRP I 922 
 HIS   0.003   0.001   HIS I 868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (17559)
  covalent geometry    : angle       0.56188 /  0.33 (24866)
  hydrogen bonds       : bond        0.12470 /  8.80 (  812)
  hydrogen bonds       : angle       4.57381 /  3.28 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7324 (mtp-110)
REVERT: B   27 GLN cc_start: 0.8007 (mp10) cc_final: 0.7703 (mp10)
REVERT: D   86 ARG cc_start: 0.8334 (mpt180) cc_final: 0.8029 (mpt180)
REVERT: G  104 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8166 (mm-40)
REVERT: H   47 GLN cc_start: 0.8266 (tt0) cc_final: 0.8023 (tt0)
REVERT: H   59 MET cc_start: 0.8525 (tpp) cc_final: 0.8184 (tpp)
REVERT: I  972 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5248 (pp)
REVERT: I 1076 TYR cc_start: 0.6876 (t80) cc_final: 0.6367 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 174
  average time/residue: 0.1771
  time to fit residues: 42.4803
Evaluate side-chains
  143 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0030
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    0.0070
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.1980
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.2608

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A  68 GLN
A  85 GLN
A 125 GLN
B  75 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
H 109 HIS
I 770 ASN
I 788 GLN
I 847 GLN
I 941 GLN
I1012 GLN
I1062 HIS
I1097 HIS
I1208 ASN
I1253 HIS
I1330 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.187105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.175113 restraints weight = 19771.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.153503 restraints weight = 47801.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.149135 restraints weight = 38636.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.149341 restraints weight = 35966.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.149310 restraints weight = 29052.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17559  Z= 0.134
  Angle     :  0.546  10.992  24866  Z= 0.307
  Chirality :  0.036   0.139   2809
  Planarity :  0.004   0.040   2196
  Dihedral  : 28.157 172.282   4546
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.26 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.45 (0.23), residues: 1346
  helix:  1.43 (0.19), residues: 807
  sheet:  0.17 (0.69), residues: 64
  loop : -1.71 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I1323 
 TYR   0.019   0.001   TYR I 560 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.011   0.001   TRP I 922 
 HIS   0.003   0.001   HIS I1253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 (17559)
  covalent geometry    : angle       0.54589 /  0.31 (24866)
  hydrogen bonds       : bond        0.04895 /  3.41 (  812)
  hydrogen bonds       : angle       3.40847 /  2.45 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7477 (mtm110)
REVERT: D   86 ARG cc_start: 0.8346 (mpt180) cc_final: 0.7990 (mpt180)
REVERT: F   84 MET cc_start: 0.8899 (tpp) cc_final: 0.8592 (tpt)
REVERT: H   47 GLN cc_start: 0.8129 (tt0) cc_final: 0.7924 (tt0)
REVERT: H   62 MET cc_start: 0.9033 (mmm) cc_final: 0.8808 (mmm)
REVERT: I  765 LEU cc_start: 0.5996 (pp) cc_final: 0.5404 (mt)
REVERT: I  972 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.4944 (pp)
REVERT: I 1011 MET cc_start: 0.7299 (tpp) cc_final: 0.6496 (ttm)
REVERT: I 1338 MET cc_start: 0.7017 (tpp) cc_final: 0.6801 (mpp)
REVERT: I 1366 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5227 (ptt)
  outliers start: 23
  outliers final: 12
  residues processed: 176
  average time/residue: 0.1895
  time to fit residues: 45.7129
Evaluate side-chains
  147 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1299 ASP
Chi-restraints excluded: chain I residue 1366 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 2 optimal weight:    0.0270
   chunk 73 optimal weight:   10.0000
   chunk 85 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 900 HIS
I1062 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.187710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.174642 restraints weight = 19605.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.156835 restraints weight = 54952.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.152042 restraints weight = 49284.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.151634 restraints weight = 48763.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.152065 restraints weight = 33564.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17559  Z= 0.145
  Angle     :  0.538   7.490  24866  Z= 0.304
  Chirality :  0.036   0.151   2809
  Planarity :  0.004   0.039   2196
  Dihedral  : 28.190 174.619   4546
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.62 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.54 (0.23), residues: 1346
  helix:  1.49 (0.19), residues: 808
  sheet:  0.21 (0.68), residues: 64
  loop : -1.68 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I1325 
 TYR   0.018   0.001   TYR I 560 
 PHE   0.009   0.001   PHE I1152 
 TRP   0.012   0.001   TRP I 922 
 HIS   0.005   0.001   HIS I1253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.15 (17559)
  covalent geometry    : angle       0.53850 /  0.30 (24866)
  hydrogen bonds       : bond        0.04855 /  3.39 (  812)
  hydrogen bonds       : angle       3.29058 /  2.36 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7411 (mtm110)
REVERT: B   27 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7566 (mp10)
REVERT: D   86 ARG cc_start: 0.8341 (mpt180) cc_final: 0.8000 (mpt180)
REVERT: F   84 MET cc_start: 0.8916 (tpp) cc_final: 0.8647 (tpt)
REVERT: H   47 GLN cc_start: 0.8243 (tt0) cc_final: 0.8029 (tt0)
REVERT: I  765 LEU cc_start: 0.5804 (pp) cc_final: 0.5129 (mt)
REVERT: I  792 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7629 (tp)
REVERT: I  972 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5174 (pp)
REVERT: I 1011 MET cc_start: 0.7292 (tpp) cc_final: 0.6747 (ttt)
REVERT: I 1317 MET cc_start: 0.6159 (mmp) cc_final: 0.5865 (mmm)
REVERT: I 1366 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5083 (ptt)
  outliers start: 30
  outliers final: 15
  residues processed: 172
  average time/residue: 0.1841
  time to fit residues: 43.6155
Evaluate side-chains
  155 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  792 LEU
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue  992 VAL
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1299 ASP
Chi-restraints excluded: chain I residue 1366 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 132 optimal weight:    0.0270
   chunk 4 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 803 ASN
I1062 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.188255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.175636 restraints weight = 19509.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.156716 restraints weight = 48628.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.151940 restraints weight = 43864.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.151580 restraints weight = 40688.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.151427 restraints weight = 32134.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17559  Z= 0.155
  Angle     :  0.541   7.670  24866  Z= 0.304
  Chirality :  0.037   0.145   2809
  Planarity :  0.004   0.046   2196
  Dihedral  : 28.248 175.254   4544
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.04 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.52 (0.23), residues: 1346
  helix:  1.45 (0.19), residues: 815
  sheet:  0.33 (0.69), residues: 64
  loop : -1.69 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 801 
 TYR   0.017   0.001   TYR I 560 
 PHE   0.009   0.001   PHE I1152 
 TRP   0.012   0.001   TRP I 922 
 HIS   0.004   0.001   HIS I1253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 (17559)
  covalent geometry    : angle       0.54122 /  0.30 (24866)
  hydrogen bonds       : bond        0.04894 /  3.40 (  812)
  hydrogen bonds       : angle       3.26901 /  2.34 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7446 (mtm180)
REVERT: C   92 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7870 (mp0)
REVERT: D   86 ARG cc_start: 0.8332 (mpt180) cc_final: 0.7991 (mpt180)
REVERT: F   84 MET cc_start: 0.8892 (tpp) cc_final: 0.8665 (tpt)
REVERT: G   58 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8591 (mm)
REVERT: G  104 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8005 (mm110)
REVERT: I  765 LEU cc_start: 0.5889 (pp) cc_final: 0.5285 (mt)
REVERT: I  924 LEU cc_start: 0.7537 (mp) cc_final: 0.7322 (mp)
REVERT: I  972 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5321 (pp)
REVERT: I 1011 MET cc_start: 0.7351 (tpp) cc_final: 0.6757 (ttt)
REVERT: I 1366 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5151 (ptt)
  outliers start: 32
  outliers final: 16
  residues processed: 165
  average time/residue: 0.1785
  time to fit residues: 40.4623
Evaluate side-chains
  152 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue  992 VAL
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1210 VAL
Chi-restraints excluded: chain I residue 1299 ASP
Chi-restraints excluded: chain I residue 1366 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 115 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 144 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I1062 HIS
I1226 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.188812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.174890 restraints weight = 19656.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.157417 restraints weight = 56146.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.152551 restraints weight = 49782.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.151863 restraints weight = 39915.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.152061 restraints weight = 33816.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17559  Z= 0.150
  Angle     :  0.540   7.576  24866  Z= 0.302
  Chirality :  0.036   0.162   2809
  Planarity :  0.004   0.040   2196
  Dihedral  : 28.229 175.804   4544
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.98 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.55 (0.23), residues: 1346
  helix:  1.47 (0.19), residues: 815
  sheet:  0.40 (0.68), residues: 64
  loop : -1.70 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I 801 
 TYR   0.016   0.001   TYR I 560 
 PHE   0.008   0.001   PHE I1152 
 TRP   0.009   0.001   TRP I 922 
 HIS   0.004   0.001   HIS I1253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 (17559)
  covalent geometry    : angle       0.53980 /  0.30 (24866)
  hydrogen bonds       : bond        0.04826 /  3.34 (  812)
  hydrogen bonds       : angle       3.23981 /  2.32 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7846 (mp0)
REVERT: D   86 ARG cc_start: 0.8345 (mpt180) cc_final: 0.8002 (mpt180)
REVERT: F   84 MET cc_start: 0.8923 (tpp) cc_final: 0.8715 (tpt)
REVERT: G   34 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8819 (mp)
REVERT: G  104 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7924 (mm110)
REVERT: I  765 LEU cc_start: 0.5807 (pp) cc_final: 0.5255 (mt)
REVERT: I  924 LEU cc_start: 0.7528 (mp) cc_final: 0.7299 (mp)
REVERT: I  972 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5400 (pp)
REVERT: I 1011 MET cc_start: 0.7339 (tpp) cc_final: 0.6757 (ttt)
REVERT: I 1105 MET cc_start: 0.7414 (mtt) cc_final: 0.7192 (mmt)
REVERT: I 1366 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5201 (ptt)
  outliers start: 26
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1702
  time to fit residues: 37.6717
Evaluate side-chains
  150 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue  992 VAL
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1210 VAL
Chi-restraints excluded: chain I residue 1299 ASP
Chi-restraints excluded: chain I residue 1366 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 149 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 105 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 154 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN
I1062 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.185882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.173324 restraints weight = 19600.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.152690 restraints weight = 48397.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.147473 restraints weight = 43130.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.147992 restraints weight = 41268.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.148477 restraints weight = 28262.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  17559  Z= 0.177
  Angle     :  0.564   8.776  24866  Z= 0.315
  Chirality :  0.038   0.149   2809
  Planarity :  0.004   0.047   2196
  Dihedral  : 28.461 176.418   4544
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.74 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.44 (0.23), residues: 1346
  helix:  1.38 (0.19), residues: 816
  sheet:  0.10 (0.67), residues: 65
  loop : -1.70 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I 801 
 TYR   0.014   0.001   TYR I 560 
 PHE   0.010   0.001   PHE A  84 
 TRP   0.010   0.001   TRP I 922 
 HIS   0.012   0.001   HIS I1054 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.18 (17559)
  covalent geometry    : angle       0.56368 /  0.32 (24866)
  hydrogen bonds       : bond        0.05201 /  3.60 (  812)
  hydrogen bonds       : angle       3.32948 /  2.38 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8244 (ttp80)
REVERT: C   92 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7903 (mp0)
REVERT: D   86 ARG cc_start: 0.8386 (mpt180) cc_final: 0.8075 (mpt180)
REVERT: G   34 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8739 (mp)
REVERT: G   58 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8664 (mm)
REVERT: G  104 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7831 (mm110)
REVERT: I  765 LEU cc_start: 0.6033 (pp) cc_final: 0.5584 (mt)
REVERT: I  924 LEU cc_start: 0.7659 (mp) cc_final: 0.7385 (mp)
REVERT: I  972 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.5759 (pp)
REVERT: I 1105 MET cc_start: 0.7753 (mtt) cc_final: 0.7292 (mmt)
REVERT: I 1366 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5123 (ptt)
  outliers start: 27
  outliers final: 16
  residues processed: 151
  average time/residue: 0.1858
  time to fit residues: 38.6893
Evaluate side-chains
  148 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue  992 VAL
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1210 VAL
Chi-restraints excluded: chain I residue 1299 ASP
Chi-restraints excluded: chain I residue 1337 LEU
Chi-restraints excluded: chain I residue 1366 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 131 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0970
   chunk 134 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 157 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 1 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  27 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I1062 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.186534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.174127 restraints weight = 19605.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.152589 restraints weight = 47030.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.148357 restraints weight = 38414.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.147902 restraints weight = 37500.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.148290 restraints weight = 30526.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17559  Z= 0.139
  Angle     :  0.532   7.983  24866  Z= 0.298
  Chirality :  0.036   0.144   2809
  Planarity :  0.004   0.046   2196
  Dihedral  : 28.214 177.199   4544
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.00 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.52 (0.23), residues: 1346
  helix:  1.46 (0.19), residues: 817
  sheet:  0.37 (0.66), residues: 64
  loop : -1.74 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 801 
 TYR   0.015   0.001   TYR D 121 
 PHE   0.009   0.001   PHE H  70 
 TRP   0.009   0.001   TRP I 922 
 HIS   0.011   0.001   HIS I1054 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 (17559)
  covalent geometry    : angle       0.53227 /  0.30 (24866)
  hydrogen bonds       : bond        0.04732 /  3.27 (  812)
  hydrogen bonds       : angle       3.20564 /  2.28 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: B   27 GLN cc_start: 0.8098 (mp-120) cc_final: 0.7537 (tm-30)
REVERT: B   92 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8224 (ttp80)
REVERT: C   92 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7870 (mp0)
REVERT: D   86 ARG cc_start: 0.8351 (mpt180) cc_final: 0.8021 (mpt180)
REVERT: G   58 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8624 (mm)
REVERT: G  104 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7764 (mm-40)
REVERT: H   59 MET cc_start: 0.8424 (tpp) cc_final: 0.8063 (mmm)
REVERT: I  765 LEU cc_start: 0.6092 (pp) cc_final: 0.5831 (mt)
REVERT: I  924 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7323 (mp)
REVERT: I  972 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.5861 (pp)
REVERT: I 1011 MET cc_start: 0.7245 (tpp) cc_final: 0.6745 (ttt)
REVERT: I 1105 MET cc_start: 0.7774 (mtt) cc_final: 0.7171 (mmt)
REVERT: I 1183 ASP cc_start: 0.6027 (OUTLIER) cc_final: 0.5661 (t70)
REVERT: I 1366 MET cc_start: 0.6295 (pmm) cc_final: 0.5244 (ptt)
  outliers start: 25
  outliers final: 13
  residues processed: 158
  average time/residue: 0.1856
  time to fit residues: 40.5630
Evaluate side-chains
  154 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  924 LEU
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue  992 VAL
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1183 ASP
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1337 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 152 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0030
   chunk 22 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 125 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 135 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I1062 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.189776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.156341 restraints weight = 19619.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.154870 restraints weight = 24597.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.155109 restraints weight = 22825.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.154720 restraints weight = 21213.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.154771 restraints weight = 19649.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17559  Z= 0.132
  Angle     :  0.535   9.015  24866  Z= 0.297
  Chirality :  0.035   0.144   2809
  Planarity :  0.004   0.064   2196
  Dihedral  : 28.112 178.408   4544
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.57 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.63 (0.23), residues: 1346
  helix:  1.58 (0.19), residues: 810
  sheet:  0.59 (0.68), residues: 64
  loop : -1.74 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG I1325 
 TYR   0.013   0.001   TYR I 560 
 PHE   0.015   0.001   PHE I1316 
 TRP   0.009   0.001   TRP I 922 
 HIS   0.010   0.001   HIS I1054 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 (17559)
  covalent geometry    : angle       0.53514 /  0.30 (24866)
  hydrogen bonds       : bond        0.04622 /  3.19 (  812)
  hydrogen bonds       : angle       3.17018 /  2.25 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7486 (mtt180)
REVERT: B   27 GLN cc_start: 0.8004 (mp-120) cc_final: 0.7406 (tm-30)
REVERT: B   92 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8257 (ttp80)
REVERT: C   92 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7896 (mp0)
REVERT: D   86 ARG cc_start: 0.8329 (mpt180) cc_final: 0.7993 (mpt180)
REVERT: G   58 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8615 (mm)
REVERT: G  104 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7867 (mm-40)
REVERT: H   59 MET cc_start: 0.8403 (tpp) cc_final: 0.8066 (mmm)
REVERT: I  765 LEU cc_start: 0.5818 (pp) cc_final: 0.5617 (mt)
REVERT: I  924 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7413 (mp)
REVERT: I  972 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.5796 (pp)
REVERT: I 1011 MET cc_start: 0.7355 (tpp) cc_final: 0.6795 (ttt)
REVERT: I 1105 MET cc_start: 0.7749 (mtt) cc_final: 0.7200 (mmt)
REVERT: I 1183 ASP cc_start: 0.5884 (OUTLIER) cc_final: 0.5572 (t70)
REVERT: I 1317 MET cc_start: 0.6703 (mmp) cc_final: 0.5967 (mmm)
REVERT: I 1366 MET cc_start: 0.6191 (pmm) cc_final: 0.5266 (ptt)
  outliers start: 30
  outliers final: 18
  residues processed: 162
  average time/residue: 0.1800
  time to fit residues: 40.5739
Evaluate side-chains
  160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  924 LEU
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1183 ASP
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1210 VAL
Chi-restraints excluded: chain I residue 1325 ARG
Chi-restraints excluded: chain I residue 1337 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 15 optimal weight:    0.0170
   chunk 103 optimal weight:    1.9990
   chunk 145 optimal weight:    4.9990
   chunk 142 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0060
   chunk 121 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 83 optimal weight:    0.2980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.3434

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I1062 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.189276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.157981 restraints weight = 19652.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.156389 restraints weight = 35142.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.156234 restraints weight = 32464.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.156090 restraints weight = 24565.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.156091 restraints weight = 22029.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17559  Z= 0.131
  Angle     :  0.543  11.069  24866  Z= 0.298
  Chirality :  0.035   0.142   2809
  Planarity :  0.004   0.043   2196
  Dihedral  : 28.084 179.337   4544
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.43 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.66 (0.23), residues: 1346
  helix:  1.60 (0.19), residues: 808
  sheet:  0.73 (0.68), residues: 64
  loop : -1.73 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG I1325 
 TYR   0.016   0.001   TYR D 121 
 PHE   0.009   0.001   PHE H  70 
 TRP   0.009   0.001   TRP I 922 
 HIS   0.010   0.001   HIS I1054 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 (17559)
  covalent geometry    : angle       0.54290 /  0.30 (24866)
  hydrogen bonds       : bond        0.04616 /  3.19 (  812)
  hydrogen bonds       : angle       3.15202 /  2.24 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7485 (mtt180)
REVERT: B   27 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7672 (tm-30)
REVERT: B   92 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8292 (ttp80)
REVERT: C   92 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7908 (mp0)
REVERT: D   86 ARG cc_start: 0.8340 (mpt180) cc_final: 0.7995 (mpt180)
REVERT: G   58 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8603 (mm)
REVERT: G  104 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7937 (mm110)
REVERT: H   59 MET cc_start: 0.8397 (tpp) cc_final: 0.8077 (mmm)
REVERT: I  924 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7441 (mp)
REVERT: I  972 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.5749 (pp)
REVERT: I 1011 MET cc_start: 0.7347 (tpp) cc_final: 0.6763 (ttt)
REVERT: I 1105 MET cc_start: 0.7743 (mtt) cc_final: 0.7201 (mmt)
REVERT: I 1183 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5657 (t70)
REVERT: I 1317 MET cc_start: 0.6478 (mmp) cc_final: 0.5806 (mmm)
REVERT: I 1366 MET cc_start: 0.6104 (pmm) cc_final: 0.5227 (ptt)
  outliers start: 27
  outliers final: 17
  residues processed: 161
  average time/residue: 0.1766
  time to fit residues: 39.7422
Evaluate side-chains
  160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  924 LEU
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1183 ASP
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1210 VAL
Chi-restraints excluded: chain I residue 1325 ARG
Chi-restraints excluded: chain I residue 1337 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0020
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0970
   chunk 50 optimal weight:    0.2980
   chunk 148 optimal weight:    2.9990
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I1062 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.189106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.176379 restraints weight = 19484.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.154072 restraints weight = 44977.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.151051 restraints weight = 37204.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.151479 restraints weight = 30194.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.151433 restraints weight = 24795.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17559  Z= 0.136
  Angle     :  0.550  12.479  24866  Z= 0.300
  Chirality :  0.036   0.144   2809
  Planarity :  0.004   0.042   2196
  Dihedral  : 28.098 179.836   4544
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.51 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.65 (0.23), residues: 1346
  helix:  1.59 (0.19), residues: 808
  sheet:  0.70 (0.69), residues: 64
  loop : -1.72 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG I1325 
 TYR   0.012   0.001   TYR I 560 
 PHE   0.009   0.001   PHE H  70 
 TRP   0.010   0.001   TRP I 764 
 HIS   0.010   0.001   HIS I1054 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.14 (17559)
  covalent geometry    : angle       0.55011 /  0.30 (24866)
  hydrogen bonds       : bond        0.04680 /  3.23 (  812)
  hydrogen bonds       : angle       3.14773 /  2.24 ( 2153)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7487 (mtt180)
REVERT: B   27 GLN cc_start: 0.8127 (mp-120) cc_final: 0.7765 (tm-30)
REVERT: B   92 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8301 (ttp80)
REVERT: C   92 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7870 (mp0)
REVERT: D   86 ARG cc_start: 0.8374 (mpt180) cc_final: 0.8043 (mpt180)
REVERT: G   58 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8609 (mm)
REVERT: G  104 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7987 (mm110)
REVERT: H   59 MET cc_start: 0.8413 (tpp) cc_final: 0.8086 (mmm)
REVERT: I  924 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7360 (mp)
REVERT: I  972 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5638 (pp)
REVERT: I 1011 MET cc_start: 0.7330 (tpp) cc_final: 0.6766 (ttt)
REVERT: I 1105 MET cc_start: 0.7821 (mtt) cc_final: 0.7281 (mmt)
REVERT: I 1183 ASP cc_start: 0.6060 (OUTLIER) cc_final: 0.5755 (t70)
REVERT: I 1317 MET cc_start: 0.6971 (mmp) cc_final: 0.6362 (mmm)
REVERT: I 1329 ARG cc_start: 0.7329 (ptp-170) cc_final: 0.6954 (ptp90)
REVERT: I 1366 MET cc_start: 0.6298 (pmm) cc_final: 0.5313 (ptt)
  outliers start: 28
  outliers final: 19
  residues processed: 157
  average time/residue: 0.1764
  time to fit residues: 38.8459
Evaluate side-chains
  156 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain I residue  754 LEU
Chi-restraints excluded: chain I residue  781 MET
Chi-restraints excluded: chain I residue  869 ILE
Chi-restraints excluded: chain I residue  875 TRP
Chi-restraints excluded: chain I residue  924 LEU
Chi-restraints excluded: chain I residue  972 LEU
Chi-restraints excluded: chain I residue 1171 VAL
Chi-restraints excluded: chain I residue 1183 ASP
Chi-restraints excluded: chain I residue 1199 VAL
Chi-restraints excluded: chain I residue 1201 VAL
Chi-restraints excluded: chain I residue 1210 VAL
Chi-restraints excluded: chain I residue 1325 ARG
Chi-restraints excluded: chain I residue 1327 GLU
Chi-restraints excluded: chain I residue 1337 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 89 optimal weight:    0.1980
   chunk 126 optimal weight:    0.0570
   chunk 119 optimal weight:    1.9990
   chunk 145 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   chunk 143 optimal weight:    1.9990
   chunk 129 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I1062 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.186975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.173186 restraints weight = 19404.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.154820 restraints weight = 50175.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.150302 restraints weight = 44452.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.150005 restraints weight = 39000.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.149849 restraints weight = 31424.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17559  Z= 0.149
  Angle     :  0.561  12.671  24866  Z= 0.306
  Chirality :  0.036   0.145   2809
  Planarity :  0.004   0.044   2196
  Dihedral  : 28.181 179.847   4544
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.43 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.61 (0.23), residues: 1346
  helix:  1.52 (0.19), residues: 814
  sheet:  0.62 (0.68), residues: 64
  loop : -1.69 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG I1325 
 TYR   0.017   0.001   TYR D 121 
 PHE   0.009   0.001   PHE H  70 
 TRP   0.010   0.001   TRP I 922 
 HIS   0.010   0.001   HIS I1054 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 (17559)
  covalent geometry    : angle       0.56080 /  0.31 (24866)
  hydrogen bonds       : bond        0.04850 /  3.35 (  812)
  hydrogen bonds       : angle       3.17329 /  2.26 ( 2153)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2451.16 seconds
wall clock time: 43 minutes 11.14 seconds (2591.14 seconds total)