Starting phenix.real_space_refine
on Sun Aug 24 02:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5z3l_6879/08_2025/5z3l_6879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5z3l_6879/08_2025/5z3l_6879.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5z3l_6879/08_2025/5z3l_6879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5z3l_6879/08_2025/5z3l_6879.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5z3l_6879/08_2025/5z3l_6879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5z3l_6879/08_2025/5z3l_6879.map"
  }
  resolution = 4.31
  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=   0.002 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     292      5.49       5
     S      29      5.16       5
     C    9670      2.51       5
     N    3091      2.21       5
     O    3701      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16783
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 703
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "C"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "D"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 718
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 672
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "G"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 815
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "O"
      Number of atoms: 4772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 581, 4772
          Classifications: {'peptide': 581}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 564}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 3.46, per 1000 atoms: 0.21
  Number of scatterers: 16783
  At special positions: 0
  Unit cell: (145.2, 126.72, 129.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P     292     15.00
     O    3701      8.00
     N    3091      7.00
     C    9670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 466.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2556

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 4 sheets defined
      63.5% alpha, 2.2% beta
      118 base pairs and 223 stacking pairs defined.
    Time for finding SS restraints: 2.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.619A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.752A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 4.376A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 48 through 76
      removed outlier: 4.422A  pdb=" N   GLU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.631A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.704A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 16 through 21'
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.866A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 98
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.926A  pdb=" N   ARG D  76 " --> pdb=" O   GLY D  72 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 102 through 120
      removed outlier: 3.699A  pdb=" N   HIS D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.619A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.753A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
      removed outlier: 3.586A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.721A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.538A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.704A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 16 through 21'
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.866A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 98
    Processing helix  chain 'H' and resid 35 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.925A  pdb=" N   ARG H  76 " --> pdb=" O   GLY H  72 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 102 through 120
      removed outlier: 3.699A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 674 through 683
      removed outlier: 4.464A  pdb=" N   THR O 680 " --> pdb=" O   ASP O 676 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   HIS O 681 " --> pdb=" O   THR O 677 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU O 682 " --> pdb=" O   ARG O 678 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 683 through 689
      removed outlier: 4.399A  pdb=" N   ASN O 687 " --> pdb=" O   LEU O 683 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 744 through 750
      removed outlier: 3.547A  pdb=" N   ALA O 748 " --> pdb=" O   TYR O 744 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 768 through 785
      removed outlier: 4.492A  pdb=" N   ASN O 784 " --> pdb=" O   SER O 780 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 797 through 810
      removed outlier: 3.687A  pdb=" N   LEU O 805 " --> pdb=" O   GLN O 801 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU O 806 " --> pdb=" O   THR O 802 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 827 through 838
      removed outlier: 3.772A  pdb=" N   PHE O 835 " --> pdb=" O   TRP O 831 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   ALA O 836 " --> pdb=" O   SER O 832 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   LYS O 837 " --> pdb=" O   SER O 833 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 850 through 863
      removed outlier: 4.080A  pdb=" N   LYS O 857 " --> pdb=" O   GLU O 853 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS O 860 " --> pdb=" O   ALA O 856 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ARG O 862 " --> pdb=" O   GLN O 858 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA O 863 " --> pdb=" O   ALA O 859 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 879 through 886
      removed outlier: 3.804A  pdb=" N   LYS O 885 " --> pdb=" O   ALA O 881 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 904 through 913
      removed outlier: 3.550A  pdb=" N   LEU O 910 " --> pdb=" O   LEU O 906 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASN O 911 " --> pdb=" O   SER O 907 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 944 through 958
      removed outlier: 3.892A  pdb=" N   SER O 948 " --> pdb=" O   LYS O 944 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   VAL O 949 " --> pdb=" O   ILE O 945 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   LYS O 950 " --> pdb=" O   PHE O 946 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   SER O 951 " --> pdb=" O   ASN O 947 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   PHE O 952 " --> pdb=" O   SER O 948 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   GLU O 954 " --> pdb=" O   LYS O 950 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   TRP O 955 " --> pdb=" O   SER O 951 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR O 958 " --> pdb=" O   GLU O 954 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 968 through 973
    Processing helix  chain 'O' and resid 975 through 987
      removed outlier: 3.578A  pdb=" N   LEU O 987 " --> pdb=" O   LEU O 983 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 995 through 999
    Processing helix  chain 'O' and resid 1020 through 1031
      removed outlier: 3.800A  pdb=" N   GLN O1024 " --> pdb=" O   GLN O1020 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG O1030 " --> pdb=" O   MET O1026 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1055 through 1061
      removed outlier: 4.032A  pdb=" N   ASN O1060 " --> pdb=" O   LYS O1056 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   HIS O1061 " --> pdb=" O   LYS O1057 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1068 through 1073
      removed outlier: 3.713A  pdb=" N   ILE O1072 " --> pdb=" O   VAL O1068 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1082 through 1085
      removed outlier: 3.706A  pdb=" N   VAL O1085 " --> pdb=" O   ILE O1082 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1082 through 1085'
    Processing helix  chain 'O' and resid 1086 through 1091
      removed outlier: 4.199A  pdb=" N   LEU O1091 " --> pdb=" O   GLY O1087 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1091 through 1103
      removed outlier: 3.976A  pdb=" N   ILE O1095 " --> pdb=" O   LEU O1091 " (cutoff:3.500A)
      Proline residue:  O1097  - end of helix
      removed outlier: 3.521A  pdb=" N   LYS O1100 " --> pdb=" O   LEU O1096 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA O1101 " --> pdb=" O   PRO O1097 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1113 through 1127
      removed outlier: 4.050A  pdb=" N   ASP O1117 " --> pdb=" O   THR O1113 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE O1118 " --> pdb=" O   GLN O1114 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   TYR O1125 " --> pdb=" O   ASP O1121 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1134 through 1138
      removed outlier: 3.520A  pdb=" N   THR O1137 " --> pdb=" O   ASP O1134 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LYS O1138 " --> pdb=" O   GLY O1135 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1134 through 1138'
    Processing helix  chain 'O' and resid 1139 through 1150
      removed outlier: 4.494A  pdb=" N   SER O1143 " --> pdb=" O   SER O1139 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU O1144 " --> pdb=" O   ASP O1140 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU O1146 " --> pdb=" O   ARG O1142 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ARG O1147 " --> pdb=" O   SER O1143 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU O1148 " --> pdb=" O   GLU O1144 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1187 through 1198
      removed outlier: 3.832A  pdb=" N   GLN O1194 " --> pdb=" O   ASP O1190 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   ASP O1195 " --> pdb=" O   LEU O1191 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA O1197 " --> pdb=" O   ALA O1193 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1217 through 1226
      removed outlier: 3.741A  pdb=" N   ILE O1221 " --> pdb=" O   VAL O1217 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU O1223 " --> pdb=" O   GLU O1219 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1229 through 1231
      No H-bonds generated for 'chain 'O' and resid 1229 through 1231'
    Processing helix  chain 'O' and resid 1232 through 1243
      removed outlier: 4.094A  pdb=" N   LYS O1240 " --> pdb=" O   ILE O1236 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1246 through 1250
      removed outlier: 3.660A  pdb=" N   GLN O1250 " --> pdb=" O   SER O1247 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1253 through 1259
      removed outlier: 4.073A  pdb=" N   LEU O1257 " --> pdb=" O   LEU O1253 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1261 through 1269
      removed outlier: 3.913A  pdb=" N   ARG O1265 " --> pdb=" O   GLU O1261 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS O1266 " --> pdb=" O   GLU O1262 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1279 through 1287
      removed outlier: 3.793A  pdb=" N   GLU O1285 " --> pdb=" O   SER O1281 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE O1286 " --> pdb=" O   GLU O1282 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1290 through 1307
      removed outlier: 3.570A  pdb=" N   THR O1298 " --> pdb=" O   MET O1294 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS O1306 " --> pdb=" O   GLU O1302 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   LYS O1307 " --> pdb=" O   ASP O1303 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1338 through 1343
    Processing helix  chain 'O' and resid 1344 through 1347
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 5.774A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.761A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'O' and resid 789 through 790
      removed outlier: 3.995A  pdb=" N   LEU O 790 " --> pdb=" O   ILE O 921 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   LEU O 820 " --> pdb=" O   ILE O 892 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL O 869 " --> pdb=" O   TYR O 819 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'O' and resid 1130 through 1131
      removed outlier: 7.266A  pdb=" N   LEU O1131 " --> pdb=" O   ILE O1160 " (cutoff:3.500A)
      removed outlier: 9.385A  pdb=" N   SER O1162 " --> pdb=" O   LEU O1131 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE O1109 " --> pdb=" O   ILE O1179 " (cutoff:3.500A)

    521 hydrogen bonds defined for protein.
    1545 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      307 hydrogen bonds
      614 hydrogen bond angles
      0 basepair planarities
      118 basepair parallelities
      223 stacking parallelities
  Total time for adding SS restraints: 3.25

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3802
        1.34 -     1.45: 4752
        1.45 -     1.57: 8477
        1.57 -     1.69: 582
        1.69 -     1.81: 53
  Bond restraints: 17666
  Sorted by residual:
  bond pdb=" C3'  DA J  14 "
       pdb=" O3'  DA J  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.468 -0.046 3.00e-02 1.11e+03 2.38e+00
  bond pdb=" C3'  DA J  71 "
       pdb=" O3'  DA J  71 "
    ideal  model  delta    sigma   weight residual
    1.422  1.468 -0.046 3.00e-02 1.11e+03 2.31e+00
  bond pdb=" C3'  DA I  20 "
       pdb=" O3'  DA I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.02e+00
  bond pdb=" C3'  DG I  40 "
       pdb=" O3'  DG I  40 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.94e+00
  bond pdb=" C3'  DG J  94 "
       pdb=" O3'  DG J  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.70e+00
  ... (remaining 17661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 24572
        1.88 -     3.77: 463
        3.77 -     5.65: 42
        5.65 -     7.53: 12
        7.53 -     9.42: 6
  Bond angle restraints: 25095
  Sorted by residual:
  angle pdb=" N   PRO O 959 "
        pdb=" CA  PRO O 959 "
        pdb=" CB  PRO O 959 "
      ideal   model   delta    sigma   weight residual
     103.25  109.96   -6.71 1.05e+00 9.07e-01 4.09e+01
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  127.29   -5.75 1.91e+00 2.74e-01 9.06e+00
  angle pdb=" C   THR E  80 "
        pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     121.54  127.20   -5.66 1.91e+00 2.74e-01 8.77e+00
  angle pdb=" C   ILE O 815 "
        pdb=" N   ARG O 816 "
        pdb=" CA  ARG O 816 "
      ideal   model   delta    sigma   weight residual
     121.54  127.06   -5.52 1.91e+00 2.74e-01 8.36e+00
  angle pdb=" C3'  DG I 128 "
        pdb=" C2'  DG I 128 "
        pdb=" C1'  DG I 128 "
      ideal   model   delta    sigma   weight residual
     101.60   97.28    4.32 1.50e+00 4.44e-01 8.28e+00
  ... (remaining 25090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.71: 8647
       35.71 -    71.41: 1261
       71.41 -   107.12: 20
      107.12 -   142.83: 5
      142.83 -   178.54: 8
  Dihedral angle restraints: 9941
    sinusoidal: 6007
      harmonic: 3934
  Sorted by residual:
  dihedral pdb=" CA  PHE O1110 "
           pdb=" C   PHE O1110 "
           pdb=" N   GLN O1111 "
           pdb=" CA  GLN O1111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.08   25.92     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ARG B  95 "
           pdb=" C   ARG B  95 "
           pdb=" N   THR B  96 "
           pdb=" CA  THR B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.39  -21.61     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" C4'  DA I  20 "
           pdb=" C3'  DA I  20 "
           pdb=" O3'  DA I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.46  178.54     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 9938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 2309
       0.042 -    0.084: 426
       0.084 -    0.126: 102
       0.126 -    0.168: 15
       0.168 -    0.210: 8
  Chirality restraints: 2860
  Sorted by residual:
  chirality pdb=" CG  LEU O1145 "
            pdb=" CB  LEU O1145 "
            pdb=" CD1 LEU O1145 "
            pdb=" CD2 LEU O1145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  PRO O 959 "
            pdb=" N   PRO O 959 "
            pdb=" C   PRO O 959 "
            pdb=" CB  PRO O 959 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CG  LEU O1170 "
            pdb=" CB  LEU O1170 "
            pdb=" CD1 LEU O1170 "
            pdb=" CD2 LEU O1170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 2857 not shown)

  Planarity restraints: 2168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H  99 "    0.029 5.00e-02 4.00e+02   4.40e-02 3.09e+00
        pdb=" N   PRO H 100 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO H 100 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO H 100 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL O1064 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   VAL O1064 "    0.030 2.00e-02 2.50e+03
        pdb=" O   VAL O1064 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PHE O1065 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  99 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO D 100 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO D 100 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 100 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 2165 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1352
        2.74 -     3.28: 16390
        3.28 -     3.82: 31004
        3.82 -     4.36: 36260
        4.36 -     4.90: 53153
  Nonbonded interactions: 138159
  Sorted by model distance:
  nonbonded pdb=" OH  TYR H  39 "
            pdb=" OP2  DG I  22 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   VAL H 108 "
            pdb=" OG1 THR H 112 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   VAL D 108 "
            pdb=" OG1 THR D 112 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ALA O 791 "
            pdb=" NH1 ARG O 993 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O2   DC I 140 "
            pdb=" N2   DG J   8 "
     model   vdw
     2.262 3.120
  ... (remaining 138154 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 40 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 24 through 101))
  selection = (chain 'F' and resid 17 through 101)
}
ncs_group {
  reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 75 through 118))
  selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 37 through 118))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 56 through 121))
}

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:             0.170
  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:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     16.160
  Find NCS groups from input model:        0.150
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
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   0.046  17666  Z= 0.134
  Angle     :  0.606   9.418  25095  Z= 0.348
  Chirality :  0.037   0.210   2860
  Planarity :  0.004   0.044   2168
  Dihedral  : 24.561 178.537   7385
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.95 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.31 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.74 (0.19), residues: 1317
  helix: -2.88 (0.14), residues: 718
  sheet: -2.02 (0.58), residues: 63
  loop : -1.67 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  95 
 TYR   0.018   0.001   TYR O 914 
 PHE   0.020   0.002   PHE O1065 
 TRP   0.015   0.001   TRP O1083 
 HIS   0.004   0.001   HIS O 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (17666)
  covalent geometry    : angle       0.60577 (25095)
  hydrogen bonds       : bond        0.15287 (  828)
  hydrogen bonds       : angle       8.10095 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 510
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8478 (tt0) cc_final: 0.7649 (tm-30)
REVERT: A  107 THR cc_start: 0.9525 (m) cc_final: 0.9264 (t)
REVERT: A  123 ASP cc_start: 0.8072 (p0) cc_final: 0.7347 (m-30)
REVERT: B   25 ASN cc_start: 0.7849 (t0) cc_final: 0.7132 (t0)
REVERT: C   92 GLU cc_start: 0.7134 (pt0) cc_final: 0.6809 (tt0)
REVERT: D   95 VAL cc_start: 0.9196 (p) cc_final: 0.8885 (p)
REVERT: D  103 LEU cc_start: 0.8666 (tp) cc_final: 0.7792 (tp)
REVERT: E   60 LEU cc_start: 0.7656 (tp) cc_final: 0.7379 (tt)
REVERT: E   81 ASP cc_start: 0.7757 (p0) cc_final: 0.7536 (p0)
REVERT: E  105 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: E  113 HIS cc_start: 0.8197 (t70) cc_final: 0.6321 (t70)
REVERT: E  125 GLN cc_start: 0.8444 (pt0) cc_final: 0.7274 (tm-30)
REVERT: F   68 ASP cc_start: 0.8897 (m-30) cc_final: 0.8155 (m-30)
REVERT: F   74 GLU cc_start: 0.8543 (tp30) cc_final: 0.8294 (tm-30)
REVERT: F   79 LYS cc_start: 0.8420 (mmtp) cc_final: 0.8020 (ttpt)
REVERT: F   88 TYR cc_start: 0.7953 (m-10) cc_final: 0.7041 (m-10)
REVERT: G   56 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8797 (mm-30)
REVERT: G   68 ASN cc_start: 0.8403 (m-40) cc_final: 0.7703 (m110)
REVERT: G   78 ILE cc_start: 0.8575 (pt) cc_final: 0.8360 (pt)
REVERT: G  113 SER cc_start: 0.9371 (m) cc_final: 0.9131 (p)
REVERT: H   56 MET cc_start: 0.8825 (tpp) cc_final: 0.8584 (tpt)
REVERT: H   90 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8221 (mm-30)
REVERT: H  102 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6939 (tp30)
REVERT: H  105 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8497 (mmtm)
REVERT: H  109 SER cc_start: 0.9040 (m) cc_final: 0.8802 (p)
REVERT: O  838 TRP cc_start: 0.7272 (m100) cc_final: 0.6844 (m100)
REVERT: O  852 ASN cc_start: 0.9103 (m-40) cc_final: 0.8595 (p0)
REVERT: O  894 ASP cc_start: 0.8484 (t70) cc_final: 0.8151 (t70)
REVERT: O  908 LEU cc_start: 0.9278 (mp) cc_final: 0.9058 (mm)
REVERT: O  912 THR cc_start: 0.9013 (m) cc_final: 0.8731 (p)
REVERT: O 1058 ILE cc_start: 0.8738 (pt) cc_final: 0.8285 (tt)
REVERT: O 1067 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7276 (tt0)
REVERT: O 1116 MET cc_start: 0.8354 (mtp) cc_final: 0.7903 (tmm)
REVERT: O 1140 ASP cc_start: 0.8691 (t0) cc_final: 0.7590 (m-30)
REVERT: O 1223 GLU cc_start: 0.8896 (mp0) cc_final: 0.8685 (pp20)
REVERT: O 1294 MET cc_start: 0.7474 (mmm) cc_final: 0.7243 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 513
  average time/residue: 0.1656
  time to fit residues: 115.1951
Evaluate side-chains
  295 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 294
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
B  18 HIS
B  25 ASN
C  68 ASN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 784 ASN
** O 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 897 HIS
O 929 ASN
O1050 ASN
O1071 GLN
O1104 HIS
O1111 GLN
** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.095905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.071461 restraints weight = 71509.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.073236 restraints weight = 40264.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.074459 restraints weight = 27509.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.075232 restraints weight = 21600.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.075592 restraints weight = 18731.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  17666  Z= 0.203
  Angle     :  0.681   8.548  25095  Z= 0.378
  Chirality :  0.041   0.194   2860
  Planarity :  0.005   0.048   2168
  Dihedral  : 29.661 179.392   4672
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  4.79 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.21), residues: 1317
  helix: -1.14 (0.17), residues: 761
  sheet: -1.66 (0.63), residues: 57
  loop : -1.89 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  36 
 TYR   0.020   0.002   TYR C  39 
 PHE   0.033   0.003   PHE O1241 
 TRP   0.026   0.003   TRP O 888 
 HIS   0.014   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (17666)
  covalent geometry    : angle       0.68118 (25095)
  hydrogen bonds       : bond        0.04603 (  828)
  hydrogen bonds       : angle       4.67822 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 353
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 SER cc_start: 0.9310 (m) cc_final: 0.9050 (t)
REVERT: A   93 GLN cc_start: 0.9161 (tt0) cc_final: 0.8352 (tm-30)
REVERT: B   75 HIS cc_start: 0.8045 (t-90) cc_final: 0.7616 (t-90)
REVERT: B   85 ASP cc_start: 0.8994 (m-30) cc_final: 0.8611 (m-30)
REVERT: B   96 THR cc_start: 0.8820 (m) cc_final: 0.8462 (m)
REVERT: D   46 HIS cc_start: 0.9023 (m-70) cc_final: 0.8576 (m170)
REVERT: D   65 ASP cc_start: 0.9091 (t0) cc_final: 0.8729 (t0)
REVERT: D   82 LYS cc_start: 0.9545 (mtmm) cc_final: 0.9202 (mtmm)
REVERT: D   93 THR cc_start: 0.9443 (p) cc_final: 0.9135 (t)
REVERT: D   98 LEU cc_start: 0.9196 (tp) cc_final: 0.8831 (tt)
REVERT: D  105 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7264 (mtmt)
REVERT: E   67 PHE cc_start: 0.9375 (t80) cc_final: 0.8800 (t80)
REVERT: E  106 ASP cc_start: 0.9031 (m-30) cc_final: 0.8773 (m-30)
REVERT: F   50 ILE cc_start: 0.8291 (mm) cc_final: 0.8064 (mm)
REVERT: F   60 VAL cc_start: 0.9168 (p) cc_final: 0.8850 (t)
REVERT: F   74 GLU cc_start: 0.8676 (tp30) cc_final: 0.8237 (tm-30)
REVERT: F   84 MET cc_start: 0.8381 (mmp) cc_final: 0.7915 (mmp)
REVERT: G   56 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8657 (mm-30)
REVERT: G   64 GLU cc_start: 0.8928 (pp20) cc_final: 0.8264 (tm-30)
REVERT: G   79 ILE cc_start: 0.8987 (tp) cc_final: 0.8708 (tp)
REVERT: G   92 GLU cc_start: 0.8795 (pp20) cc_final: 0.7952 (pm20)
REVERT: H   39 TYR cc_start: 0.7908 (t80) cc_final: 0.7528 (t80)
REVERT: H   44 GLN cc_start: 0.9020 (tt0) cc_final: 0.8730 (tm-30)
REVERT: H   90 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8819 (mm-30)
REVERT: H  105 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8417 (mmtm)
REVERT: H  109 SER cc_start: 0.9261 (m) cc_final: 0.9000 (p)
REVERT: O  745 TYR cc_start: 0.4998 (OUTLIER) cc_final: 0.4717 (m-10)
REVERT: O  852 ASN cc_start: 0.9109 (m-40) cc_final: 0.8673 (p0)
REVERT: O  879 GLU cc_start: 0.7722 (pt0) cc_final: 0.7218 (pt0)
REVERT: O  891 MET cc_start: 0.9095 (tmm) cc_final: 0.8811 (tmm)
REVERT: O  920 LEU cc_start: 0.9054 (mm) cc_final: 0.8831 (mm)
REVERT: O 1116 MET cc_start: 0.8702 (mtp) cc_final: 0.7951 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 354
  average time/residue: 0.1353
  time to fit residues: 69.4124
Evaluate side-chains
  246 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 86 optimal weight:   30.0000
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 145 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
D  92 GLN
F  27 GLN
G  94 ASN
G 112 GLN
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 929 ASN
** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.092690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.067526 restraints weight = 74784.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.069044 restraints weight = 44728.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.070139 restraints weight = 31822.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.070846 restraints weight = 25775.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.071247 restraints weight = 22786.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  17666  Z= 0.192
  Angle     :  0.646   8.463  25095  Z= 0.360
  Chirality :  0.039   0.195   2860
  Planarity :  0.005   0.056   2168
  Dihedral  : 29.758 179.970   4672
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.22), residues: 1317
  helix: -0.36 (0.18), residues: 779
  sheet: -1.15 (0.61), residues: 61
  loop : -1.71 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O 880 
 TYR   0.024   0.002   TYR B  88 
 PHE   0.025   0.002   PHE O1241 
 TRP   0.016   0.003   TRP O 777 
 HIS   0.011   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (17666)
  covalent geometry    : angle       0.64608 (25095)
  hydrogen bonds       : bond        0.04317 (  828)
  hydrogen bonds       : angle       4.35969 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9333 (tt0) cc_final: 0.8477 (tm-30)
REVERT: A  123 ASP cc_start: 0.8355 (m-30) cc_final: 0.7878 (t70)
REVERT: B   49 LEU cc_start: 0.8180 (mp) cc_final: 0.7948 (mp)
REVERT: B   53 GLU cc_start: 0.8186 (tp30) cc_final: 0.7934 (tp30)
REVERT: B   75 HIS cc_start: 0.8274 (t-90) cc_final: 0.8005 (t-90)
REVERT: B   88 TYR cc_start: 0.8761 (m-10) cc_final: 0.7940 (m-10)
REVERT: B   98 TYR cc_start: 0.8710 (m-10) cc_final: 0.8474 (m-10)
REVERT: C   35 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7956 (ttp-110)
REVERT: C   41 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7542 (tm-30)
REVERT: C   57 TYR cc_start: 0.9050 (t80) cc_final: 0.8727 (t80)
REVERT: D   65 ASP cc_start: 0.9241 (t0) cc_final: 0.8839 (t0)
REVERT: D   75 SER cc_start: 0.9424 (p) cc_final: 0.9014 (m)
REVERT: D   80 TYR cc_start: 0.8198 (m-10) cc_final: 0.7534 (m-80)
REVERT: D   98 LEU cc_start: 0.9369 (tp) cc_final: 0.9082 (tt)
REVERT: D  105 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7681 (mtmt)
REVERT: E   71 VAL cc_start: 0.9457 (t) cc_final: 0.9144 (t)
REVERT: E  105 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: E  106 ASP cc_start: 0.8807 (m-30) cc_final: 0.8506 (m-30)
REVERT: F   40 ARG cc_start: 0.8338 (ttm170) cc_final: 0.7999 (ttm170)
REVERT: F   59 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8558 (ttmm)
REVERT: F   74 GLU cc_start: 0.8571 (tp30) cc_final: 0.8364 (tm-30)
REVERT: F   84 MET cc_start: 0.8245 (mmp) cc_final: 0.7830 (mmp)
REVERT: F   91 LYS cc_start: 0.9441 (tttm) cc_final: 0.9163 (ttpt)
REVERT: G   59 THR cc_start: 0.9272 (m) cc_final: 0.8948 (p)
REVERT: G   64 GLU cc_start: 0.8827 (pp20) cc_final: 0.8346 (tm-30)
REVERT: G   94 ASN cc_start: 0.8954 (t0) cc_final: 0.8638 (t0)
REVERT: G  111 ILE cc_start: 0.7647 (mp) cc_final: 0.7424 (mm)
REVERT: G  112 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7781 (mm-40)
REVERT: H   38 VAL cc_start: 0.9456 (t) cc_final: 0.9118 (m)
REVERT: H   44 GLN cc_start: 0.8952 (tt0) cc_final: 0.8547 (tm-30)
REVERT: H   54 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8629 (mmtp)
REVERT: H  109 SER cc_start: 0.9430 (m) cc_final: 0.9180 (p)
REVERT: O  831 TRP cc_start: 0.8268 (m100) cc_final: 0.7495 (m100)
REVERT: O  852 ASN cc_start: 0.9048 (m-40) cc_final: 0.8605 (p0)
REVERT: O  879 GLU cc_start: 0.7753 (pt0) cc_final: 0.7361 (pt0)
REVERT: O  891 MET cc_start: 0.9165 (tmm) cc_final: 0.8867 (tmm)
REVERT: O  894 ASP cc_start: 0.8387 (t70) cc_final: 0.7588 (p0)
REVERT: O 1058 ILE cc_start: 0.8328 (mp) cc_final: 0.7981 (tt)
REVERT: O 1116 MET cc_start: 0.8781 (mtp) cc_final: 0.7623 (tmm)
REVERT: O 1122 PHE cc_start: 0.7792 (t80) cc_final: 0.7495 (t80)
REVERT: O 1142 ARG cc_start: 0.8806 (mtt180) cc_final: 0.8439 (mtt180)
REVERT: O 1144 GLU cc_start: 0.8892 (pt0) cc_final: 0.8339 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.1201
  time to fit residues: 54.5557
Evaluate side-chains
  248 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 117 optimal weight:    0.0060
   chunk 33 optimal weight:    2.9990
   chunk 146 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 137 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    2.6004

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C  68 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 929 ASN
** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O1186 ASN
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.091963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.066490 restraints weight = 73805.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.068094 restraints weight = 42264.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.069267 restraints weight = 29469.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.069995 restraints weight = 23601.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.070415 restraints weight = 20743.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17666  Z= 0.172
  Angle     :  0.628   9.387  25095  Z= 0.350
  Chirality :  0.039   0.165   2860
  Planarity :  0.004   0.055   2168
  Dihedral  : 29.833 179.421   4672
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.23), residues: 1317
  helix:  0.07 (0.19), residues: 781
  sheet: -0.89 (0.63), residues: 62
  loop : -1.54 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 128 
 TYR   0.019   0.002   TYR H  80 
 PHE   0.024   0.002   PHE O1241 
 TRP   0.023   0.002   TRP O 888 
 HIS   0.010   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (17666)
  covalent geometry    : angle       0.62811 (25095)
  hydrogen bonds       : bond        0.04099 (  828)
  hydrogen bonds       : angle       4.13076 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9369 (tt0) cc_final: 0.8510 (tm-30)
REVERT: B   16 LYS cc_start: 0.7541 (tmtt) cc_final: 0.7214 (pttm)
REVERT: B   53 GLU cc_start: 0.8145 (tp30) cc_final: 0.7934 (tp30)
REVERT: B   84 MET cc_start: 0.8884 (tpp) cc_final: 0.8194 (mmm)
REVERT: B   88 TYR cc_start: 0.8706 (m-10) cc_final: 0.7943 (m-10)
REVERT: B   98 TYR cc_start: 0.8660 (m-10) cc_final: 0.8447 (m-10)
REVERT: C   57 TYR cc_start: 0.9073 (t80) cc_final: 0.8800 (t80)
REVERT: C   68 ASN cc_start: 0.9494 (m-40) cc_final: 0.9261 (m110)
REVERT: C   91 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7944 (mt-10)
REVERT: C  110 ASN cc_start: 0.7985 (p0) cc_final: 0.7723 (m-40)
REVERT: D   46 HIS cc_start: 0.9087 (m90) cc_final: 0.8877 (m90)
REVERT: D   65 ASP cc_start: 0.9282 (t0) cc_final: 0.8852 (t0)
REVERT: D   68 GLU cc_start: 0.8270 (tp30) cc_final: 0.8063 (tp30)
REVERT: E   71 VAL cc_start: 0.9503 (t) cc_final: 0.9192 (t)
REVERT: E   93 GLN cc_start: 0.7849 (mt0) cc_final: 0.7293 (tm-30)
REVERT: E  105 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7972 (tm-30)
REVERT: E  106 ASP cc_start: 0.8779 (m-30) cc_final: 0.8325 (m-30)
REVERT: F   84 MET cc_start: 0.8292 (mmp) cc_final: 0.7810 (mmp)
REVERT: F   91 LYS cc_start: 0.9414 (tttm) cc_final: 0.9116 (ttpt)
REVERT: G   56 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8533 (mm-30)
REVERT: G   64 GLU cc_start: 0.8898 (pp20) cc_final: 0.8201 (tm-30)
REVERT: G   94 ASN cc_start: 0.9123 (t0) cc_final: 0.8863 (t0)
REVERT: G  112 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7990 (mm-40)
REVERT: H   56 MET cc_start: 0.8956 (tpt) cc_final: 0.8669 (tpp)
REVERT: H  109 SER cc_start: 0.9464 (m) cc_final: 0.9239 (p)
REVERT: O  794 MET cc_start: 0.7377 (tmm) cc_final: 0.7058 (mpp)
REVERT: O  823 VAL cc_start: 0.8419 (m) cc_final: 0.7061 (t)
REVERT: O  831 TRP cc_start: 0.8376 (m100) cc_final: 0.7547 (m100)
REVERT: O  852 ASN cc_start: 0.9049 (m-40) cc_final: 0.8629 (p0)
REVERT: O  891 MET cc_start: 0.9214 (tmm) cc_final: 0.8878 (tmm)
REVERT: O  894 ASP cc_start: 0.8463 (t70) cc_final: 0.7434 (p0)
REVERT: O 1058 ILE cc_start: 0.8629 (mp) cc_final: 0.8247 (tt)
REVERT: O 1116 MET cc_start: 0.8825 (mtp) cc_final: 0.7691 (tmm)
REVERT: O 1142 ARG cc_start: 0.8769 (mtt180) cc_final: 0.7729 (mtt-85)
REVERT: O 1144 GLU cc_start: 0.8806 (pt0) cc_final: 0.8273 (pp20)
REVERT: O 1162 SER cc_start: 0.9387 (t) cc_final: 0.9178 (p)
REVERT: O 1346 TYR cc_start: 0.3284 (m-80) cc_final: 0.2344 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 0.1364
  time to fit residues: 58.9597
Evaluate side-chains
  241 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 123 optimal weight:    0.0970
   chunk 132 optimal weight:    7.9990
   chunk 142 optimal weight:    0.0070
   chunk 140 optimal weight:    0.8980
   chunk 113 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   overall best weight:    3.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O1071 GLN
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.089523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.063920 restraints weight = 74731.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.065416 restraints weight = 43199.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.066522 restraints weight = 30509.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.067175 restraints weight = 24745.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.067351 restraints weight = 21999.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.5985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  17666  Z= 0.191
  Angle     :  0.648  10.017  25095  Z= 0.360
  Chirality :  0.039   0.224   2860
  Planarity :  0.004   0.059   2168
  Dihedral  : 29.940 179.897   4672
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.23), residues: 1317
  helix:  0.24 (0.19), residues: 767
  sheet: -1.12 (0.62), residues: 68
  loop : -1.32 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E  69 
 TYR   0.016   0.002   TYR B  88 
 PHE   0.023   0.002   PHE O1241 
 TRP   0.016   0.002   TRP O 888 
 HIS   0.015   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (17666)
  covalent geometry    : angle       0.64791 (25095)
  hydrogen bonds       : bond        0.04383 (  828)
  hydrogen bonds       : angle       4.18021 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   16 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7049 (pttm)
REVERT: B   88 TYR cc_start: 0.8828 (m-10) cc_final: 0.8411 (m-10)
REVERT: B   98 TYR cc_start: 0.8665 (m-10) cc_final: 0.8106 (m-10)
REVERT: C   35 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7933 (ttp-110)
REVERT: C   82 HIS cc_start: 0.9190 (m90) cc_final: 0.8862 (m90)
REVERT: C   91 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8196 (mt-10)
REVERT: D   46 HIS cc_start: 0.9107 (m90) cc_final: 0.8870 (m90)
REVERT: D   65 ASP cc_start: 0.9341 (t0) cc_final: 0.8867 (t0)
REVERT: D   80 TYR cc_start: 0.8361 (m-10) cc_final: 0.8048 (m-80)
REVERT: E   67 PHE cc_start: 0.9088 (t80) cc_final: 0.8763 (t80)
REVERT: E   71 VAL cc_start: 0.9614 (t) cc_final: 0.9389 (t)
REVERT: E  105 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: E  106 ASP cc_start: 0.8766 (m-30) cc_final: 0.8286 (m-30)
REVERT: F   91 LYS cc_start: 0.9386 (tttm) cc_final: 0.9109 (ttpt)
REVERT: G   57 TYR cc_start: 0.8749 (t80) cc_final: 0.8290 (t80)
REVERT: G   64 GLU cc_start: 0.8857 (pp20) cc_final: 0.8649 (tm-30)
REVERT: G   95 LYS cc_start: 0.9154 (tppp) cc_final: 0.8930 (tppp)
REVERT: G  112 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8138 (mm-40)
REVERT: H   54 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8708 (mmtp)
REVERT: H   56 MET cc_start: 0.8962 (tpt) cc_final: 0.8567 (tpp)
REVERT: H  109 SER cc_start: 0.9508 (m) cc_final: 0.9308 (p)
REVERT: H  119 THR cc_start: 0.8764 (m) cc_final: 0.8500 (t)
REVERT: O  794 MET cc_start: 0.7585 (tmm) cc_final: 0.7038 (mpp)
REVERT: O  823 VAL cc_start: 0.8779 (m) cc_final: 0.7393 (t)
REVERT: O  831 TRP cc_start: 0.8480 (m100) cc_final: 0.7685 (m100)
REVERT: O  852 ASN cc_start: 0.9090 (m-40) cc_final: 0.8665 (p0)
REVERT: O  888 TRP cc_start: 0.6886 (m100) cc_final: 0.6312 (m-10)
REVERT: O  891 MET cc_start: 0.9240 (tmm) cc_final: 0.8940 (tmm)
REVERT: O  894 ASP cc_start: 0.8472 (t70) cc_final: 0.7609 (p0)
REVERT: O 1116 MET cc_start: 0.8928 (mtp) cc_final: 0.7763 (tmm)
REVERT: O 1142 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8082 (mtt180)
REVERT: O 1162 SER cc_start: 0.9318 (t) cc_final: 0.9113 (p)
REVERT: O 1294 MET cc_start: 0.7425 (mmm) cc_final: 0.6992 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 282
  average time/residue: 0.1304
  time to fit residues: 54.0195
Evaluate side-chains
  228 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 152 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 100 optimal weight:   30.0000
   chunk 147 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 156 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 146 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 139 optimal weight:   10.0000
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
G  38 ASN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 858 GLN
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.088563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.062918 restraints weight = 75526.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.064468 restraints weight = 43449.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.065615 restraints weight = 30717.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.066244 restraints weight = 24875.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.066532 restraints weight = 22137.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.6399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17666  Z= 0.196
  Angle     :  0.659   9.685  25095  Z= 0.365
  Chirality :  0.040   0.179   2860
  Planarity :  0.004   0.054   2168
  Dihedral  : 30.034 178.701   4672
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.22 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.23), residues: 1317
  helix:  0.32 (0.19), residues: 767
  sheet: -0.93 (0.61), residues: 68
  loop : -1.34 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  72 
 TYR   0.017   0.002   TYR D  37 
 PHE   0.020   0.002   PHE O1241 
 TRP   0.014   0.002   TRP O1083 
 HIS   0.012   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (17666)
  covalent geometry    : angle       0.65862 (25095)
  hydrogen bonds       : bond        0.04452 (  828)
  hydrogen bonds       : angle       4.14168 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 283
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.9657 (tp) cc_final: 0.9390 (tp)
REVERT: A  123 ASP cc_start: 0.8715 (m-30) cc_final: 0.7933 (t70)
REVERT: B   16 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7047 (pttm)
REVERT: B   26 ILE cc_start: 0.9304 (tp) cc_final: 0.9048 (tp)
REVERT: B   66 ILE cc_start: 0.9507 (mm) cc_final: 0.9293 (mm)
REVERT: B   84 MET cc_start: 0.8873 (tpp) cc_final: 0.8216 (mmm)
REVERT: C   57 TYR cc_start: 0.9044 (t80) cc_final: 0.8638 (t80)
REVERT: C   68 ASN cc_start: 0.9543 (m-40) cc_final: 0.9312 (m110)
REVERT: C   91 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8341 (mt-10)
REVERT: D   33 SER cc_start: 0.7595 (t) cc_final: 0.7371 (t)
REVERT: D   46 HIS cc_start: 0.9078 (m90) cc_final: 0.8853 (m90)
REVERT: D   65 ASP cc_start: 0.9424 (t0) cc_final: 0.9125 (t0)
REVERT: D   80 TYR cc_start: 0.8352 (m-10) cc_final: 0.8029 (m-80)
REVERT: D   90 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8829 (mm-30)
REVERT: E   67 PHE cc_start: 0.9095 (t80) cc_final: 0.8775 (t80)
REVERT: E   97 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8107 (tp30)
REVERT: E  105 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: F   24 ASP cc_start: 0.6824 (t0) cc_final: 0.6555 (t0)
REVERT: F   84 MET cc_start: 0.8342 (mmp) cc_final: 0.8052 (mmp)
REVERT: F   91 LYS cc_start: 0.9355 (tttm) cc_final: 0.9047 (ttpt)
REVERT: G   64 GLU cc_start: 0.8822 (pp20) cc_final: 0.8578 (tm-30)
REVERT: H   32 GLU cc_start: 0.8430 (pm20) cc_final: 0.8129 (pm20)
REVERT: H   56 MET cc_start: 0.8966 (tpt) cc_final: 0.8593 (tpp)
REVERT: H   90 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8648 (tp30)
REVERT: H  109 SER cc_start: 0.9468 (m) cc_final: 0.9259 (p)
REVERT: H  119 THR cc_start: 0.8776 (m) cc_final: 0.8543 (t)
REVERT: O  752 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7224 (mmmt)
REVERT: O  794 MET cc_start: 0.7547 (tmm) cc_final: 0.7194 (mpp)
REVERT: O  823 VAL cc_start: 0.8891 (m) cc_final: 0.7497 (t)
REVERT: O  831 TRP cc_start: 0.8606 (m100) cc_final: 0.7727 (m100)
REVERT: O  852 ASN cc_start: 0.9085 (m-40) cc_final: 0.8697 (p0)
REVERT: O  888 TRP cc_start: 0.6582 (m100) cc_final: 0.6371 (m-10)
REVERT: O  891 MET cc_start: 0.9273 (tmm) cc_final: 0.8939 (tmm)
REVERT: O  894 ASP cc_start: 0.8225 (t70) cc_final: 0.7451 (p0)
REVERT: O 1116 MET cc_start: 0.8881 (mtp) cc_final: 0.8092 (ppp)
REVERT: O 1181 PHE cc_start: 0.7489 (m-80) cc_final: 0.6944 (m-10)
REVERT: O 1248 GLU cc_start: 0.7957 (pm20) cc_final: 0.7579 (mp0)
REVERT: O 1346 TYR cc_start: 0.4124 (m-10) cc_final: 0.2970 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 284
  average time/residue: 0.1142
  time to fit residues: 48.4826
Evaluate side-chains
  233 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0670
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.4122

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.090286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.065033 restraints weight = 73640.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.066657 restraints weight = 41919.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.067824 restraints weight = 29306.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.068490 restraints weight = 23637.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.068722 restraints weight = 20857.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.6439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  17666  Z= 0.150
  Angle     :  0.629   9.723  25095  Z= 0.349
  Chirality :  0.038   0.165   2860
  Planarity :  0.004   0.053   2168
  Dihedral  : 29.975 177.044   4672
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.22 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.23), residues: 1317
  helix:  0.51 (0.19), residues: 756
  sheet: -0.62 (0.64), residues: 68
  loop : -1.11 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O1337 
 TYR   0.019   0.002   TYR O1029 
 PHE   0.021   0.002   PHE O1241 
 TRP   0.014   0.002   TRP O1083 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (17666)
  covalent geometry    : angle       0.62900 (25095)
  hydrogen bonds       : bond        0.03974 (  828)
  hydrogen bonds       : angle       3.98717 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 298
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9407 (tt0) cc_final: 0.8307 (tm-30)
REVERT: A  123 ASP cc_start: 0.8715 (m-30) cc_final: 0.7935 (t70)
REVERT: B   16 LYS cc_start: 0.7621 (tmtt) cc_final: 0.6810 (pttt)
REVERT: B   88 TYR cc_start: 0.8736 (m-10) cc_final: 0.8132 (m-10)
REVERT: B   98 TYR cc_start: 0.8595 (m-10) cc_final: 0.8327 (m-10)
REVERT: C   68 ASN cc_start: 0.9492 (m-40) cc_final: 0.9258 (m-40)
REVERT: C   91 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8367 (mt-10)
REVERT: D   61 SER cc_start: 0.9603 (t) cc_final: 0.9373 (t)
REVERT: D   65 ASP cc_start: 0.9338 (t0) cc_final: 0.9079 (t0)
REVERT: D   80 TYR cc_start: 0.8368 (m-10) cc_final: 0.7751 (m-80)
REVERT: E   67 PHE cc_start: 0.8899 (t80) cc_final: 0.8696 (t80)
REVERT: E  105 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7812 (tm-30)
REVERT: E  120 MET cc_start: 0.8698 (mmm) cc_final: 0.8318 (mmm)
REVERT: E  125 GLN cc_start: 0.8524 (pt0) cc_final: 0.7614 (tm-30)
REVERT: F   24 ASP cc_start: 0.7108 (t0) cc_final: 0.6257 (m-30)
REVERT: F   40 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8418 (ttm170)
REVERT: F   84 MET cc_start: 0.8379 (mmp) cc_final: 0.8022 (mmp)
REVERT: F   88 TYR cc_start: 0.8491 (m-10) cc_final: 0.8065 (m-10)
REVERT: F   91 LYS cc_start: 0.9335 (tttm) cc_final: 0.8968 (ttpt)
REVERT: G   56 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8867 (mm-30)
REVERT: H   54 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8635 (mmtp)
REVERT: H   56 MET cc_start: 0.8892 (tpt) cc_final: 0.8634 (tpp)
REVERT: H  109 SER cc_start: 0.9452 (m) cc_final: 0.9251 (p)
REVERT: H  119 THR cc_start: 0.8957 (m) cc_final: 0.8649 (t)
REVERT: O  752 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7164 (mmmt)
REVERT: O  823 VAL cc_start: 0.8878 (m) cc_final: 0.7537 (t)
REVERT: O  831 TRP cc_start: 0.8528 (m100) cc_final: 0.7634 (m100)
REVERT: O  852 ASN cc_start: 0.9101 (m-40) cc_final: 0.8672 (p0)
REVERT: O  888 TRP cc_start: 0.7107 (m100) cc_final: 0.6700 (m-10)
REVERT: O  891 MET cc_start: 0.9280 (tmm) cc_final: 0.9003 (tmm)
REVERT: O  894 ASP cc_start: 0.8235 (t70) cc_final: 0.7442 (p0)
REVERT: O  978 LEU cc_start: 0.6411 (tp) cc_final: 0.6204 (tp)
REVERT: O 1116 MET cc_start: 0.8829 (mtp) cc_final: 0.8077 (ppp)
REVERT: O 1294 MET cc_start: 0.7252 (mmm) cc_final: 0.6747 (mmm)
REVERT: O 1346 TYR cc_start: 0.4154 (m-10) cc_final: 0.3614 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 298
  average time/residue: 0.1138
  time to fit residues: 50.2224
Evaluate side-chains
  238 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 149 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 131 optimal weight:    9.9990
   chunk 86 optimal weight:   30.0000
   chunk 137 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 47 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 147 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
O1192 GLN
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.087277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.062412 restraints weight = 75216.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.063734 restraints weight = 44960.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.064668 restraints weight = 32476.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.065258 restraints weight = 26785.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.065518 restraints weight = 24010.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.6931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  17666  Z= 0.211
  Angle     :  0.683  10.271  25095  Z= 0.377
  Chirality :  0.041   0.234   2860
  Planarity :  0.004   0.051   2168
  Dihedral  : 30.098 179.643   4672
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.23), residues: 1317
  helix:  0.34 (0.19), residues: 765
  sheet: -0.53 (0.66), residues: 68
  loop : -1.10 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E  53 
 TYR   0.025   0.002   TYR G  57 
 PHE   0.019   0.002   PHE O1241 
 TRP   0.018   0.002   TRP O1083 
 HIS   0.010   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (17666)
  covalent geometry    : angle       0.68317 (25095)
  hydrogen bonds       : bond        0.04834 (  828)
  hydrogen bonds       : angle       4.22008 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.9607 (tp) cc_final: 0.9369 (tp)
REVERT: A   93 GLN cc_start: 0.9454 (tt0) cc_final: 0.8428 (tm-30)
REVERT: A   94 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8586 (tm-30)
REVERT: A  123 ASP cc_start: 0.8715 (m-30) cc_final: 0.7940 (t70)
REVERT: B   16 LYS cc_start: 0.7550 (tmtt) cc_final: 0.6729 (pttt)
REVERT: B   26 ILE cc_start: 0.9289 (tp) cc_final: 0.9047 (tp)
REVERT: B   98 TYR cc_start: 0.8576 (m-10) cc_final: 0.8152 (m-10)
REVERT: C   35 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8085 (ttp-110)
REVERT: D   46 HIS cc_start: 0.9190 (m-70) cc_final: 0.8957 (m90)
REVERT: D   65 ASP cc_start: 0.9419 (t0) cc_final: 0.9209 (t0)
REVERT: D   80 TYR cc_start: 0.8292 (m-10) cc_final: 0.7746 (m-80)
REVERT: E   67 PHE cc_start: 0.9089 (t80) cc_final: 0.8827 (t80)
REVERT: E  105 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: F   24 ASP cc_start: 0.7226 (t0) cc_final: 0.6382 (m-30)
REVERT: F   68 ASP cc_start: 0.8285 (m-30) cc_final: 0.7725 (m-30)
REVERT: F   91 LYS cc_start: 0.9360 (tttm) cc_final: 0.9020 (ttpt)
REVERT: H   32 GLU cc_start: 0.8311 (pm20) cc_final: 0.8092 (pm20)
REVERT: H  119 THR cc_start: 0.8925 (m) cc_final: 0.8690 (t)
REVERT: O  752 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7040 (mmmt)
REVERT: O  823 VAL cc_start: 0.9017 (m) cc_final: 0.7594 (t)
REVERT: O  831 TRP cc_start: 0.8630 (m100) cc_final: 0.7732 (m100)
REVERT: O  852 ASN cc_start: 0.9118 (m-40) cc_final: 0.8721 (p0)
REVERT: O  888 TRP cc_start: 0.7035 (m100) cc_final: 0.6619 (m-10)
REVERT: O  891 MET cc_start: 0.9281 (tmm) cc_final: 0.8959 (tmm)
REVERT: O  894 ASP cc_start: 0.8062 (t70) cc_final: 0.7538 (p0)
REVERT: O 1116 MET cc_start: 0.8955 (mtp) cc_final: 0.7763 (tmm)
REVERT: O 1248 GLU cc_start: 0.8127 (pm20) cc_final: 0.7650 (mp0)
REVERT: O 1346 TYR cc_start: 0.4409 (m-10) cc_final: 0.3977 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.1120
  time to fit residues: 48.4362
Evaluate side-chains
  227 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 85 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   chunk 116 optimal weight:    0.6980
   chunk 103 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
O 929 ASN
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.090608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.065411 restraints weight = 74674.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.066980 restraints weight = 43174.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.068128 restraints weight = 30491.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.068819 restraints weight = 24650.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.069042 restraints weight = 21798.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.6852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17666  Z= 0.145
  Angle     :  0.640  10.962  25095  Z= 0.351
  Chirality :  0.039   0.174   2860
  Planarity :  0.004   0.050   2168
  Dihedral  : 29.993 175.906   4672
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.24), residues: 1317
  helix:  0.51 (0.19), residues: 769
  sheet: -0.27 (0.67), residues: 68
  loop : -0.96 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E  53 
 TYR   0.029   0.002   TYR G  57 
 PHE   0.021   0.002   PHE O1241 
 TRP   0.022   0.002   TRP O1083 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (17666)
  covalent geometry    : angle       0.63956 (25095)
  hydrogen bonds       : bond        0.03920 (  828)
  hydrogen bonds       : angle       3.93796 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8493 (t80) cc_final: 0.8190 (t80)
REVERT: A   74 ILE cc_start: 0.9575 (tp) cc_final: 0.9344 (tp)
REVERT: A   93 GLN cc_start: 0.9249 (tt0) cc_final: 0.8319 (tm-30)
REVERT: A  115 LYS cc_start: 0.9250 (mtmm) cc_final: 0.9003 (mttm)
REVERT: A  123 ASP cc_start: 0.8640 (m-30) cc_final: 0.8039 (t70)
REVERT: B   16 LYS cc_start: 0.7618 (tmtt) cc_final: 0.6766 (pttt)
REVERT: B   84 MET cc_start: 0.8702 (tpp) cc_final: 0.8358 (mmm)
REVERT: B   98 TYR cc_start: 0.8638 (m-10) cc_final: 0.8392 (m-10)
REVERT: C   39 TYR cc_start: 0.7792 (m-80) cc_final: 0.7451 (m-80)
REVERT: C   41 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: C   68 ASN cc_start: 0.9472 (m-40) cc_final: 0.9267 (m-40)
REVERT: C  110 ASN cc_start: 0.8420 (p0) cc_final: 0.8077 (p0)
REVERT: D   65 ASP cc_start: 0.9351 (t0) cc_final: 0.9036 (t0)
REVERT: E   50 GLU cc_start: 0.8780 (mm-30) cc_final: 0.7952 (tm-30)
REVERT: E   53 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7995 (ttp80)
REVERT: E   70 LEU cc_start: 0.9120 (tp) cc_final: 0.8859 (tp)
REVERT: E  105 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: E  125 GLN cc_start: 0.8553 (pt0) cc_final: 0.7563 (tm-30)
REVERT: F   24 ASP cc_start: 0.7027 (t0) cc_final: 0.6335 (m-30)
REVERT: F   68 ASP cc_start: 0.8149 (m-30) cc_final: 0.7854 (m-30)
REVERT: F   88 TYR cc_start: 0.8078 (m-10) cc_final: 0.7755 (m-10)
REVERT: F   91 LYS cc_start: 0.9353 (tttm) cc_final: 0.8978 (ttpt)
REVERT: G   56 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: G   64 GLU cc_start: 0.8805 (pp20) cc_final: 0.8581 (tm-30)
REVERT: G   72 ASP cc_start: 0.8529 (t70) cc_final: 0.8312 (t70)
REVERT: H   32 GLU cc_start: 0.8287 (pm20) cc_final: 0.8076 (pm20)
REVERT: H   44 GLN cc_start: 0.9110 (tt0) cc_final: 0.8845 (tm-30)
REVERT: H   54 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8610 (mmtp)
REVERT: H  119 THR cc_start: 0.8964 (m) cc_final: 0.8702 (t)
REVERT: O  794 MET cc_start: 0.7472 (tmm) cc_final: 0.6684 (mpp)
REVERT: O  823 VAL cc_start: 0.8932 (m) cc_final: 0.8483 (t)
REVERT: O  831 TRP cc_start: 0.8462 (m100) cc_final: 0.8057 (m100)
REVERT: O  852 ASN cc_start: 0.8988 (m-40) cc_final: 0.8611 (p0)
REVERT: O  888 TRP cc_start: 0.7226 (m100) cc_final: 0.6884 (m-10)
REVERT: O  894 ASP cc_start: 0.8166 (t70) cc_final: 0.7920 (t70)
REVERT: O 1111 GLN cc_start: 0.8660 (mm110) cc_final: 0.7967 (mm110)
REVERT: O 1116 MET cc_start: 0.8862 (mtp) cc_final: 0.7712 (tmm)
REVERT: O 1294 MET cc_start: 0.7284 (mmm) cc_final: 0.6786 (mmm)
REVERT: O 1346 TYR cc_start: 0.4229 (m-10) cc_final: 0.3674 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1473
  time to fit residues: 64.9019
Evaluate side-chains
  245 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 139 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 65 optimal weight:    8.9990
   chunk 137 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 85 optimal weight:   20.0000
   chunk 135 optimal weight:    4.9990
   chunk 152 optimal weight:    8.9990
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.084885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.059744 restraints weight = 76269.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.061192 restraints weight = 44293.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.062182 restraints weight = 31641.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.062831 restraints weight = 25773.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.063076 restraints weight = 22930.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.7514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  17666  Z= 0.288
  Angle     :  0.768   9.584  25095  Z= 0.423
  Chirality :  0.044   0.309   2860
  Planarity :  0.005   0.056   2168
  Dihedral  : 30.188 179.716   4672
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.24), residues: 1317
  helix:  0.29 (0.19), residues: 760
  sheet: -0.62 (0.64), residues: 68
  loop : -1.15 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O1147 
 TYR   0.028   0.003   TYR G  57 
 PHE   0.036   0.003   PHE E  67 
 TRP   0.014   0.003   TRP O1083 
 HIS   0.014   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 (17666)
  covalent geometry    : angle       0.76820 (25095)
  hydrogen bonds       : bond        0.05527 (  828)
  hydrogen bonds       : angle       4.45935 ( 2159)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.9213 (tp) cc_final: 0.8972 (tt)
REVERT: A   68 GLN cc_start: 0.8899 (tm130) cc_final: 0.8611 (tm-30)
REVERT: A   74 ILE cc_start: 0.9699 (tp) cc_final: 0.9432 (tp)
REVERT: A   87 SER cc_start: 0.9565 (m) cc_final: 0.9067 (p)
REVERT: A   93 GLN cc_start: 0.9448 (tt0) cc_final: 0.8683 (tm-30)
REVERT: A  123 ASP cc_start: 0.8696 (m-30) cc_final: 0.8305 (m-30)
REVERT: B   16 LYS cc_start: 0.7582 (tmtt) cc_final: 0.6775 (pttt)
REVERT: B   26 ILE cc_start: 0.9337 (tp) cc_final: 0.9126 (tp)
REVERT: B   84 MET cc_start: 0.8983 (tpp) cc_final: 0.8510 (mmm)
REVERT: C   35 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8011 (ttp-110)
REVERT: D   76 ARG cc_start: 0.9171 (ptm160) cc_final: 0.8894 (ptm160)
REVERT: D   77 LEU cc_start: 0.9410 (tt) cc_final: 0.9186 (tt)
REVERT: D   90 GLU cc_start: 0.9232 (mp0) cc_final: 0.8960 (mp0)
REVERT: E   50 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8189 (tm-30)
REVERT: E   53 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8131 (ttp80)
REVERT: E   70 LEU cc_start: 0.9263 (tp) cc_final: 0.9035 (tp)
REVERT: E  120 MET cc_start: 0.8800 (mmp) cc_final: 0.8322 (mmm)
REVERT: F   24 ASP cc_start: 0.7062 (t0) cc_final: 0.6189 (m-30)
REVERT: F   50 ILE cc_start: 0.8864 (mm) cc_final: 0.8557 (tp)
REVERT: F   68 ASP cc_start: 0.8504 (m-30) cc_final: 0.7973 (m-30)
REVERT: F   91 LYS cc_start: 0.9430 (tttm) cc_final: 0.9097 (ttpt)
REVERT: G   64 GLU cc_start: 0.8881 (pp20) cc_final: 0.8515 (tm-30)
REVERT: G   68 ASN cc_start: 0.9049 (m-40) cc_final: 0.8818 (m-40)
REVERT: G   91 GLU cc_start: 0.8231 (pp20) cc_final: 0.7939 (tm-30)
REVERT: H   54 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8696 (mmtp)
REVERT: H  119 THR cc_start: 0.9006 (m) cc_final: 0.8747 (t)
REVERT: O  823 VAL cc_start: 0.8894 (m) cc_final: 0.7449 (t)
REVERT: O  831 TRP cc_start: 0.8561 (m100) cc_final: 0.8196 (m100)
REVERT: O  852 ASN cc_start: 0.9131 (m-40) cc_final: 0.8731 (p0)
REVERT: O  888 TRP cc_start: 0.7193 (m100) cc_final: 0.6800 (m100)
REVERT: O  894 ASP cc_start: 0.8069 (t70) cc_final: 0.7602 (p0)
REVERT: O 1111 GLN cc_start: 0.8705 (mm110) cc_final: 0.8441 (mm-40)
REVERT: O 1116 MET cc_start: 0.8853 (mtp) cc_final: 0.7713 (tmm)
REVERT: O 1142 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8199 (mtt180)
REVERT: O 1248 GLU cc_start: 0.8283 (pm20) cc_final: 0.7701 (mp0)
REVERT: O 1294 MET cc_start: 0.7401 (mmm) cc_final: 0.6943 (mmm)
REVERT: O 1346 TYR cc_start: 0.4470 (m-10) cc_final: 0.4070 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1418
  time to fit residues: 59.4289
Evaluate side-chains
  225 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 154 optimal weight:   30.0000
   chunk 56 optimal weight:    0.0980
   chunk 117 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.087991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.062209 restraints weight = 75445.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.063710 restraints weight = 43222.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.064842 restraints weight = 30616.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.065489 restraints weight = 24931.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.065659 restraints weight = 22242.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.7488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  17666  Z= 0.172
  Angle     :  0.688  10.641  25095  Z= 0.375
  Chirality :  0.040   0.255   2860
  Planarity :  0.004   0.053   2168
  Dihedral  : 30.139 177.537   4672
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.24), residues: 1317
  helix:  0.50 (0.19), residues: 759
  sheet: -0.46 (0.65), residues: 68
  loop : -0.98 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  53 
 TYR   0.031   0.002   TYR G  57 
 PHE   0.019   0.002   PHE O1241 
 TRP   0.020   0.002   TRP O1083 
 HIS   0.014   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (17666)
  covalent geometry    : angle       0.68773 (25095)
  hydrogen bonds       : bond        0.04251 (  828)
  hydrogen bonds       : angle       4.12312 ( 2159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2863.68 seconds
wall clock time: 50 minutes 4.43 seconds (3004.43 seconds total)