Starting phenix.real_space_refine
on Tue Nov 18 19:08:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5z3o_6880/11_2025/5z3o_6880.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5z3o_6880/11_2025/5z3o_6880.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5z3o_6880/11_2025/5z3o_6880.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5z3o_6880/11_2025/5z3o_6880.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5z3o_6880/11_2025/5z3o_6880.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5z3o_6880/11_2025/5z3o_6880.map"
  }
  resolution = 3.62
  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=   0.001 sd=   0.008
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: 6
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     Mg      1      5.21       5
     S      29      5.16       5
     C    9675      2.51       5
     N    3095      2.21       5
     O    3708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16802
  Number of models: 1
  Model: ""
    Number of chains: 12
    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: 4763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4763
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 563}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "O"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.57, per 1000 atoms: 0.21
  Number of scatterers: 16802
  At special positions: 0
  Unit cell: (149.16, 117.48, 135.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      29     16.00
     P     294     15.00
     Mg      1     11.99
     O    3708      8.00
     N    3095      7.00
     C    9675      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: 1.38
  Conformation dependent library (CDL) restraints added in 506.6 milliseconds
  

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2554

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 8 sheets defined
      64.6% alpha, 3.0% beta
      114 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 2.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.502A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.625A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.513A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG A 128 " --> pdb=" O   ILE A 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.659A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 3.797A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.571A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.704A  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
      removed outlier: 3.746A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    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: 3.745A  pdb=" N   ARG D  76 " --> pdb=" O   GLY D  72 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.589A  pdb=" N   LEU D  99 " --> pdb=" O   VAL D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 120
      removed outlier: 4.006A  pdb=" N   HIS D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA D 107 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.502A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.625A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.514A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG E 128 " --> pdb=" O   ILE E 124 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
      removed outlier: 3.653A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.630A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.705A  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
      removed outlier: 3.747A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    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: 3.746A  pdb=" N   ARG H  76 " --> pdb=" O   GLY H  72 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.588A  pdb=" N   LEU H  99 " --> pdb=" O   VAL H  95 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 102 through 120
      removed outlier: 4.007A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA H 107 " --> pdb=" O   LEU H 103 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 671 through 683
    Processing helix  chain 'O' and resid 683 through 690
      removed outlier: 4.427A  pdb=" N   ASN O 687 " --> pdb=" O   LEU O 683 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 745 through 750
    Processing helix  chain 'O' and resid 768 through 784
      removed outlier: 3.640A  pdb=" N   ASN O 784 " --> pdb=" O   SER O 780 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 797 through 812
    Processing helix  chain 'O' and resid 824 through 838
      removed outlier: 4.241A  pdb=" N   SER O 829 " --> pdb=" O   LEU O 825 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   ASN O 830 " --> pdb=" O   SER O 826 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA O 836 " --> pdb=" O   SER O 832 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS O 837 " --> pdb=" O   SER O 833 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 849 through 863
      removed outlier: 3.984A  pdb=" N   ALA O 856 " --> pdb=" O   ASN O 852 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LYS O 857 " --> pdb=" O   GLU O 853 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA O 863 " --> pdb=" O   ALA O 859 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 873 through 879
      removed outlier: 3.885A  pdb=" N   ILE O 877 " --> pdb=" O   PHE O 873 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 879 through 886
    Processing helix  chain 'O' and resid 895 through 900
    Processing helix  chain 'O' and resid 904 through 912
    Processing helix  chain 'O' and resid 942 through 958
      removed outlier: 4.237A  pdb=" N   ASN O 947 " --> pdb=" O   PRO O 943 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LYS O 950 " --> pdb=" O   PHE O 946 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   SER O 951 " --> pdb=" O   ASN O 947 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   PHE O 952 " --> pdb=" O   SER O 948 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP O 953 " --> pdb=" O   VAL O 949 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   GLU O 954 " --> pdb=" O   LYS O 950 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP O 955 " --> pdb=" O   SER O 951 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 968 through 973
    Processing helix  chain 'O' and resid 976 through 987
      removed outlier: 3.771A  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: 3.780A  pdb=" N   GLN O1024 " --> pdb=" O   GLN O1020 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1049 through 1059
      removed outlier: 4.055A  pdb=" N   LEU O1055 " --> pdb=" O   GLN O1051 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LYS O1056 " --> pdb=" O   ILE O1052 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1068 through 1073
    Processing helix  chain 'O' and resid 1082 through 1085
      removed outlier: 3.571A  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 1103
      removed outlier: 3.729A  pdb=" N   GLU O1090 " --> pdb=" O   ALA O1086 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU O1091 " --> pdb=" O   GLY O1087 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU O1092 " --> pdb=" O   LYS O1088 " (cutoff:3.500A)
      Proline residue:  O1097  - end of helix
    Processing helix  chain 'O' and resid 1113 through 1126
    Processing helix  chain 'O' and resid 1139 through 1150
      removed outlier: 3.918A  pdb=" N   LEU O1146 " --> pdb=" O   ARG O1142 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ARG O1147 " --> pdb=" O   SER O1143 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU O1148 " --> pdb=" O   GLU O1144 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1187 through 1199
      removed outlier: 4.469A  pdb=" N   ASP O1195 " --> pdb=" O   LEU O1191 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA O1197 " --> pdb=" O   ALA O1193 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG O1199 " --> pdb=" O   ASP O1195 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1216 through 1226
      removed outlier: 4.227A  pdb=" N   VAL O1220 " --> pdb=" O   SER O1216 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1227 through 1231
      removed outlier: 4.012A  pdb=" N   ILE O1231 " --> pdb=" O   LYS O1228 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1232 through 1241
      removed outlier: 4.154A  pdb=" N   LYS O1240 " --> pdb=" O   ILE O1236 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE O1241 " --> pdb=" O   GLN O1237 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1246 through 1250
      removed outlier: 3.935A  pdb=" N   GLN O1250 " --> pdb=" O   SER O1247 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1251 through 1263
      removed outlier: 4.221A  pdb=" N   ALA O1260 " --> pdb=" O   SER O1256 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1264 through 1268
    Processing helix  chain 'O' and resid 1279 through 1286
    Processing helix  chain 'O' and resid 1290 through 1307
      removed outlier: 3.625A  pdb=" N   VAL O1296 " --> pdb=" O   GLU O1292 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LYS O1306 " --> pdb=" O   GLU O1302 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LYS O1307 " --> pdb=" O   ASP O1303 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1337 through 1341
      removed outlier: 3.622A  pdb=" N   GLU O1341 " --> pdb=" O   ARG O1337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1337 through 1341'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.606A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.607A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.269A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.852A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'O' and resid 788 through 790
      removed outlier: 3.922A  pdb=" N   GLY O 788 " --> pdb=" O   ARG O 919 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ILE O 921 " --> pdb=" O   GLY O 788 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU O 790 " --> pdb=" O   ILE O 921 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU O 922 " --> pdb=" O   ILE O 893 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   LEU O 820 " --> pdb=" O   ILE O 892 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'O' and resid 1130 through 1131
      removed outlier: 6.810A  pdb=" N   LEU O1131 " --> pdb=" O   ILE O1160 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   SER O1162 " --> pdb=" O   LEU O1131 " (cutoff:3.500A)

    557 hydrogen bonds defined for protein.
    1647 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      297 hydrogen bonds
      594 hydrogen bond angles
      0 basepair planarities
      114 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 3.73

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3371
        1.33 -     1.45: 5070
        1.45 -     1.57: 8607
        1.57 -     1.69: 585
        1.69 -     1.81: 53
  Bond restraints: 17686
  Sorted by residual:
  bond pdb=" C3'  DA I  20 "
       pdb=" O3'  DA I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.466 -0.044 3.00e-02 1.11e+03 2.12e+00
  bond pdb=" C   ARG A 131 "
       pdb=" O   ARG A 131 "
    ideal  model  delta    sigma   weight residual
    1.236  1.217  0.019 1.29e-02 6.01e+03 2.07e+00
  bond pdb=" C   ASP E 106 "
       pdb=" O   ASP E 106 "
    ideal  model  delta    sigma   weight residual
    1.237  1.220  0.017 1.17e-02 7.31e+03 2.05e+00
  bond pdb=" C3'  DA J  14 "
       pdb=" O3'  DA J  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.96e+00
  bond pdb=" C3'  DG J 137 "
       pdb=" O3'  DG J 137 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.80e+00
  ... (remaining 17681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 24643
        2.05 -     4.09: 435
        4.09 -     6.14: 39
        6.14 -     8.19: 9
        8.19 -    10.24: 2
  Bond angle restraints: 25128
  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  110.03   -6.78 1.05e+00 9.07e-01 4.17e+01
  angle pdb=" C   ILE O1058 "
        pdb=" N   CYS O1059 "
        pdb=" CA  CYS O1059 "
      ideal   model   delta    sigma   weight residual
     122.06  116.26    5.80 1.86e+00 2.89e-01 9.73e+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  127.49   -5.95 1.91e+00 2.74e-01 9.72e+00
  angle pdb=" CA  LEU O 927 "
        pdb=" CB  LEU O 927 "
        pdb=" CG  LEU O 927 "
      ideal   model   delta    sigma   weight residual
     116.30  126.54  -10.24 3.50e+00 8.16e-02 8.55e+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   97.59    4.01 1.50e+00 4.44e-01 7.15e+00
  ... (remaining 25123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.72: 8659
       35.72 -    71.44: 1259
       71.44 -   107.16: 20
      107.16 -   142.88: 2
      142.88 -   178.60: 7
  Dihedral angle restraints: 9947
    sinusoidal: 6016
      harmonic: 3931
  Sorted by residual:
  dihedral pdb=" CA  PRO O 932 "
           pdb=" C   PRO O 932 "
           pdb=" N   GLU O 933 "
           pdb=" CA  GLU O 933 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.54  -27.46     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  HIS O 913 "
           pdb=" C   HIS O 913 "
           pdb=" N   TYR O 914 "
           pdb=" CA  TYR O 914 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.19  -25.81     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  LEU O1258 "
           pdb=" C   LEU O1258 "
           pdb=" N   ASP O1259 "
           pdb=" CA  ASP O1259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.60   24.40     0      5.00e+00 4.00e-02 2.38e+01
  ... (remaining 9944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 2460
       0.051 -    0.102: 332
       0.102 -    0.153: 60
       0.153 -    0.204: 8
       0.204 -    0.255: 3
  Chirality restraints: 2863
  Sorted by residual:
  chirality pdb=" CG  LEU O1258 "
            pdb=" CB  LEU O1258 "
            pdb=" CD1 LEU O1258 "
            pdb=" CD2 LEU O1258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CG  LEU O1222 "
            pdb=" CB  LEU O1222 "
            pdb=" CD1 LEU O1222 "
            pdb=" CD2 LEU O1222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.27e+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 1.13e+00
  ... (remaining 2860 not shown)

  Planarity restraints: 2167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  39 "   -0.027 2.00e-02 2.50e+03   1.36e-02 5.06e+00
        pdb=" N9   DA I  39 "    0.016 2.00e-02 2.50e+03
        pdb=" C8   DA I  39 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I  39 "    0.006 2.00e-02 2.50e+03
        pdb=" C5   DA I  39 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  39 "   -0.025 2.00e-02 2.50e+03
        pdb=" N6   DA I  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1   DA I  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  39 "    0.010 2.00e-02 2.50e+03
        pdb=" N3   DA I  39 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4   DA I  39 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E 120 "    0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO E 121 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E 121 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 121 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 120 "   -0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO A 121 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 121 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 121 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2164 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 295
        2.62 -     3.19: 14733
        3.19 -     3.76: 29374
        3.76 -     4.33: 38774
        4.33 -     4.90: 56567
  Nonbonded interactions: 139743
  Sorted by model distance:
  nonbonded pdb=" O1B ADP O1501 "
            pdb="MG    MG O1502 "
     model   vdw
     2.055 2.170
  nonbonded pdb=" O1A ADP O1501 "
            pdb="MG    MG O1502 "
     model   vdw
     2.065 2.170
  nonbonded pdb=" O   ALA O 748 "
            pdb=" ND2 ASN O 784 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OP1  DA I  97 "
            pdb=" ND2 ASN O1186 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   LEU O 971 "
            pdb=" OG1 THR O 976 "
     model   vdw
     2.236 3.040
  ... (remaining 139738 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:             0.480
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.800
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
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   0.044  17686  Z= 0.153
  Angle     :  0.634  10.236  25128  Z= 0.363
  Chirality :  0.038   0.255   2863
  Planarity :  0.004   0.048   2167
  Dihedral  : 24.397 178.604   7393
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.27 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  1.74 %
    Favored  : 97.82 %
  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 are not related in a simple way.
  whole: -3.57 (0.19), residues: 1316
  helix: -2.37 (0.15), residues: 742
  sheet: -2.49 (0.55), residues: 65
  loop : -2.07 (0.23), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O 919 
 TYR   0.018   0.002   TYR F  98 
 PHE   0.022   0.002   PHE O1241 
 TRP   0.014   0.001   TRP O1083 
 HIS   0.004   0.001   HIS O 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (17686)
  covalent geometry    : angle       0.63399 (25128)
  hydrogen bonds       : bond        0.10872 (  854)
  hydrogen bonds       : angle       8.10821 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 454
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7457 (mtt-85)
REVERT: A   59 GLU cc_start: 0.8859 (pt0) cc_final: 0.8504 (mm-30)
REVERT: B   82 THR cc_start: 0.9479 (p) cc_final: 0.9205 (p)
REVERT: D   51 ILE cc_start: 0.8053 (tt) cc_final: 0.7778 (tt)
REVERT: E   60 LEU cc_start: 0.8606 (tp) cc_final: 0.7926 (tp)
REVERT: F   80 THR cc_start: 0.9092 (m) cc_final: 0.8892 (p)
REVERT: G   90 ASP cc_start: 0.8364 (t0) cc_final: 0.8114 (t0)
REVERT: O  806 LEU cc_start: 0.8832 (mt) cc_final: 0.8630 (mt)
REVERT: O  891 MET cc_start: 0.6384 (ptp) cc_final: 0.6108 (ptp)
REVERT: O  895 GLU cc_start: 0.7322 (tp30) cc_final: 0.7101 (tp30)
REVERT: O 1184 ASP cc_start: 0.7980 (m-30) cc_final: 0.6869 (m-30)
REVERT: O 1188 HIS cc_start: 0.7937 (p-80) cc_final: 0.7449 (p-80)
REVERT: O 1222 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8474 (tm)
  outliers start: 5
  outliers final: 3
  residues processed: 457
  average time/residue: 0.1793
  time to fit residues: 112.2288
Evaluate side-chains
  242 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 238
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  25 ASN
D  92 GLN
E  68 GLN
E 125 GLN
G  38 ASN
G  73 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
** O 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 897 HIS
O1104 HIS
O1198 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.096105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.068112 restraints weight = 61040.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.069733 restraints weight = 31889.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.070579 restraints weight = 22171.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.071266 restraints weight = 18646.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.071449 restraints weight = 16922.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  17686  Z= 0.232
  Angle     :  0.715   9.572  25128  Z= 0.388
  Chirality :  0.041   0.240   2863
  Planarity :  0.006   0.049   2167
  Dihedral  : 29.645 178.146   4690
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 12.62 %
    Favored  : 82.85 %
  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 are not related in a simple way.
  whole: -1.54 (0.22), residues: 1316
  helix: -0.40 (0.18), residues: 761
  sheet: -2.19 (0.61), residues: 64
  loop : -1.72 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  71 
 TYR   0.027   0.002   TYR F  98 
 PHE   0.021   0.003   PHE O 873 
 TRP   0.010   0.002   TRP O 777 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 (17686)
  covalent geometry    : angle       0.71541 (25128)
  hydrogen bonds       : bond        0.04575 (  854)
  hydrogen bonds       : angle       4.81898 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 253
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 ASN cc_start: 0.8616 (m-40) cc_final: 0.8159 (m110)
REVERT: B   74 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: B   84 MET cc_start: 0.8355 (mmm) cc_final: 0.8102 (mmm)
REVERT: C   64 GLU cc_start: 0.8466 (tt0) cc_final: 0.7949 (pt0)
REVERT: C   72 ASP cc_start: 0.8278 (m-30) cc_final: 0.7893 (m-30)
REVERT: C   75 LYS cc_start: 0.9036 (mptt) cc_final: 0.8720 (mmmt)
REVERT: C   77 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7241 (mtt-85)
REVERT: E  122 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8689 (ptpp)
REVERT: F   27 GLN cc_start: 0.8645 (pp30) cc_final: 0.8375 (pp30)
REVERT: F   88 TYR cc_start: 0.8691 (m-10) cc_final: 0.8300 (m-80)
REVERT: G   95 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8551 (mtpp)
REVERT: H   39 TYR cc_start: 0.8095 (t80) cc_final: 0.7710 (t80)
REVERT: H   59 MET cc_start: 0.9104 (tpp) cc_final: 0.8620 (tpp)
REVERT: H   80 TYR cc_start: 0.7903 (m-10) cc_final: 0.7468 (m-10)
REVERT: O  790 LEU cc_start: 0.8922 (tp) cc_final: 0.8558 (tt)
REVERT: O 1015 MET cc_start: 0.7925 (mmt) cc_final: 0.7354 (mmp)
REVERT: O 1112 MET cc_start: 0.7273 (mmt) cc_final: 0.6919 (mmm)
REVERT: O 1183 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8178 (p)
REVERT: O 1294 MET cc_start: 0.8604 (mmm) cc_final: 0.8394 (mmm)
  outliers start: 52
  outliers final: 29
  residues processed: 288
  average time/residue: 0.1669
  time to fit residues: 68.7621
Evaluate side-chains
  236 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 205
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  882 LEU
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  897 HIS
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  954 GLU
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1163 THR
Chi-restraints excluded: chain O residue 1183 THR
Chi-restraints excluded: chain O residue 1248 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 118 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
E  68 GLN
G  38 ASN
G  73 ASN
H  46 HIS
** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 749 HIS
** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 897 HIS
O 915 HIS
O 929 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.097543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.069838 restraints weight = 61255.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.071559 restraints weight = 30466.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.072636 restraints weight = 20608.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.073228 restraints weight = 16838.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.073474 restraints weight = 15275.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17686  Z= 0.146
  Angle     :  0.629   9.348  25128  Z= 0.342
  Chirality :  0.037   0.188   2863
  Planarity :  0.004   0.056   2167
  Dihedral  : 29.474 177.858   4686
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.93 %
    Favored  : 80.59 %
  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 are not related in a simple way.
  whole: -0.63 (0.23), residues: 1316
  helix:  0.40 (0.19), residues: 765
  sheet: -1.96 (0.57), residues: 72
  loop : -1.41 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  71 
 TYR   0.023   0.002   TYR B  98 
 PHE   0.018   0.002   PHE O 946 
 TRP   0.010   0.002   TRP O 777 
 HIS   0.015   0.001   HIS O 897 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (17686)
  covalent geometry    : angle       0.62860 (25128)
  hydrogen bonds       : bond        0.03709 (  854)
  hydrogen bonds       : angle       4.21727 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 249
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8707 (tt0)
REVERT: A  112 ILE cc_start: 0.9434 (pt) cc_final: 0.9198 (mt)
REVERT: B   64 ASN cc_start: 0.8560 (m-40) cc_final: 0.7995 (m110)
REVERT: B   91 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8439 (tttm)
REVERT: C   64 GLU cc_start: 0.8448 (tt0) cc_final: 0.8086 (pt0)
REVERT: C   72 ASP cc_start: 0.8171 (m-30) cc_final: 0.7788 (m-30)
REVERT: C   73 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7957 (t0)
REVERT: C   77 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.6999 (mmt180)
REVERT: D   44 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8644 (tm-30)
REVERT: D   68 GLU cc_start: 0.8255 (tp30) cc_final: 0.8038 (tp30)
REVERT: D   73 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8351 (tp30)
REVERT: E   59 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7753 (tm-30)
REVERT: E   93 GLN cc_start: 0.8722 (tt0) cc_final: 0.8074 (tp40)
REVERT: F   27 GLN cc_start: 0.8655 (pp30) cc_final: 0.8324 (pp30)
REVERT: F   88 TYR cc_start: 0.8602 (m-10) cc_final: 0.8311 (m-80)
REVERT: F   91 LYS cc_start: 0.9050 (tppt) cc_final: 0.8741 (tttm)
REVERT: G   95 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8385 (mtpp)
REVERT: H   39 TYR cc_start: 0.8076 (t80) cc_final: 0.7659 (t80)
REVERT: H   80 TYR cc_start: 0.7835 (m-10) cc_final: 0.7274 (m-10)
REVERT: H  102 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: O  775 LEU cc_start: 0.9106 (tt) cc_final: 0.8900 (pp)
REVERT: O  790 LEU cc_start: 0.8878 (tp) cc_final: 0.8564 (tt)
REVERT: O  794 MET cc_start: 0.8381 (tmm) cc_final: 0.8157 (tmm)
REVERT: O 1015 MET cc_start: 0.7772 (mmt) cc_final: 0.7539 (mmp)
REVERT: O 1053 MET cc_start: 0.8518 (ppp) cc_final: 0.7939 (ppp)
REVERT: O 1112 MET cc_start: 0.7303 (mmt) cc_final: 0.7052 (mmm)
REVERT: O 1183 THR cc_start: 0.8217 (p) cc_final: 0.8013 (p)
  outliers start: 40
  outliers final: 17
  residues processed: 269
  average time/residue: 0.1596
  time to fit residues: 61.9118
Evaluate side-chains
  236 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 215
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 143 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 130 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
G  38 ASN
** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 783 ASN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.096993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069009 restraints weight = 60485.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.070694 restraints weight = 30342.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.071759 restraints weight = 20759.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.072333 restraints weight = 17061.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.072568 restraints weight = 15509.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17686  Z= 0.153
  Angle     :  0.613   8.859  25128  Z= 0.337
  Chirality :  0.036   0.182   2863
  Planarity :  0.004   0.057   2167
  Dihedral  : 29.522 178.960   4686
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.93 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.88 %
    Favored  : 79.81 %
  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 are not related in a simple way.
  whole: -0.24 (0.23), residues: 1316
  helix:  0.75 (0.19), residues: 756
  sheet: -1.69 (0.60), residues: 72
  loop : -1.30 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.016   0.002   TYR F  98 
 PHE   0.017   0.002   PHE O1063 
 TRP   0.013   0.002   TRP O 777 
 HIS   0.008   0.001   HIS O 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (17686)
  covalent geometry    : angle       0.61261 (25128)
  hydrogen bonds       : bond        0.03709 (  854)
  hydrogen bonds       : angle       4.02307 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 226
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8726 (tt0)
REVERT: A  112 ILE cc_start: 0.9516 (pt) cc_final: 0.9184 (mt)
REVERT: B   80 THR cc_start: 0.9338 (m) cc_final: 0.9118 (p)
REVERT: B   84 MET cc_start: 0.8485 (mmm) cc_final: 0.8220 (mmm)
REVERT: C   56 GLU cc_start: 0.7689 (tt0) cc_final: 0.7164 (tt0)
REVERT: C   64 GLU cc_start: 0.8450 (tt0) cc_final: 0.8168 (pt0)
REVERT: C   72 ASP cc_start: 0.8126 (m-30) cc_final: 0.7760 (m-30)
REVERT: C   75 LYS cc_start: 0.9157 (mptt) cc_final: 0.8903 (mmmt)
REVERT: C   77 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7061 (mmt180)
REVERT: D   37 TYR cc_start: 0.8635 (m-80) cc_final: 0.8343 (m-80)
REVERT: D   44 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: D   68 GLU cc_start: 0.8327 (tp30) cc_final: 0.8044 (tp30)
REVERT: D   73 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8246 (tp30)
REVERT: E   93 GLN cc_start: 0.8738 (tt0) cc_final: 0.8114 (tp40)
REVERT: F   27 GLN cc_start: 0.8744 (pp30) cc_final: 0.8482 (pp30)
REVERT: F   91 LYS cc_start: 0.9056 (tppt) cc_final: 0.8762 (tttm)
REVERT: G   24 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8127 (mp10)
REVERT: G   95 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8440 (mtpp)
REVERT: H   39 TYR cc_start: 0.8101 (t80) cc_final: 0.7669 (t80)
REVERT: H   80 TYR cc_start: 0.7955 (m-10) cc_final: 0.7427 (m-10)
REVERT: H  102 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: O  775 LEU cc_start: 0.9115 (tt) cc_final: 0.8877 (pp)
REVERT: O  790 LEU cc_start: 0.8887 (tp) cc_final: 0.8540 (tt)
REVERT: O 1015 MET cc_start: 0.7803 (mmt) cc_final: 0.7527 (mmp)
REVERT: O 1053 MET cc_start: 0.8466 (ppp) cc_final: 0.8062 (ppp)
REVERT: O 1112 MET cc_start: 0.7258 (mmt) cc_final: 0.6976 (mmm)
REVERT: O 1300 MET cc_start: 0.7268 (ttm) cc_final: 0.6431 (ptm)
  outliers start: 38
  outliers final: 24
  residues processed: 247
  average time/residue: 0.1455
  time to fit residues: 53.1369
Evaluate side-chains
  230 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain O residue  766 THR
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 139 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  64 ASN
G  38 ASN
O 687 ASN
O 785 HIS
** O 801 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.094780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.066261 restraints weight = 60164.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.067870 restraints weight = 30454.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.068908 restraints weight = 20861.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.069473 restraints weight = 17229.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.069665 restraints weight = 15715.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  17686  Z= 0.190
  Angle     :  0.640  10.847  25128  Z= 0.351
  Chirality :  0.037   0.189   2863
  Planarity :  0.004   0.055   2167
  Dihedral  : 29.681 178.721   4686
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.40 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.06 %
    Favored  : 78.85 %
  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 are not related in a simple way.
  whole: -0.03 (0.23), residues: 1316
  helix:  0.96 (0.19), residues: 756
  sheet: -1.41 (0.65), residues: 66
  loop : -1.32 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG O1299 
 TYR   0.014   0.002   TYR F  98 
 PHE   0.020   0.002   PHE O1063 
 TRP   0.012   0.002   TRP O 777 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (17686)
  covalent geometry    : angle       0.63965 (25128)
  hydrogen bonds       : bond        0.04058 (  854)
  hydrogen bonds       : angle       3.99818 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 213
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8587 (mmm) cc_final: 0.8226 (mmm)
REVERT: C   56 GLU cc_start: 0.7773 (tt0) cc_final: 0.7463 (tt0)
REVERT: C   64 GLU cc_start: 0.8448 (tt0) cc_final: 0.8075 (pt0)
REVERT: C   72 ASP cc_start: 0.8112 (m-30) cc_final: 0.7765 (m-30)
REVERT: C   75 LYS cc_start: 0.9145 (mptt) cc_final: 0.8853 (mmmt)
REVERT: D   37 TYR cc_start: 0.8842 (m-80) cc_final: 0.8625 (m-80)
REVERT: D   39 TYR cc_start: 0.7516 (t80) cc_final: 0.7308 (t80)
REVERT: D   44 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8661 (tm-30)
REVERT: D   68 GLU cc_start: 0.8364 (tp30) cc_final: 0.8059 (tp30)
REVERT: D   73 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8270 (tp30)
REVERT: E   93 GLN cc_start: 0.8746 (tt0) cc_final: 0.8055 (tp40)
REVERT: F   27 GLN cc_start: 0.8773 (pp30) cc_final: 0.8452 (pp30)
REVERT: F   88 TYR cc_start: 0.8540 (m-80) cc_final: 0.8183 (m-80)
REVERT: G   24 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8197 (mp10)
REVERT: G   95 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8526 (mtpp)
REVERT: H   42 LEU cc_start: 0.9551 (tp) cc_final: 0.9246 (tt)
REVERT: H  102 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7564 (tm-30)
REVERT: O  760 SER cc_start: 0.8948 (m) cc_final: 0.8704 (p)
REVERT: O  775 LEU cc_start: 0.9087 (tt) cc_final: 0.8885 (pp)
REVERT: O  790 LEU cc_start: 0.8933 (tp) cc_final: 0.8530 (tt)
REVERT: O 1015 MET cc_start: 0.7912 (mmt) cc_final: 0.7564 (mmp)
REVERT: O 1112 MET cc_start: 0.7411 (mmt) cc_final: 0.7102 (mmm)
  outliers start: 47
  outliers final: 36
  residues processed: 241
  average time/residue: 0.1499
  time to fit residues: 53.6940
Evaluate side-chains
  236 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 200
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain O residue  766 THR
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  891 MET
Chi-restraints excluded: chain O residue  918 TYR
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue  954 GLU
Chi-restraints excluded: chain O residue  999 VAL
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 149 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0010
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 127 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 117 optimal weight:    9.9990
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
D  81 ASN
G  38 ASN
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1284 ASN ** 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 = 0.3830 r_free = 0.3830 target = 0.096051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.068067 restraints weight = 60161.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.069764 restraints weight = 30129.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.070824 restraints weight = 20512.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.071389 restraints weight = 16872.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.071679 restraints weight = 15370.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17686  Z= 0.148
  Angle     :  0.618  10.891  25128  Z= 0.338
  Chirality :  0.036   0.186   2863
  Planarity :  0.004   0.055   2167
  Dihedral  : 29.543 179.632   4686
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.32 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.71 %
    Favored  : 77.98 %
  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 are not related in a simple way.
  whole:  0.31 (0.24), residues: 1316
  helix:  1.25 (0.20), residues: 756
  sheet: -1.55 (0.62), residues: 72
  loop : -1.14 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.026   0.002   TYR H  80 
 PHE   0.021   0.001   PHE O1063 
 TRP   0.018   0.002   TRP O 777 
 HIS   0.005   0.001   HIS O 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (17686)
  covalent geometry    : angle       0.61815 (25128)
  hydrogen bonds       : bond        0.03606 (  854)
  hydrogen bonds       : angle       3.83143 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8390 (mmm) cc_final: 0.8141 (mmm)
REVERT: C   56 GLU cc_start: 0.7708 (tt0) cc_final: 0.7449 (tt0)
REVERT: C   64 GLU cc_start: 0.8427 (tt0) cc_final: 0.8023 (pt0)
REVERT: C   72 ASP cc_start: 0.8102 (m-30) cc_final: 0.7721 (m-30)
REVERT: C   75 LYS cc_start: 0.9116 (mptt) cc_final: 0.8816 (mmmt)
REVERT: D   39 TYR cc_start: 0.7489 (t80) cc_final: 0.7205 (t80)
REVERT: D   44 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8638 (tm-30)
REVERT: D   68 GLU cc_start: 0.8351 (tp30) cc_final: 0.8053 (tp30)
REVERT: E   93 GLN cc_start: 0.8644 (tt0) cc_final: 0.7964 (tp40)
REVERT: F   27 GLN cc_start: 0.8673 (pp30) cc_final: 0.8369 (pp30)
REVERT: F   44 LYS cc_start: 0.8476 (tttm) cc_final: 0.8037 (mtpt)
REVERT: F   91 LYS cc_start: 0.9039 (tppt) cc_final: 0.8831 (tttm)
REVERT: G   90 ASP cc_start: 0.8137 (t0) cc_final: 0.7575 (t0)
REVERT: G   92 GLU cc_start: 0.8143 (pp20) cc_final: 0.7832 (pm20)
REVERT: G   95 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8466 (mtpp)
REVERT: H  102 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7075 (tm-30)
REVERT: O  760 SER cc_start: 0.8907 (m) cc_final: 0.8676 (p)
REVERT: O  775 LEU cc_start: 0.9086 (tt) cc_final: 0.8873 (pp)
REVERT: O  790 LEU cc_start: 0.8967 (tp) cc_final: 0.8604 (tt)
REVERT: O  895 GLU cc_start: 0.6794 (tp30) cc_final: 0.6581 (tp30)
REVERT: O 1015 MET cc_start: 0.7905 (mmt) cc_final: 0.7577 (mmp)
REVERT: O 1053 MET cc_start: 0.8477 (ppp) cc_final: 0.8054 (ppp)
REVERT: O 1112 MET cc_start: 0.7371 (mmt) cc_final: 0.7028 (mmm)
  outliers start: 38
  outliers final: 27
  residues processed: 237
  average time/residue: 0.1434
  time to fit residues: 50.6376
Evaluate side-chains
  233 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 206
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  891 MET
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue  999 VAL
Chi-restraints excluded: chain O residue 1059 CYS
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 120 optimal weight:    9.9990
   chunk 67 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0070
   chunk 78 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
G  38 ASN
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O1284 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.096105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.067967 restraints weight = 59815.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.069652 restraints weight = 30026.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.070697 restraints weight = 20534.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.071260 restraints weight = 16935.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.071491 restraints weight = 15437.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17686  Z= 0.147
  Angle     :  0.616   9.480  25128  Z= 0.337
  Chirality :  0.036   0.183   2863
  Planarity :  0.004   0.058   2167
  Dihedral  : 29.521 179.881   4686
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.09 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.80 %
    Favored  : 77.89 %
  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 are not related in a simple way.
  whole:  0.40 (0.24), residues: 1316
  helix:  1.30 (0.20), residues: 756
  sheet: -1.54 (0.62), residues: 72
  loop : -1.07 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.042   0.002   TYR H  80 
 PHE   0.021   0.001   PHE O1063 
 TRP   0.019   0.002   TRP O 777 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (17686)
  covalent geometry    : angle       0.61558 (25128)
  hydrogen bonds       : bond        0.03575 (  854)
  hydrogen bonds       : angle       3.79479 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 220
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8399 (mmm) cc_final: 0.8094 (mmm)
REVERT: C   56 GLU cc_start: 0.7704 (tt0) cc_final: 0.7451 (tt0)
REVERT: C   64 GLU cc_start: 0.8433 (tt0) cc_final: 0.8037 (pt0)
REVERT: C   72 ASP cc_start: 0.8082 (m-30) cc_final: 0.7763 (m-30)
REVERT: C   75 LYS cc_start: 0.9103 (mptt) cc_final: 0.8815 (mmmt)
REVERT: D   37 TYR cc_start: 0.8523 (m-80) cc_final: 0.8202 (m-80)
REVERT: D   39 TYR cc_start: 0.7441 (t80) cc_final: 0.7168 (t80)
REVERT: D   44 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8718 (tm-30)
REVERT: D   68 GLU cc_start: 0.8356 (tp30) cc_final: 0.8031 (tp30)
REVERT: E   93 GLN cc_start: 0.8617 (tt0) cc_final: 0.7967 (tp40)
REVERT: F   27 GLN cc_start: 0.8666 (pp30) cc_final: 0.8385 (pp30)
REVERT: F   44 LYS cc_start: 0.8479 (tttm) cc_final: 0.8187 (mtpt)
REVERT: G   24 GLN cc_start: 0.8618 (mp10) cc_final: 0.8187 (mm-40)
REVERT: G   95 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8412 (mtpp)
REVERT: H  103 LEU cc_start: 0.9008 (mt) cc_final: 0.8739 (mt)
REVERT: O  760 SER cc_start: 0.8921 (m) cc_final: 0.8692 (p)
REVERT: O  775 LEU cc_start: 0.9082 (tt) cc_final: 0.8879 (pp)
REVERT: O  790 LEU cc_start: 0.8976 (tp) cc_final: 0.8616 (tt)
REVERT: O  895 GLU cc_start: 0.6852 (tp30) cc_final: 0.6630 (tp30)
REVERT: O 1015 MET cc_start: 0.7942 (mmt) cc_final: 0.7606 (mmp)
REVERT: O 1053 MET cc_start: 0.8503 (ppp) cc_final: 0.8064 (ppp)
REVERT: O 1112 MET cc_start: 0.7577 (mmt) cc_final: 0.7161 (mmm)
REVERT: O 1119 MET cc_start: 0.8921 (tpp) cc_final: 0.8712 (tpp)
  outliers start: 38
  outliers final: 31
  residues processed: 241
  average time/residue: 0.1387
  time to fit residues: 50.1319
Evaluate side-chains
  234 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   91 ILE
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue  999 VAL
Chi-restraints excluded: chain O residue 1059 CYS
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 142 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 130 optimal weight:    9.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
G  38 ASN
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O1111 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.093540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.065337 restraints weight = 60451.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.066943 restraints weight = 30885.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.067942 restraints weight = 21353.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.068477 restraints weight = 17701.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.068663 restraints weight = 16181.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  17686  Z= 0.212
  Angle     :  0.670   9.624  25128  Z= 0.363
  Chirality :  0.038   0.195   2863
  Planarity :  0.005   0.059   2167
  Dihedral  : 29.747 179.393   4686
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.40 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.97 %
    Favored  : 77.28 %
  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 are not related in a simple way.
  whole:  0.35 (0.24), residues: 1316
  helix:  1.17 (0.19), residues: 763
  sheet: -1.55 (0.62), residues: 72
  loop : -0.95 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.055   0.002   TYR H  80 
 PHE   0.021   0.002   PHE O1063 
 TRP   0.020   0.002   TRP O 777 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (17686)
  covalent geometry    : angle       0.66962 (25128)
  hydrogen bonds       : bond        0.04174 (  854)
  hydrogen bonds       : angle       3.96457 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8531 (mmm) cc_final: 0.8300 (mmm)
REVERT: C   64 GLU cc_start: 0.8474 (tt0) cc_final: 0.8115 (pt0)
REVERT: C   72 ASP cc_start: 0.8103 (m-30) cc_final: 0.7765 (m-30)
REVERT: C   75 LYS cc_start: 0.9149 (mptt) cc_final: 0.8845 (mmmt)
REVERT: D   37 TYR cc_start: 0.8664 (m-80) cc_final: 0.8279 (m-80)
REVERT: D   39 TYR cc_start: 0.7509 (t80) cc_final: 0.7176 (t80)
REVERT: D   44 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8765 (tm-30)
REVERT: D   68 GLU cc_start: 0.8364 (tp30) cc_final: 0.8114 (tp30)
REVERT: F   25 ASN cc_start: 0.6028 (m110) cc_final: 0.5617 (m-40)
REVERT: F   27 GLN cc_start: 0.8586 (pp30) cc_final: 0.8235 (pp30)
REVERT: G   24 GLN cc_start: 0.8601 (mp10) cc_final: 0.8228 (mm-40)
REVERT: G   95 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8517 (mtpp)
REVERT: O  760 SER cc_start: 0.8970 (m) cc_final: 0.8765 (p)
REVERT: O  790 LEU cc_start: 0.9028 (tp) cc_final: 0.8687 (tt)
REVERT: O  895 GLU cc_start: 0.7018 (tp30) cc_final: 0.6772 (tp30)
REVERT: O 1015 MET cc_start: 0.8074 (mmt) cc_final: 0.7638 (mmp)
REVERT: O 1053 MET cc_start: 0.8469 (ppp) cc_final: 0.7975 (ppp)
REVERT: O 1112 MET cc_start: 0.7600 (mmt) cc_final: 0.7156 (mmm)
  outliers start: 43
  outliers final: 35
  residues processed: 218
  average time/residue: 0.1350
  time to fit residues: 44.4025
Evaluate side-chains
  220 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain O residue  766 THR
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  918 TYR
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue  999 VAL
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 121 optimal weight:    0.2980
   chunk 73 optimal weight:    7.9990
   chunk 113 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 45 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 137 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E  93 GLN
G  38 ASN
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1284 ASN ** 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 = 0.3831 r_free = 0.3831 target = 0.096153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.068217 restraints weight = 60633.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.069887 restraints weight = 30913.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.070923 restraints weight = 21295.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.071489 restraints weight = 17592.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.071627 restraints weight = 16050.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.5161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17686  Z= 0.147
  Angle     :  0.635   9.485  25128  Z= 0.347
  Chirality :  0.036   0.187   2863
  Planarity :  0.004   0.058   2167
  Dihedral  : 29.523 179.937   4686
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.64 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.63 %
    Favored  : 76.76 %
  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 are not related in a simple way.
  whole:  0.37 (0.24), residues: 1316
  helix:  1.23 (0.20), residues: 766
  sheet: -1.54 (0.62), residues: 72
  loop : -1.04 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  63 
 TYR   0.040   0.002   TYR H  80 
 PHE   0.022   0.001   PHE O1063 
 TRP   0.022   0.002   TRP O 777 
 HIS   0.005   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (17686)
  covalent geometry    : angle       0.63548 (25128)
  hydrogen bonds       : bond        0.03591 (  854)
  hydrogen bonds       : angle       3.81027 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.8840 (mppt) cc_final: 0.8552 (mmtm)
REVERT: C   64 GLU cc_start: 0.8446 (tt0) cc_final: 0.8036 (pt0)
REVERT: C   72 ASP cc_start: 0.8102 (m-30) cc_final: 0.7755 (m-30)
REVERT: C   75 LYS cc_start: 0.9123 (mptt) cc_final: 0.8840 (mmmt)
REVERT: D   39 TYR cc_start: 0.7465 (t80) cc_final: 0.7076 (t80)
REVERT: D   44 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: D   68 GLU cc_start: 0.8335 (tp30) cc_final: 0.8103 (tp30)
REVERT: F   25 ASN cc_start: 0.6205 (m110) cc_final: 0.5755 (m-40)
REVERT: F   27 GLN cc_start: 0.8574 (pp30) cc_final: 0.8269 (pp30)
REVERT: F   44 LYS cc_start: 0.8580 (tttm) cc_final: 0.8016 (mtpt)
REVERT: G   24 GLN cc_start: 0.8602 (mp10) cc_final: 0.8222 (mm-40)
REVERT: G   95 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8339 (mtpp)
REVERT: O  760 SER cc_start: 0.8933 (m) cc_final: 0.8705 (p)
REVERT: O  790 LEU cc_start: 0.9043 (tp) cc_final: 0.8714 (tt)
REVERT: O  895 GLU cc_start: 0.6866 (tp30) cc_final: 0.6638 (tp30)
REVERT: O 1015 MET cc_start: 0.7960 (mmt) cc_final: 0.7629 (mmp)
REVERT: O 1053 MET cc_start: 0.8553 (ppp) cc_final: 0.8143 (ppp)
REVERT: O 1112 MET cc_start: 0.7587 (mmt) cc_final: 0.7136 (mmm)
REVERT: O 1116 MET cc_start: 0.7561 (tmt) cc_final: 0.7184 (tmm)
  outliers start: 30
  outliers final: 25
  residues processed: 230
  average time/residue: 0.1378
  time to fit residues: 47.1273
Evaluate side-chains
  217 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  891 MET
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue  999 VAL
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 19 optimal weight:    0.0270
   chunk 123 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 117 optimal weight:   10.0000
   chunk 132 optimal weight:    0.7980
   chunk 135 optimal weight:    4.9990
   chunk 128 optimal weight:   30.0000
   chunk 126 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   overall best weight:    1.7644

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

Flipped N/Q/H residues before XYZ refinement:
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.094661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066412 restraints weight = 60594.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.068039 restraints weight = 31140.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.069047 restraints weight = 21529.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.069595 restraints weight = 17863.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.069823 restraints weight = 16309.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  17686  Z= 0.184
  Angle     :  0.657   9.435  25128  Z= 0.357
  Chirality :  0.037   0.202   2863
  Planarity :  0.004   0.058   2167
  Dihedral  : 29.653 178.943   4686
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.62 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.71 %
    Favored  : 76.68 %
  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 are not related in a simple way.
  whole:  0.33 (0.24), residues: 1316
  helix:  1.20 (0.20), residues: 765
  sheet: -1.60 (0.61), residues: 72
  loop : -1.04 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  77 
 TYR   0.044   0.002   TYR H  80 
 PHE   0.022   0.002   PHE O1063 
 TRP   0.022   0.002   TRP O 777 
 HIS   0.005   0.001   HIS O 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (17686)
  covalent geometry    : angle       0.65738 (25128)
  hydrogen bonds       : bond        0.03883 (  854)
  hydrogen bonds       : angle       3.87832 ( 2241)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLN cc_start: 0.8083 (mt0) cc_final: 0.7790 (mt0)
REVERT: B   84 MET cc_start: 0.8338 (mmm) cc_final: 0.7953 (tpp)
REVERT: C   64 GLU cc_start: 0.8457 (tt0) cc_final: 0.8094 (pt0)
REVERT: C   72 ASP cc_start: 0.8127 (m-30) cc_final: 0.7809 (m-30)
REVERT: C   75 LYS cc_start: 0.9221 (mptt) cc_final: 0.8911 (mmmt)
REVERT: D   39 TYR cc_start: 0.7496 (t80) cc_final: 0.7078 (t80)
REVERT: D   56 MET cc_start: 0.8709 (tpt) cc_final: 0.8506 (tpt)
REVERT: D   68 GLU cc_start: 0.8352 (tp30) cc_final: 0.8119 (tp30)
REVERT: F   25 ASN cc_start: 0.6043 (m110) cc_final: 0.5692 (m-40)
REVERT: F   27 GLN cc_start: 0.8532 (pp30) cc_final: 0.8198 (pp30)
REVERT: F   44 LYS cc_start: 0.8587 (tttm) cc_final: 0.8057 (mtpt)
REVERT: G   24 GLN cc_start: 0.8593 (mp10) cc_final: 0.8261 (mm-40)
REVERT: O  760 SER cc_start: 0.8959 (m) cc_final: 0.8747 (p)
REVERT: O  790 LEU cc_start: 0.9056 (tp) cc_final: 0.8734 (tt)
REVERT: O 1015 MET cc_start: 0.8075 (mmt) cc_final: 0.7668 (mmp)
REVERT: O 1053 MET cc_start: 0.8473 (ppp) cc_final: 0.7991 (ppp)
REVERT: O 1112 MET cc_start: 0.7501 (mmt) cc_final: 0.7066 (mmm)
REVERT: O 1116 MET cc_start: 0.7609 (tmt) cc_final: 0.7304 (tmm)
  outliers start: 30
  outliers final: 28
  residues processed: 214
  average time/residue: 0.1357
  time to fit residues: 44.1987
Evaluate side-chains
  223 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain O residue  823 VAL
Chi-restraints excluded: chain O residue  891 MET
Chi-restraints excluded: chain O residue  927 LEU
Chi-restraints excluded: chain O residue  931 LEU
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue  999 VAL
Chi-restraints excluded: chain O residue 1023 TYR
Chi-restraints excluded: chain O residue 1158 CYS
Chi-restraints excluded: chain O residue 1220 VAL
Chi-restraints excluded: chain O residue 1222 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 141 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 138 optimal weight:    8.9990
   chunk 80 optimal weight:    6.9990
   chunk 153 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.091005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.062633 restraints weight = 60310.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.064184 restraints weight = 31287.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.065153 restraints weight = 21774.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.065681 restraints weight = 18122.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.065809 restraints weight = 16590.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.5838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  17686  Z= 0.277
  Angle     :  0.744  10.154  25128  Z= 0.403
  Chirality :  0.041   0.234   2863
  Planarity :  0.005   0.062   2167
  Dihedral  : 30.147 179.393   4686
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.93 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.28 %
    Favored  : 76.68 %
  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 are not related in a simple way.
  whole:  0.11 (0.24), residues: 1316
  helix:  1.00 (0.19), residues: 769
  sheet: -1.61 (0.64), residues: 66
  loop : -1.15 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  99 
 TYR   0.052   0.003   TYR H  80 
 PHE   0.022   0.002   PHE O1063 
 TRP   0.022   0.003   TRP O 777 
 HIS   0.008   0.002   HIS O 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 (17686)
  covalent geometry    : angle       0.74401 (25128)
  hydrogen bonds       : bond        0.04822 (  854)
  hydrogen bonds       : angle       4.22673 ( 2241)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3402.17 seconds
wall clock time: 59 minutes 12.45 seconds (3552.45 seconds total)