Starting phenix.real_space_refine on Tue Aug 26 04:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bfn_16020/08_2025/8bfn_16020_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bfn_16020/08_2025/8bfn_16020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bfn_16020/08_2025/8bfn_16020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bfn_16020/08_2025/8bfn_16020.map" model { file = "/net/cci-nas-00/data/ceres_data/8bfn_16020/08_2025/8bfn_16020_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bfn_16020/08_2025/8bfn_16020_trim.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 20848 2.51 5 N 6120 2.21 5 O 6360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33400 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "F" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "G" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "H" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "I" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "J" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.41, per 1000 atoms: 0.22 Number of scatterers: 33400 At special positions: 0 Unit cell: (163.786, 177.725, 160.301, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 6360 8.00 N 6120 7.00 C 20848 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7820 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 26 sheets defined 61.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.619A pdb=" N SER A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 6' Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 152 through 175 removed outlier: 8.341A pdb=" N THR A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.735A pdb=" N TYR A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.916A pdb=" N PHE A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 231 through 283 removed outlier: 3.580A pdb=" N ALA A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 783 through 808 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.735A pdb=" N GLU A 814 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 835 removed outlier: 3.549A pdb=" N TYR A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.772A pdb=" N ASN A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 883 removed outlier: 3.648A pdb=" N GLU A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 947 through 955 Processing helix chain 'A' and resid 956 through 959 removed outlier: 3.706A pdb=" N ARG A 959 " --> pdb=" O PRO A 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 985 through 1006 Processing helix chain 'A' and resid 1028 through 1042 removed outlier: 3.607A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.727A pdb=" N GLY B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 6 through 11 removed outlier: 4.489A pdb=" N LYS B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 152 through 175 removed outlier: 8.774A pdb=" N THR B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.561A pdb=" N TYR B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.776A pdb=" N PHE B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 removed outlier: 3.708A pdb=" N GLU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 283 Proline residue: B 264 - end of helix removed outlier: 3.705A pdb=" N TRP B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.944A pdb=" N GLU B 789 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing helix chain 'B' and resid 821 through 835 removed outlier: 3.535A pdb=" N TYR B 825 " --> pdb=" O ASP B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 851 Processing helix chain 'B' and resid 856 through 884 removed outlier: 3.767A pdb=" N VAL B 884 " --> pdb=" O THR B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 918 removed outlier: 3.606A pdb=" N ARG B 905 " --> pdb=" O HIS B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 944 Processing helix chain 'B' and resid 947 through 955 Processing helix chain 'B' and resid 956 through 959 Processing helix chain 'B' and resid 986 through 1006 Processing helix chain 'B' and resid 1028 through 1042 removed outlier: 3.568A pdb=" N ARG B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 Processing helix chain 'C' and resid 45 through 59 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.549A pdb=" N GLU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.882A pdb=" N LEU C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix removed outlier: 4.038A pdb=" N TYR C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 192 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.879A pdb=" N HIS C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'D' and resid 45 through 59 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 126 through 148 Processing helix chain 'D' and resid 158 through 170 Proline residue: D 163 - end of helix removed outlier: 3.792A pdb=" N TYR D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 4.028A pdb=" N LEU D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 removed outlier: 3.753A pdb=" N ARG E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 Processing helix chain 'E' and resid 29 through 44 removed outlier: 4.091A pdb=" N LYS E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.923A pdb=" N ASP E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 144 Processing helix chain 'E' and resid 146 through 170 removed outlier: 3.680A pdb=" N ARG E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 220 Processing helix chain 'E' and resid 224 through 232 removed outlier: 5.435A pdb=" N ARG E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.758A pdb=" N GLN E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 273 through 280 removed outlier: 3.946A pdb=" N SER E 277 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 290 through 318 Processing helix chain 'E' and resid 321 through 339 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 378 through 391 Processing helix chain 'E' and resid 398 through 406 removed outlier: 3.739A pdb=" N TRP E 402 " --> pdb=" O GLY E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 425 Processing helix chain 'E' and resid 429 through 437 Processing helix chain 'E' and resid 442 through 456 removed outlier: 3.838A pdb=" N VAL E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 495 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.666A pdb=" N GLY F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.637A pdb=" N LEU F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 152 through 175 removed outlier: 7.808A pdb=" N THR F 165 " --> pdb=" O HIS F 161 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.605A pdb=" N TYR F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 208 removed outlier: 3.959A pdb=" N PHE F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 231 through 283 removed outlier: 3.868A pdb=" N ALA F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Proline residue: F 264 - end of helix Processing helix chain 'F' and resid 783 through 807 Processing helix chain 'F' and resid 810 through 814 removed outlier: 3.787A pdb=" N GLU F 814 " --> pdb=" O ALA F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 820 No H-bonds generated for 'chain 'F' and resid 818 through 820' Processing helix chain 'F' and resid 821 through 835 Processing helix chain 'F' and resid 835 through 851 removed outlier: 3.506A pdb=" N ASN F 849 " --> pdb=" O LEU F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 856 through 882 removed outlier: 3.919A pdb=" N GLU F 879 " --> pdb=" O ASN F 875 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 918 removed outlier: 3.518A pdb=" N ARG F 905 " --> pdb=" O HIS F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 944 Processing helix chain 'F' and resid 947 through 955 Processing helix chain 'F' and resid 956 through 959 removed outlier: 3.697A pdb=" N ARG F 959 " --> pdb=" O PRO F 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 956 through 959' Processing helix chain 'F' and resid 985 through 1006 Processing helix chain 'F' and resid 1028 through 1042 removed outlier: 4.016A pdb=" N ARG F1034 " --> pdb=" O ALA F1030 " (cutoff:3.500A) Processing helix chain 'F' and resid 1054 through 1060 removed outlier: 3.994A pdb=" N ASP F1060 " --> pdb=" O ARG F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1094 Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.802A pdb=" N GLY G 6 " --> pdb=" O ASN G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 6 through 11 removed outlier: 4.493A pdb=" N LYS G 10 " --> pdb=" O GLY G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 79 through 86 Processing helix chain 'G' and resid 152 through 175 removed outlier: 8.652A pdb=" N THR G 165 " --> pdb=" O HIS G 161 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 196 removed outlier: 3.545A pdb=" N PHE G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 210 removed outlier: 3.825A pdb=" N PHE G 202 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY G 210 " --> pdb=" O ASN G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 223 removed outlier: 3.634A pdb=" N GLU G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 283 Proline residue: G 264 - end of helix removed outlier: 3.701A pdb=" N TRP G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 808 removed outlier: 3.874A pdb=" N GLU G 789 " --> pdb=" O ARG G 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 807 " --> pdb=" O GLU G 803 " (cutoff:3.500A) Processing helix chain 'G' and resid 818 through 820 No H-bonds generated for 'chain 'G' and resid 818 through 820' Processing helix chain 'G' and resid 821 through 835 Processing helix chain 'G' and resid 835 through 851 Processing helix chain 'G' and resid 856 through 884 removed outlier: 3.635A pdb=" N VAL G 884 " --> pdb=" O THR G 880 " (cutoff:3.500A) Processing helix chain 'G' and resid 901 through 918 Processing helix chain 'G' and resid 924 through 944 Processing helix chain 'G' and resid 947 through 955 Processing helix chain 'G' and resid 956 through 959 Processing helix chain 'G' and resid 986 through 1006 Processing helix chain 'G' and resid 1028 through 1042 removed outlier: 3.944A pdb=" N ARG G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) Processing helix chain 'G' and resid 1054 through 1061 Processing helix chain 'H' and resid 45 through 59 Processing helix chain 'H' and resid 66 through 76 Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 126 through 146 Processing helix chain 'H' and resid 158 through 170 removed outlier: 3.800A pdb=" N LEU H 162 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Proline residue: H 163 - end of helix removed outlier: 3.580A pdb=" N ILE H 167 " --> pdb=" O PRO H 163 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 192 removed outlier: 3.501A pdb=" N HIS H 192 " --> pdb=" O GLN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 214 removed outlier: 3.888A pdb=" N HIS H 212 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 234 Processing helix chain 'I' and resid 45 through 59 Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 76 through 85 Processing helix chain 'I' and resid 126 through 148 Processing helix chain 'I' and resid 158 through 170 Proline residue: I 163 - end of helix removed outlier: 3.942A pdb=" N TYR I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 192 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 215 through 234 removed outlier: 4.072A pdb=" N LEU I 219 " --> pdb=" O ASP I 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 19 removed outlier: 3.622A pdb=" N ARG J 8 " --> pdb=" O ASN J 4 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 27 Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.972A pdb=" N LYS J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.704A pdb=" N HIS J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 90 Processing helix chain 'J' and resid 104 through 118 removed outlier: 3.880A pdb=" N ASP J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 142 Processing helix chain 'J' and resid 146 through 170 removed outlier: 3.587A pdb=" N ARG J 150 " --> pdb=" O ASN J 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 156 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG J 157 " --> pdb=" O THR J 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 158 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 170 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 194 removed outlier: 3.550A pdb=" N ALA J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL J 182 " --> pdb=" O THR J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 198 through 220 removed outlier: 3.546A pdb=" N GLU J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 232 removed outlier: 3.657A pdb=" N VAL J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG J 230 " --> pdb=" O ASP J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 256 Processing helix chain 'J' and resid 258 through 272 Processing helix chain 'J' and resid 273 through 280 removed outlier: 3.884A pdb=" N SER J 277 " --> pdb=" O HIS J 273 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP J 278 " --> pdb=" O PRO J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 290 Processing helix chain 'J' and resid 290 through 318 Processing helix chain 'J' and resid 321 through 339 Processing helix chain 'J' and resid 340 through 342 No H-bonds generated for 'chain 'J' and resid 340 through 342' Processing helix chain 'J' and resid 346 through 351 Processing helix chain 'J' and resid 368 through 370 No H-bonds generated for 'chain 'J' and resid 368 through 370' Processing helix chain 'J' and resid 378 through 391 Processing helix chain 'J' and resid 398 through 406 removed outlier: 3.930A pdb=" N TRP J 402 " --> pdb=" O GLY J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 425 Processing helix chain 'J' and resid 429 through 437 Processing helix chain 'J' and resid 442 through 456 removed outlier: 3.502A pdb=" N PHE J 446 " --> pdb=" O ASP J 442 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL J 448 " --> pdb=" O GLU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.067A pdb=" N GLY A 28 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 21 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS A 30 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 19 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 32 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG A 17 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU A 15 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU A 115 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 17 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP A 23 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N VAL A 107 " --> pdb=" O TRP A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1017 through 1021 removed outlier: 6.394A pdb=" N ILE A1018 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A1049 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A1020 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 40 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A1068 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 42 " --> pdb=" O VAL A1068 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ARG A1070 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.590A pdb=" N GLY B 28 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 21 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS B 30 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU B 19 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 32 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG B 17 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU B 15 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU B 115 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 17 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP B 23 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N VAL B 107 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1017 through 1020 removed outlier: 6.590A pdb=" N ILE B1018 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE B1049 " --> pdb=" O ILE B1018 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B1020 " --> pdb=" O ILE B1049 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 39 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 40 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B1068 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 42 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG B1070 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 893 through 895 removed outlier: 4.120A pdb=" N ALA B 963 " --> pdb=" O ASP B 895 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 966 " --> pdb=" O ILE B 975 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 62 Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.082A pdb=" N GLN D 123 " --> pdb=" O ARG E 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.693A pdb=" N ALA D 154 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'E' and resid 461 through 465 Processing sheet with id=AB5, first strand: chain 'F' and resid 26 through 32 removed outlier: 6.066A pdb=" N GLY F 28 " --> pdb=" O PHE F 21 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE F 21 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS F 30 " --> pdb=" O GLU F 19 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU F 19 " --> pdb=" O HIS F 30 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA F 32 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG F 17 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR F 113 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 18 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA F 111 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU F 20 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY F 109 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASN F 22 " --> pdb=" O VAL F 107 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL F 107 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 144 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 1017 through 1021 removed outlier: 6.553A pdb=" N ILE F1018 " --> pdb=" O VAL F1047 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE F1049 " --> pdb=" O ILE F1018 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F1020 " --> pdb=" O ILE F1049 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 39 " --> pdb=" O ALA F1046 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA F 40 " --> pdb=" O ILE F1066 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F1068 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 42 " --> pdb=" O VAL F1068 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG F1070 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 892 through 895 Processing sheet with id=AB8, first strand: chain 'G' and resid 26 through 33 removed outlier: 7.155A pdb=" N GLY G 28 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU G 15 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU G 115 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG G 17 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TRP G 23 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N VAL G 107 " --> pdb=" O TRP G 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 124 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1017 through 1020 removed outlier: 6.605A pdb=" N ILE G1018 " --> pdb=" O VAL G1047 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE G1049 " --> pdb=" O ILE G1018 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU G1020 " --> pdb=" O ILE G1049 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR G 39 " --> pdb=" O ALA G1046 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA G 40 " --> pdb=" O ILE G1066 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL G1068 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 42 " --> pdb=" O VAL G1068 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ARG G1070 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER G1081 " --> pdb=" O ASN J 481 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 893 through 895 removed outlier: 4.040A pdb=" N ALA G 963 " --> pdb=" O ASP G 895 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL G 966 " --> pdb=" O ILE G 975 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 60 through 62 Processing sheet with id=AC3, first strand: chain 'H' and resid 155 through 157 Processing sheet with id=AC4, first strand: chain 'I' and resid 60 through 62 Processing sheet with id=AC5, first strand: chain 'I' and resid 123 through 124 removed outlier: 6.058A pdb=" N GLN I 123 " --> pdb=" O ARG J 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC7, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AC8, first strand: chain 'J' and resid 461 through 465 1985 hydrogen bonds defined for protein. 5820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 3.99 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: 9557 1.33 - 1.45: 5161 1.45 - 1.57: 19124 1.57 - 1.69: 16 1.69 - 1.81: 114 Bond restraints: 33972 Sorted by residual: bond pdb=" C5 ADP F1101 " pdb=" C6 ADP F1101 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C5 ADP A1101 " pdb=" C6 ADP A1101 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C5 ADP B1101 " pdb=" C6 ADP B1101 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C5 ADP G1101 " pdb=" C6 ADP G1101 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C5 ADP B1101 " pdb=" N7 ADP B1101 " ideal model delta sigma weight residual 1.350 1.474 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 33967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 45817 3.77 - 7.55: 114 7.55 - 11.32: 17 11.32 - 15.09: 4 15.09 - 18.86: 12 Bond angle restraints: 45964 Sorted by residual: angle pdb=" CA PRO D 198 " pdb=" N PRO D 198 " pdb=" CD PRO D 198 " ideal model delta sigma weight residual 112.00 101.73 10.27 1.40e+00 5.10e-01 5.38e+01 angle pdb=" O1A ADP G1101 " pdb=" PA ADP G1101 " pdb=" O2A ADP G1101 " ideal model delta sigma weight residual 119.90 101.04 18.86 3.00e+00 1.11e-01 3.95e+01 angle pdb=" O1A ADP B1101 " pdb=" PA ADP B1101 " pdb=" O2A ADP B1101 " ideal model delta sigma weight residual 119.90 101.07 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" O1A ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sigma weight residual 119.90 101.53 18.37 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O1A ADP F1101 " pdb=" PA ADP F1101 " pdb=" O2A ADP F1101 " ideal model delta sigma weight residual 119.90 101.54 18.36 3.00e+00 1.11e-01 3.74e+01 ... (remaining 45959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 19579 33.17 - 66.33: 976 66.33 - 99.50: 104 99.50 - 132.66: 0 132.66 - 165.83: 5 Dihedral angle restraints: 20664 sinusoidal: 8614 harmonic: 12050 Sorted by residual: dihedral pdb=" C5' ADP F1101 " pdb=" O5' ADP F1101 " pdb=" PA ADP F1101 " pdb=" O2A ADP F1101 " ideal model delta sinusoidal sigma weight residual -60.00 105.83 -165.83 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual -60.00 103.30 -163.30 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1101 " pdb=" O3A ADP A1101 " pdb=" PB ADP A1101 " pdb=" PA ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 142.55 157.45 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 20661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3453 0.030 - 0.059: 1118 0.059 - 0.089: 372 0.089 - 0.118: 187 0.118 - 0.148: 16 Chirality restraints: 5146 Sorted by residual: chirality pdb=" CG LEU F 224 " pdb=" CB LEU F 224 " pdb=" CD1 LEU F 224 " pdb=" CD2 LEU F 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE E 366 " pdb=" N ILE E 366 " pdb=" C ILE E 366 " pdb=" CB ILE E 366 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE J 366 " pdb=" N ILE J 366 " pdb=" C ILE J 366 " pdb=" CB ILE J 366 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 5143 not shown) Planarity restraints: 6034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 197 " -0.067 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO D 198 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 887 " 0.058 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO F 888 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 888 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 888 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 887 " -0.057 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO A 888 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " -0.047 5.00e-02 4.00e+02 ... (remaining 6031 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 355 2.52 - 3.11: 28284 3.11 - 3.71: 54376 3.71 - 4.30: 74232 4.30 - 4.90: 122741 Nonbonded interactions: 279988 Sorted by model distance: nonbonded pdb=" OG SER F 971 " pdb=" OD1 ASN F 973 " model vdw 1.921 3.040 nonbonded pdb=" OG SER A 971 " pdb=" OD1 ASN A 973 " model vdw 1.921 3.040 nonbonded pdb=" O ASN B 22 " pdb=" OG1 THR B 108 " model vdw 1.934 3.040 nonbonded pdb=" O LEU B1058 " pdb=" OG1 THR B1062 " model vdw 1.945 3.040 nonbonded pdb=" O SER A 852 " pdb=" OG1 THR A 857 " model vdw 1.949 3.040 ... (remaining 279983 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.490 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.005 0.174 33972 Z= 0.219 Angle : 0.668 18.863 45964 Z= 0.324 Chirality : 0.037 0.148 5146 Planarity : 0.004 0.095 6034 Dihedral : 19.102 165.826 12844 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 45.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Rotamer: Outliers : 0.48 % Allowed : 33.16 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 4136 helix: 1.96 (0.11), residues: 2346 sheet: -0.91 (0.23), residues: 520 loop : -1.44 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 792 TYR 0.025 0.001 TYR A 891 PHE 0.017 0.001 PHE G 194 TRP 0.021 0.001 TRP B 156 HIS 0.007 0.001 HIS G1029 Details of bonding type rmsd covalent geometry : bond 0.00471 (33972) covalent geometry : angle 0.66814 (45964) hydrogen bonds : bond 0.17853 ( 1985) hydrogen bonds : angle 6.49648 ( 5820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 818 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 MET cc_start: 0.6401 (ptt) cc_final: 0.6042 (ptt) REVERT: F 801 MET cc_start: 0.7293 (mtt) cc_final: 0.6870 (mmt) REVERT: G 34 ILE cc_start: 0.8630 (mp) cc_final: 0.8380 (mp) REVERT: G 172 GLU cc_start: 0.6299 (tt0) cc_final: 0.4556 (tp30) REVERT: G 234 ARG cc_start: 0.3446 (mmm-85) cc_final: 0.2982 (mtt-85) REVERT: G 801 MET cc_start: 0.7427 (ttm) cc_final: 0.7195 (ttt) REVERT: J 211 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7580 (ttm110) REVERT: J 263 MET cc_start: 0.7795 (mtt) cc_final: 0.7258 (mtm) REVERT: J 454 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7199 (ttt180) outliers start: 17 outliers final: 12 residues processed: 829 average time/residue: 0.2108 time to fit residues: 274.8498 Evaluate side-chains 800 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 788 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 283 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 273 GLN B 278 GLN B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 830 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G 213 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS G1073 GLN H 218 ASN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.170033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131157 restraints weight = 52308.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130068 restraints weight = 26991.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130582 restraints weight = 24321.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131106 restraints weight = 19312.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131599 restraints weight = 17570.868| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33972 Z= 0.177 Angle : 0.726 15.151 45964 Z= 0.360 Chirality : 0.044 0.194 5146 Planarity : 0.005 0.057 6034 Dihedral : 7.535 154.148 4661 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.54 % Favored : 94.25 % Rotamer: Outliers : 5.06 % Allowed : 26.93 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.13), residues: 4136 helix: 1.78 (0.10), residues: 2400 sheet: -0.75 (0.23), residues: 480 loop : -1.43 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 792 TYR 0.023 0.002 TYR A 891 PHE 0.019 0.002 PHE B 242 TRP 0.019 0.001 TRP G 128 HIS 0.012 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00403 (33972) covalent geometry : angle 0.72557 (45964) hydrogen bonds : bond 0.05009 ( 1985) hydrogen bonds : angle 4.86389 ( 5820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 921 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 67 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6579 (m110) REVERT: A 794 ASN cc_start: 0.8486 (t0) cc_final: 0.8211 (t0) REVERT: A 801 MET cc_start: 0.6988 (mtt) cc_final: 0.6682 (mtt) REVERT: A 1054 GLU cc_start: 0.8050 (mp0) cc_final: 0.7396 (mt-10) REVERT: A 1092 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6400 (tmm-80) REVERT: B 172 GLU cc_start: 0.6607 (tm-30) cc_final: 0.6379 (tm-30) REVERT: B 186 GLN cc_start: 0.7889 (tt0) cc_final: 0.7633 (pt0) REVERT: B 219 GLU cc_start: 0.8056 (mp0) cc_final: 0.7417 (tt0) REVERT: B 234 ARG cc_start: 0.3354 (mmm-85) cc_final: 0.2644 (mtp85) REVERT: B 792 ARG cc_start: 0.6950 (mtm110) cc_final: 0.6688 (ptt-90) REVERT: B 978 ARG cc_start: 0.1884 (OUTLIER) cc_final: 0.0580 (ptm160) REVERT: B 1076 ASN cc_start: 0.7017 (OUTLIER) cc_final: 0.6402 (p0) REVERT: C 46 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 76 HIS cc_start: 0.8033 (m90) cc_final: 0.7413 (m90) REVERT: C 146 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6361 (tm-30) REVERT: D 54 GLU cc_start: 0.7315 (tp30) cc_final: 0.7070 (mm-30) REVERT: E 442 ASP cc_start: 0.7411 (m-30) cc_final: 0.7182 (t70) REVERT: E 443 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7675 (pt) REVERT: E 461 ILE cc_start: 0.7595 (pt) cc_final: 0.7321 (mp) REVERT: E 494 ASP cc_start: 0.6037 (OUTLIER) cc_final: 0.5665 (t70) REVERT: F 185 LYS cc_start: 0.8502 (tppt) cc_final: 0.8211 (mtmm) REVERT: F 881 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8200 (mtm) REVERT: F 1054 GLU cc_start: 0.7886 (mp0) cc_final: 0.7479 (mt-10) REVERT: G 34 ILE cc_start: 0.8750 (mp) cc_final: 0.8454 (mp) REVERT: G 144 LEU cc_start: 0.7136 (mt) cc_final: 0.6910 (mt) REVERT: G 155 HIS cc_start: 0.7527 (t-170) cc_final: 0.7274 (t-170) REVERT: G 172 GLU cc_start: 0.6104 (tt0) cc_final: 0.4629 (tp30) REVERT: G 234 ARG cc_start: 0.3669 (mmm-85) cc_final: 0.3196 (mtp85) REVERT: G 248 ILE cc_start: 0.7597 (mt) cc_final: 0.7231 (mp) REVERT: G 270 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: G 789 GLU cc_start: 0.6848 (tt0) cc_final: 0.6639 (tt0) REVERT: G 978 ARG cc_start: 0.1834 (OUTLIER) cc_final: 0.0464 (ptm160) REVERT: G 1076 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6653 (p0) REVERT: I 215 ASP cc_start: 0.7414 (p0) cc_final: 0.7122 (p0) REVERT: I 227 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7539 (ttm110) REVERT: J 96 GLU cc_start: 0.6718 (tp30) cc_final: 0.6436 (tp30) REVERT: J 134 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6046 (mtm180) REVERT: J 161 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5764 (mt) REVERT: J 188 VAL cc_start: 0.9244 (t) cc_final: 0.9043 (p) REVERT: J 211 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7671 (ttm110) REVERT: J 263 MET cc_start: 0.7784 (mtt) cc_final: 0.7450 (mtm) REVERT: J 399 ASP cc_start: 0.7540 (t0) cc_final: 0.7290 (t0) REVERT: J 409 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6558 (p0) REVERT: J 452 MET cc_start: 0.7373 (mmt) cc_final: 0.7038 (mmt) outliers start: 180 outliers final: 89 residues processed: 1034 average time/residue: 0.2121 time to fit residues: 345.3419 Evaluate side-chains 908 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 806 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 881 MET Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1002 SER Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1029 HIS Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain G residue 1077 MET Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 409 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 274 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 282 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 830 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1073 GLN H 53 GLN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN ** J 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126019 restraints weight = 53214.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124465 restraints weight = 30156.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125133 restraints weight = 27923.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125502 restraints weight = 22674.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125858 restraints weight = 19569.491| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33972 Z= 0.214 Angle : 0.715 14.597 45964 Z= 0.354 Chirality : 0.044 0.311 5146 Planarity : 0.005 0.061 6034 Dihedral : 7.400 152.032 4642 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 5.90 % Allowed : 26.56 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.13), residues: 4136 helix: 1.55 (0.10), residues: 2392 sheet: -0.86 (0.23), residues: 480 loop : -1.53 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 957 TYR 0.032 0.002 TYR B 891 PHE 0.024 0.002 PHE A 221 TRP 0.015 0.001 TRP B 128 HIS 0.024 0.001 HIS G1029 Details of bonding type rmsd covalent geometry : bond 0.00495 (33972) covalent geometry : angle 0.71490 (45964) hydrogen bonds : bond 0.04809 ( 1985) hydrogen bonds : angle 4.78817 ( 5820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 849 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6826 (m110) REVERT: A 115 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7134 (mt-10) REVERT: A 267 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 976 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6601 (tp30) REVERT: A 1054 GLU cc_start: 0.8031 (mp0) cc_final: 0.7512 (mt-10) REVERT: B 219 GLU cc_start: 0.7959 (mp0) cc_final: 0.7756 (pm20) REVERT: B 248 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7301 (mp) REVERT: B 253 GLU cc_start: 0.5458 (mm-30) cc_final: 0.4949 (mm-30) REVERT: B 270 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: B 792 ARG cc_start: 0.6969 (mtm110) cc_final: 0.6711 (ptt-90) REVERT: B 796 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 800 ARG cc_start: 0.7272 (mmp-170) cc_final: 0.6676 (mmm160) REVERT: B 978 ARG cc_start: 0.1566 (OUTLIER) cc_final: 0.0529 (ptm160) REVERT: B 1003 TYR cc_start: 0.7624 (t80) cc_final: 0.6977 (t80) REVERT: B 1062 THR cc_start: 0.7721 (p) cc_final: 0.7466 (p) REVERT: C 46 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 146 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6837 (tm-30) REVERT: D 54 GLU cc_start: 0.7373 (tp30) cc_final: 0.7170 (mm-30) REVERT: D 215 ASP cc_start: 0.7186 (p0) cc_final: 0.6756 (p0) REVERT: E 96 GLU cc_start: 0.6798 (tp30) cc_final: 0.6506 (tp30) REVERT: E 134 ARG cc_start: 0.6893 (mtm180) cc_final: 0.6436 (mtm180) REVERT: E 227 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7928 (mm) REVERT: E 230 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7848 (ttp-110) REVERT: E 376 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: E 409 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6035 (p0) REVERT: E 442 ASP cc_start: 0.7380 (m-30) cc_final: 0.7096 (t70) REVERT: E 461 ILE cc_start: 0.7778 (pt) cc_final: 0.7419 (mp) REVERT: E 465 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6903 (mmp80) REVERT: E 494 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5640 (t70) REVERT: F 115 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7141 (mt-10) REVERT: F 921 ASP cc_start: 0.7668 (t0) cc_final: 0.7266 (t0) REVERT: F 929 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: F 976 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6555 (tp30) REVERT: F 1054 GLU cc_start: 0.8002 (mp0) cc_final: 0.7515 (mt-10) REVERT: G 34 ILE cc_start: 0.8774 (mp) cc_final: 0.8517 (mp) REVERT: G 155 HIS cc_start: 0.7484 (t-170) cc_final: 0.7268 (t-170) REVERT: G 173 LYS cc_start: 0.5783 (mmmt) cc_final: 0.5555 (mmtp) REVERT: G 216 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7648 (p) REVERT: G 219 GLU cc_start: 0.7934 (pm20) cc_final: 0.7562 (tt0) REVERT: G 234 ARG cc_start: 0.3837 (mmm-85) cc_final: 0.3630 (mtp85) REVERT: G 248 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7314 (mp) REVERT: G 253 GLU cc_start: 0.5404 (mm-30) cc_final: 0.4386 (mm-30) REVERT: G 270 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: G 978 ARG cc_start: 0.1714 (OUTLIER) cc_final: 0.0571 (ptm160) REVERT: I 54 GLU cc_start: 0.7256 (tp30) cc_final: 0.6948 (tp30) REVERT: I 215 ASP cc_start: 0.7317 (p0) cc_final: 0.6952 (p0) REVERT: J 134 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6233 (mtm180) REVERT: J 161 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5650 (mt) REVERT: J 188 VAL cc_start: 0.9244 (t) cc_final: 0.9022 (p) REVERT: J 211 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7602 (ttm110) REVERT: J 291 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7793 (tt) REVERT: J 294 ARG cc_start: 0.7678 (ptp-110) cc_final: 0.7255 (ptp-170) REVERT: J 399 ASP cc_start: 0.7554 (t0) cc_final: 0.7240 (t0) REVERT: J 409 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6436 (p0) REVERT: J 418 LEU cc_start: 0.7479 (pp) cc_final: 0.7236 (pp) REVERT: J 452 MET cc_start: 0.7444 (mmt) cc_final: 0.7061 (mmt) outliers start: 210 outliers final: 110 residues processed: 977 average time/residue: 0.2011 time to fit residues: 311.2903 Evaluate side-chains 925 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 795 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 795 ILE Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 218 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 208 optimal weight: 0.0050 chunk 258 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 264 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN G1029 HIS G1073 GLN J 396 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127587 restraints weight = 52873.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126126 restraints weight = 29277.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126868 restraints weight = 26305.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127193 restraints weight = 22200.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127641 restraints weight = 19012.501| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33972 Z= 0.154 Angle : 0.672 13.555 45964 Z= 0.331 Chirality : 0.042 0.203 5146 Planarity : 0.004 0.061 6034 Dihedral : 7.151 154.728 4642 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.15 % Rotamer: Outliers : 5.42 % Allowed : 27.88 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.13), residues: 4136 helix: 1.61 (0.10), residues: 2396 sheet: -0.87 (0.23), residues: 464 loop : -1.38 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 142 TYR 0.023 0.002 TYR G 891 PHE 0.017 0.002 PHE B 194 TRP 0.020 0.001 TRP B 128 HIS 0.012 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00347 (33972) covalent geometry : angle 0.67224 (45964) hydrogen bonds : bond 0.04291 ( 1985) hydrogen bonds : angle 4.57815 ( 5820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 897 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6990 (OUTLIER) cc_final: 0.6528 (m110) REVERT: A 1054 GLU cc_start: 0.8059 (mp0) cc_final: 0.7652 (mt-10) REVERT: B 186 GLN cc_start: 0.7971 (tt0) cc_final: 0.7681 (pt0) REVERT: B 269 TRP cc_start: 0.7435 (t-100) cc_final: 0.7099 (t-100) REVERT: B 792 ARG cc_start: 0.7016 (mtm110) cc_final: 0.6782 (ptt-90) REVERT: B 796 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 800 ARG cc_start: 0.7330 (mmp-170) cc_final: 0.6737 (mmm160) REVERT: B 960 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6475 (pt) REVERT: B 1003 TYR cc_start: 0.7456 (t80) cc_final: 0.7011 (t80) REVERT: C 46 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7522 (tm-30) REVERT: C 146 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6856 (tm-30) REVERT: C 175 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: D 215 ASP cc_start: 0.7202 (p0) cc_final: 0.6794 (p0) REVERT: E 96 GLU cc_start: 0.6759 (tp30) cc_final: 0.6438 (tp30) REVERT: E 134 ARG cc_start: 0.6603 (mtm180) cc_final: 0.6211 (mtm180) REVERT: E 227 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7823 (mm) REVERT: E 294 ARG cc_start: 0.7668 (ptp-110) cc_final: 0.6986 (mtm180) REVERT: E 409 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6098 (p0) REVERT: E 442 ASP cc_start: 0.7292 (m-30) cc_final: 0.7062 (t70) REVERT: E 494 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5688 (t70) REVERT: F 67 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6889 (m110) REVERT: F 267 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8229 (tt) REVERT: F 921 ASP cc_start: 0.7889 (t0) cc_final: 0.7502 (t0) REVERT: F 929 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8330 (mtmm) REVERT: F 976 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6463 (tp30) REVERT: F 1054 GLU cc_start: 0.8004 (mp0) cc_final: 0.7731 (mt-10) REVERT: G 34 ILE cc_start: 0.8752 (mp) cc_final: 0.8502 (mp) REVERT: G 155 HIS cc_start: 0.7489 (t-170) cc_final: 0.7219 (t-170) REVERT: G 172 GLU cc_start: 0.6503 (tt0) cc_final: 0.4783 (tp30) REVERT: G 173 LYS cc_start: 0.5754 (mmmt) cc_final: 0.5552 (mmtp) REVERT: G 234 ARG cc_start: 0.3726 (mmm-85) cc_final: 0.3109 (mtp85) REVERT: G 253 GLU cc_start: 0.5330 (mm-30) cc_final: 0.4959 (mm-30) REVERT: G 270 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: G 275 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6841 (tp40) REVERT: G 789 GLU cc_start: 0.6794 (tt0) cc_final: 0.6485 (tt0) REVERT: G 893 ARG cc_start: 0.6712 (ptt180) cc_final: 0.6213 (mtp-110) REVERT: G 1076 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.6340 (p0) REVERT: H 45 LEU cc_start: 0.8753 (mp) cc_final: 0.8208 (tp) REVERT: I 54 GLU cc_start: 0.7185 (tp30) cc_final: 0.6940 (tp30) REVERT: I 215 ASP cc_start: 0.7452 (p0) cc_final: 0.7129 (p0) REVERT: J 3 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6222 (pm20) REVERT: J 134 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6366 (mtm180) REVERT: J 161 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5824 (mt) REVERT: J 201 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7607 (ttt90) REVERT: J 211 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7594 (ttm110) REVERT: J 294 ARG cc_start: 0.7802 (ptp-110) cc_final: 0.7335 (ptp-170) REVERT: J 409 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6381 (p0) REVERT: J 452 MET cc_start: 0.7633 (mmt) cc_final: 0.6753 (mtp) REVERT: J 467 PHE cc_start: 0.6701 (m-80) cc_final: 0.6400 (m-80) outliers start: 193 outliers final: 113 residues processed: 1009 average time/residue: 0.1851 time to fit residues: 297.0385 Evaluate side-chains 947 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 818 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1029 HIS Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1029 HIS Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 275 GLN Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 802 SER Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 383 optimal weight: 0.8980 chunk 330 optimal weight: 0.0030 chunk 334 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 227 optimal weight: 0.6980 chunk 314 optimal weight: 0.9990 chunk 380 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 HIS ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN G1029 HIS G1073 GLN J 396 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127493 restraints weight = 53054.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125976 restraints weight = 29423.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126680 restraints weight = 26389.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127217 restraints weight = 20524.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127734 restraints weight = 18630.099| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33972 Z= 0.157 Angle : 0.677 12.631 45964 Z= 0.334 Chirality : 0.042 0.209 5146 Planarity : 0.004 0.062 6034 Dihedral : 7.072 155.037 4642 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 5.37 % Allowed : 28.58 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.13), residues: 4136 helix: 1.59 (0.10), residues: 2394 sheet: -0.85 (0.23), residues: 464 loop : -1.46 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 78 TYR 0.026 0.002 TYR F 891 PHE 0.020 0.002 PHE G 194 TRP 0.019 0.001 TRP B 128 HIS 0.019 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00361 (33972) covalent geometry : angle 0.67719 (45964) hydrogen bonds : bond 0.04234 ( 1985) hydrogen bonds : angle 4.56110 ( 5820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 865 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8239 (tt) REVERT: A 976 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6487 (tp30) REVERT: A 1054 GLU cc_start: 0.8051 (mp0) cc_final: 0.7566 (mt-10) REVERT: B 219 GLU cc_start: 0.7975 (pm20) cc_final: 0.7457 (tt0) REVERT: B 792 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6892 (ptt-90) REVERT: B 796 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 800 ARG cc_start: 0.7364 (mmp-170) cc_final: 0.6837 (mmm160) REVERT: B 819 LEU cc_start: 0.6763 (pt) cc_final: 0.5865 (mm) REVERT: B 978 ARG cc_start: 0.1048 (OUTLIER) cc_final: 0.0158 (ptm160) REVERT: B 990 GLU cc_start: 0.8677 (tp30) cc_final: 0.8078 (tp30) REVERT: B 1003 TYR cc_start: 0.7445 (t80) cc_final: 0.7021 (t80) REVERT: B 1076 ASN cc_start: 0.6462 (OUTLIER) cc_final: 0.6127 (p0) REVERT: C 146 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6911 (tm-30) REVERT: C 175 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: D 178 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7302 (mp0) REVERT: D 215 ASP cc_start: 0.7282 (p0) cc_final: 0.6852 (p0) REVERT: E 134 ARG cc_start: 0.6635 (mtm180) cc_final: 0.6227 (mtm180) REVERT: E 142 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7362 (mtp85) REVERT: E 163 ARG cc_start: 0.7285 (mtm110) cc_final: 0.6972 (ptp-110) REVERT: E 198 ASP cc_start: 0.8032 (m-30) cc_final: 0.7514 (m-30) REVERT: E 227 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7750 (mm) REVERT: E 294 ARG cc_start: 0.7696 (ptp-110) cc_final: 0.7026 (mtm180) REVERT: E 409 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6044 (p0) REVERT: E 442 ASP cc_start: 0.7163 (m-30) cc_final: 0.6939 (t0) REVERT: E 478 TRP cc_start: 0.6790 (OUTLIER) cc_final: 0.6510 (m100) REVERT: E 494 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5674 (t70) REVERT: F 234 ARG cc_start: 0.8029 (tpt170) cc_final: 0.7806 (tpt170) REVERT: F 267 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8214 (tt) REVERT: F 921 ASP cc_start: 0.7911 (t0) cc_final: 0.7508 (t0) REVERT: F 929 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8337 (mtmm) REVERT: F 976 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6488 (tp30) REVERT: F 1054 GLU cc_start: 0.8006 (mp0) cc_final: 0.7572 (mt-10) REVERT: G 34 ILE cc_start: 0.8743 (mp) cc_final: 0.8479 (mp) REVERT: G 155 HIS cc_start: 0.7599 (t-170) cc_final: 0.7280 (t-170) REVERT: G 172 GLU cc_start: 0.6502 (tt0) cc_final: 0.4825 (tp30) REVERT: G 219 GLU cc_start: 0.7840 (pm20) cc_final: 0.7388 (tt0) REVERT: G 270 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: G 819 LEU cc_start: 0.6349 (pt) cc_final: 0.5421 (mm) REVERT: G 871 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6566 (tm-30) REVERT: G 893 ARG cc_start: 0.6740 (ptt180) cc_final: 0.6252 (mtp-110) REVERT: G 1056 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7124 (ttp-110) REVERT: G 1076 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.6400 (p0) REVERT: H 45 LEU cc_start: 0.8775 (mp) cc_final: 0.8250 (tp) REVERT: H 179 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7933 (mtp85) REVERT: H 220 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7236 (tm-30) REVERT: H 233 GLN cc_start: 0.7096 (pp30) cc_final: 0.6868 (pp30) REVERT: I 215 ASP cc_start: 0.7420 (p0) cc_final: 0.7112 (p0) REVERT: J 6 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7263 (mtm110) REVERT: J 134 ARG cc_start: 0.6854 (mtm-85) cc_final: 0.6431 (mtm180) REVERT: J 161 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5815 (mt) REVERT: J 201 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7550 (ttt90) REVERT: J 211 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7528 (ttm110) REVERT: J 409 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6295 (p0) REVERT: J 452 MET cc_start: 0.7656 (mmt) cc_final: 0.6917 (mtp) REVERT: J 467 PHE cc_start: 0.6921 (m-80) cc_final: 0.6651 (m-80) outliers start: 191 outliers final: 129 residues processed: 980 average time/residue: 0.1880 time to fit residues: 293.9545 Evaluate side-chains 978 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 832 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 802 SER Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 165 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 230 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN E 481 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN G 275 GLN G 927 HIS G 932 GLN G1029 HIS J 11 ASN J 396 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126832 restraints weight = 52899.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125426 restraints weight = 29409.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126053 restraints weight = 27210.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126396 restraints weight = 22656.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126751 restraints weight = 19524.826| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33972 Z= 0.180 Angle : 0.691 12.580 45964 Z= 0.342 Chirality : 0.042 0.194 5146 Planarity : 0.004 0.068 6034 Dihedral : 7.057 154.183 4642 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.03 % Rotamer: Outliers : 5.79 % Allowed : 27.85 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.13), residues: 4136 helix: 1.52 (0.10), residues: 2398 sheet: -0.99 (0.23), residues: 492 loop : -1.48 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 156 TYR 0.026 0.002 TYR A 891 PHE 0.019 0.002 PHE B 194 TRP 0.017 0.001 TRP I 115 HIS 0.006 0.001 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00416 (33972) covalent geometry : angle 0.69087 (45964) hydrogen bonds : bond 0.04325 ( 1985) hydrogen bonds : angle 4.58734 ( 5820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 871 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 921 ASP cc_start: 0.7818 (t0) cc_final: 0.7533 (t0) REVERT: A 929 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: A 976 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: A 1054 GLU cc_start: 0.8070 (mp0) cc_final: 0.7837 (mt-10) REVERT: B 219 GLU cc_start: 0.8017 (pm20) cc_final: 0.7473 (tt0) REVERT: B 237 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7197 (mm-30) REVERT: B 253 GLU cc_start: 0.5651 (mm-30) cc_final: 0.4896 (mm-30) REVERT: B 796 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 800 ARG cc_start: 0.7478 (mmp-170) cc_final: 0.6906 (mmm160) REVERT: B 819 LEU cc_start: 0.6712 (pt) cc_final: 0.5864 (mm) REVERT: B 821 ASP cc_start: 0.6837 (t0) cc_final: 0.6630 (t0) REVERT: B 978 ARG cc_start: 0.0923 (OUTLIER) cc_final: -0.0203 (ptm160) REVERT: B 1003 TYR cc_start: 0.7407 (t80) cc_final: 0.6954 (t80) REVERT: B 1076 ASN cc_start: 0.6717 (OUTLIER) cc_final: 0.6400 (p0) REVERT: C 146 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6999 (tm-30) REVERT: C 233 GLN cc_start: 0.7108 (pp30) cc_final: 0.6799 (pp30) REVERT: D 178 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7321 (mp0) REVERT: D 215 ASP cc_start: 0.7399 (p0) cc_final: 0.6936 (p0) REVERT: E 227 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7785 (mm) REVERT: E 291 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7714 (tt) REVERT: E 442 ASP cc_start: 0.7288 (m-30) cc_final: 0.6950 (t0) REVERT: E 461 ILE cc_start: 0.7685 (pt) cc_final: 0.7347 (mp) REVERT: E 478 TRP cc_start: 0.6759 (OUTLIER) cc_final: 0.6473 (m100) REVERT: E 494 ASP cc_start: 0.6006 (OUTLIER) cc_final: 0.5661 (t70) REVERT: F 234 ARG cc_start: 0.8025 (tpt170) cc_final: 0.7818 (tpt170) REVERT: F 267 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8243 (tt) REVERT: F 921 ASP cc_start: 0.7963 (t0) cc_final: 0.7670 (t0) REVERT: F 929 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8324 (mtmm) REVERT: F 931 LEU cc_start: 0.9303 (tp) cc_final: 0.9029 (tp) REVERT: F 976 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6418 (tp30) REVERT: F 1054 GLU cc_start: 0.7992 (mp0) cc_final: 0.7581 (mt-10) REVERT: G 34 ILE cc_start: 0.8743 (mp) cc_final: 0.8467 (mp) REVERT: G 155 HIS cc_start: 0.7561 (t-170) cc_final: 0.7270 (t-170) REVERT: G 172 GLU cc_start: 0.6931 (tt0) cc_final: 0.5066 (tp30) REVERT: G 219 GLU cc_start: 0.7861 (pm20) cc_final: 0.7385 (tt0) REVERT: G 279 LEU cc_start: 0.6280 (tt) cc_final: 0.6071 (pp) REVERT: G 819 LEU cc_start: 0.6355 (pt) cc_final: 0.5390 (mm) REVERT: G 893 ARG cc_start: 0.6709 (ptt180) cc_final: 0.6225 (mtp-110) REVERT: G 978 ARG cc_start: 0.0874 (OUTLIER) cc_final: -0.0232 (ptm160) REVERT: G 1040 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6335 (ttm-80) REVERT: H 45 LEU cc_start: 0.8706 (mp) cc_final: 0.8227 (tp) REVERT: H 146 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6098 (tm-30) REVERT: H 233 GLN cc_start: 0.7109 (pp30) cc_final: 0.6878 (pp30) REVERT: I 215 ASP cc_start: 0.7460 (p0) cc_final: 0.7140 (p0) REVERT: I 227 ARG cc_start: 0.7367 (mtp85) cc_final: 0.6960 (mmm160) REVERT: J 6 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7280 (mtm110) REVERT: J 161 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5780 (mt) REVERT: J 201 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7509 (ttt90) REVERT: J 409 ASP cc_start: 0.6500 (OUTLIER) cc_final: 0.6207 (p0) REVERT: J 452 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6929 (mtp) outliers start: 206 outliers final: 145 residues processed: 993 average time/residue: 0.1967 time to fit residues: 309.5836 Evaluate side-chains 990 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 827 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1053 LYS Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 975 ILE Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1040 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 7 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 360 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 306 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN B 927 HIS ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 396 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 932 GLN G1029 HIS J 396 GLN ** J 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127541 restraints weight = 53184.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126013 restraints weight = 28709.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126672 restraints weight = 26783.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127313 restraints weight = 20554.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127728 restraints weight = 18540.584| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33972 Z= 0.172 Angle : 0.698 17.481 45964 Z= 0.345 Chirality : 0.043 0.182 5146 Planarity : 0.004 0.069 6034 Dihedral : 6.989 154.852 4642 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 5.42 % Allowed : 28.61 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.13), residues: 4136 helix: 1.50 (0.10), residues: 2398 sheet: -1.03 (0.23), residues: 492 loop : -1.50 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 156 TYR 0.026 0.002 TYR A 891 PHE 0.034 0.002 PHE B 194 TRP 0.018 0.001 TRP I 115 HIS 0.006 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00396 (33972) covalent geometry : angle 0.69834 (45964) hydrogen bonds : bond 0.04279 ( 1985) hydrogen bonds : angle 4.58663 ( 5820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 851 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6834 (OUTLIER) cc_final: 0.6134 (m110) REVERT: A 226 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (pp) REVERT: A 267 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 909 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8461 (mtpp) REVERT: A 929 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8179 (mtmm) REVERT: A 976 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6396 (tp30) REVERT: A 1054 GLU cc_start: 0.7980 (mp0) cc_final: 0.7777 (mt-10) REVERT: B 144 LEU cc_start: 0.7402 (mp) cc_final: 0.6545 (pp) REVERT: B 184 LYS cc_start: 0.7872 (tttt) cc_final: 0.7500 (ttpp) REVERT: B 186 GLN cc_start: 0.7685 (tt0) cc_final: 0.7398 (pt0) REVERT: B 219 GLU cc_start: 0.7991 (pm20) cc_final: 0.7354 (tt0) REVERT: B 237 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7186 (mm-30) REVERT: B 794 ASN cc_start: 0.8174 (t0) cc_final: 0.7972 (t0) REVERT: B 800 ARG cc_start: 0.7481 (mmp-170) cc_final: 0.6889 (mmm160) REVERT: B 821 ASP cc_start: 0.7023 (t0) cc_final: 0.6706 (t0) REVERT: B 961 GLU cc_start: 0.7301 (mp0) cc_final: 0.6867 (mp0) REVERT: B 1003 TYR cc_start: 0.7410 (t80) cc_final: 0.6951 (t80) REVERT: B 1040 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6418 (ttm-80) REVERT: B 1076 ASN cc_start: 0.6721 (OUTLIER) cc_final: 0.6360 (p0) REVERT: C 146 GLU cc_start: 0.7239 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 233 GLN cc_start: 0.7085 (pp30) cc_final: 0.6814 (pp30) REVERT: D 215 ASP cc_start: 0.7411 (p0) cc_final: 0.6941 (p0) REVERT: E 227 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7797 (mm) REVERT: E 291 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7782 (tt) REVERT: E 376 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: E 442 ASP cc_start: 0.7261 (m-30) cc_final: 0.6952 (t0) REVERT: E 461 ILE cc_start: 0.7736 (pt) cc_final: 0.7406 (mp) REVERT: E 478 TRP cc_start: 0.6891 (OUTLIER) cc_final: 0.6653 (m100) REVERT: E 494 ASP cc_start: 0.6013 (OUTLIER) cc_final: 0.5559 (t0) REVERT: F 234 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7805 (tpt170) REVERT: F 267 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8217 (tt) REVERT: F 921 ASP cc_start: 0.7990 (t0) cc_final: 0.7709 (t0) REVERT: F 929 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8331 (mtmm) REVERT: F 931 LEU cc_start: 0.9290 (tp) cc_final: 0.9015 (tp) REVERT: F 976 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6455 (tp30) REVERT: F 1054 GLU cc_start: 0.7979 (mp0) cc_final: 0.7586 (mt-10) REVERT: G 34 ILE cc_start: 0.8694 (mp) cc_final: 0.8414 (mp) REVERT: G 128 TRP cc_start: 0.7196 (p90) cc_final: 0.6970 (p90) REVERT: G 155 HIS cc_start: 0.7519 (t-170) cc_final: 0.7263 (t-170) REVERT: G 172 GLU cc_start: 0.6960 (tt0) cc_final: 0.5164 (tp30) REVERT: G 173 LYS cc_start: 0.5353 (pttm) cc_final: 0.4792 (ptmm) REVERT: G 184 LYS cc_start: 0.7987 (tttt) cc_final: 0.7594 (ttpp) REVERT: G 219 GLU cc_start: 0.7872 (pm20) cc_final: 0.7366 (tt0) REVERT: G 270 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: G 819 LEU cc_start: 0.6166 (pt) cc_final: 0.5273 (mm) REVERT: G 893 ARG cc_start: 0.6702 (ptt180) cc_final: 0.6222 (mtp-110) REVERT: G 1040 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6358 (ttm-80) REVERT: H 45 LEU cc_start: 0.8717 (mp) cc_final: 0.8230 (tp) REVERT: H 146 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6247 (tm-30) REVERT: H 220 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7223 (tm-30) REVERT: H 233 GLN cc_start: 0.7102 (pp30) cc_final: 0.6633 (pp30) REVERT: I 103 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8468 (ptpp) REVERT: I 215 ASP cc_start: 0.7477 (p0) cc_final: 0.7177 (p0) REVERT: J 134 ARG cc_start: 0.6798 (mtm180) cc_final: 0.6428 (mtm180) REVERT: J 201 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7460 (ttt90) REVERT: J 409 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6112 (p0) REVERT: J 452 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6926 (mtp) REVERT: J 467 PHE cc_start: 0.7021 (m-80) cc_final: 0.6759 (m-80) outliers start: 193 outliers final: 141 residues processed: 971 average time/residue: 0.2154 time to fit residues: 331.9091 Evaluate side-chains 970 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 809 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1040 ARG Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 17 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 406 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 374 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 396 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 133 GLN J 396 GLN J 481 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.169871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131481 restraints weight = 52535.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131177 restraints weight = 25398.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131934 restraints weight = 23006.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132229 restraints weight = 19724.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132683 restraints weight = 16949.999| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33972 Z= 0.152 Angle : 0.700 15.095 45964 Z= 0.346 Chirality : 0.042 0.223 5146 Planarity : 0.004 0.068 6034 Dihedral : 6.872 157.742 4640 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 5.31 % Allowed : 29.01 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.13), residues: 4136 helix: 1.55 (0.10), residues: 2384 sheet: -1.00 (0.23), residues: 492 loop : -1.43 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 156 TYR 0.026 0.002 TYR G 187 PHE 0.020 0.002 PHE J 467 TRP 0.018 0.001 TRP I 115 HIS 0.007 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00346 (33972) covalent geometry : angle 0.70017 (45964) hydrogen bonds : bond 0.04172 ( 1985) hydrogen bonds : angle 4.57278 ( 5820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 858 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8537 (pp) REVERT: A 267 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 271 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8193 (mtmt) REVERT: A 886 PHE cc_start: 0.8649 (t80) cc_final: 0.8421 (t80) REVERT: A 976 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6483 (tp30) REVERT: A 1054 GLU cc_start: 0.7933 (mp0) cc_final: 0.7727 (mt-10) REVERT: B 17 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7861 (tpp80) REVERT: B 144 LEU cc_start: 0.7494 (mp) cc_final: 0.6650 (pp) REVERT: B 184 LYS cc_start: 0.7737 (tttt) cc_final: 0.7494 (ttpp) REVERT: B 219 GLU cc_start: 0.7963 (pm20) cc_final: 0.7433 (tt0) REVERT: B 237 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7175 (mm-30) REVERT: B 819 LEU cc_start: 0.6837 (pt) cc_final: 0.5934 (mm) REVERT: B 821 ASP cc_start: 0.7056 (t0) cc_final: 0.6778 (t0) REVERT: B 961 GLU cc_start: 0.7260 (mp0) cc_final: 0.6961 (mp0) REVERT: B 1076 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6583 (p0) REVERT: C 233 GLN cc_start: 0.7005 (pp30) cc_final: 0.6744 (pp30) REVERT: D 215 ASP cc_start: 0.7315 (p0) cc_final: 0.6834 (p0) REVERT: E 227 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7771 (mm) REVERT: E 291 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7718 (tt) REVERT: E 376 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: E 461 ILE cc_start: 0.7525 (pt) cc_final: 0.7194 (mp) REVERT: E 494 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.5501 (t0) REVERT: F 56 LEU cc_start: 0.8984 (tt) cc_final: 0.8595 (tt) REVERT: F 234 ARG cc_start: 0.8000 (tpt170) cc_final: 0.7797 (tpt170) REVERT: F 267 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7840 (tt) REVERT: F 271 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8062 (mtmt) REVERT: F 921 ASP cc_start: 0.7828 (t0) cc_final: 0.7584 (t0) REVERT: F 929 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8338 (mtmm) REVERT: F 931 LEU cc_start: 0.9246 (tp) cc_final: 0.8962 (tp) REVERT: F 976 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: F 1054 GLU cc_start: 0.7951 (mp0) cc_final: 0.7556 (mt-10) REVERT: G 34 ILE cc_start: 0.8724 (mp) cc_final: 0.8439 (mp) REVERT: G 128 TRP cc_start: 0.7073 (p90) cc_final: 0.6857 (p90) REVERT: G 172 GLU cc_start: 0.6951 (tt0) cc_final: 0.5306 (tp30) REVERT: G 173 LYS cc_start: 0.5153 (pttm) cc_final: 0.4536 (ptmm) REVERT: G 184 LYS cc_start: 0.7833 (tttt) cc_final: 0.7510 (ttpp) REVERT: G 219 GLU cc_start: 0.7872 (pm20) cc_final: 0.7374 (tt0) REVERT: G 270 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: G 789 GLU cc_start: 0.6819 (tt0) cc_final: 0.6411 (tt0) REVERT: G 819 LEU cc_start: 0.6221 (pt) cc_final: 0.5482 (mm) REVERT: G 893 ARG cc_start: 0.6634 (ptt180) cc_final: 0.6225 (mtp-110) REVERT: G 1040 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6313 (ttm-80) REVERT: H 45 LEU cc_start: 0.8672 (mp) cc_final: 0.8242 (tp) REVERT: H 146 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6134 (tm-30) REVERT: H 220 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7189 (tm-30) REVERT: H 233 GLN cc_start: 0.7000 (pp30) cc_final: 0.6573 (pp30) REVERT: I 215 ASP cc_start: 0.7352 (p0) cc_final: 0.7064 (p0) REVERT: J 134 ARG cc_start: 0.6878 (mtm180) cc_final: 0.6401 (mtm180) REVERT: J 201 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7509 (ttt90) REVERT: J 263 MET cc_start: 0.8087 (mmt) cc_final: 0.7626 (mtp) REVERT: J 409 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6151 (p0) REVERT: J 452 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6918 (mtp) outliers start: 189 outliers final: 146 residues processed: 968 average time/residue: 0.2027 time to fit residues: 311.2113 Evaluate side-chains 976 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 814 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 863 ILE Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 THR Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1040 ARG Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 326 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 404 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 256 optimal weight: 0.0870 chunk 288 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G1029 HIS J 396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128154 restraints weight = 53122.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126977 restraints weight = 28484.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127595 restraints weight = 25795.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128207 restraints weight = 20034.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128563 restraints weight = 18143.733| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33972 Z= 0.158 Angle : 0.716 14.770 45964 Z= 0.355 Chirality : 0.043 0.234 5146 Planarity : 0.004 0.069 6034 Dihedral : 6.843 160.317 4640 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.32 % Rotamer: Outliers : 5.03 % Allowed : 29.45 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.13), residues: 4136 helix: 1.51 (0.10), residues: 2384 sheet: -1.00 (0.23), residues: 492 loop : -1.43 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 843 TYR 0.025 0.002 TYR A 891 PHE 0.021 0.002 PHE J 467 TRP 0.018 0.001 TRP B 128 HIS 0.007 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00362 (33972) covalent geometry : angle 0.71597 (45964) hydrogen bonds : bond 0.04192 ( 1985) hydrogen bonds : angle 4.60622 ( 5820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 847 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 271 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8186 (mtmt) REVERT: A 793 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7568 (mt) REVERT: A 886 PHE cc_start: 0.8679 (t80) cc_final: 0.8457 (t80) REVERT: A 909 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8457 (mtpp) REVERT: A 976 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6453 (tp30) REVERT: A 1054 GLU cc_start: 0.7943 (mp0) cc_final: 0.7738 (mt-10) REVERT: B 17 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7853 (tpp80) REVERT: B 144 LEU cc_start: 0.7613 (mp) cc_final: 0.6906 (pp) REVERT: B 184 LYS cc_start: 0.7953 (tttt) cc_final: 0.7582 (ttpp) REVERT: B 219 GLU cc_start: 0.8033 (pm20) cc_final: 0.7453 (tt0) REVERT: B 237 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7215 (mm-30) REVERT: B 819 LEU cc_start: 0.7038 (pt) cc_final: 0.6078 (mm) REVERT: B 821 ASP cc_start: 0.7171 (t0) cc_final: 0.6751 (t0) REVERT: B 961 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 1076 ASN cc_start: 0.6878 (OUTLIER) cc_final: 0.6593 (p0) REVERT: C 233 GLN cc_start: 0.6990 (pp30) cc_final: 0.6520 (pp30) REVERT: D 103 LYS cc_start: 0.8824 (pttm) cc_final: 0.8100 (pttm) REVERT: D 215 ASP cc_start: 0.7381 (p0) cc_final: 0.6891 (p0) REVERT: E 227 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7776 (mm) REVERT: E 263 MET cc_start: 0.7693 (mmt) cc_final: 0.7055 (mtt) REVERT: E 376 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: E 461 ILE cc_start: 0.7666 (pt) cc_final: 0.7335 (mp) REVERT: E 494 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5578 (t70) REVERT: F 56 LEU cc_start: 0.8976 (tt) cc_final: 0.8607 (tt) REVERT: F 267 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7835 (tt) REVERT: F 271 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8049 (mtmt) REVERT: F 921 ASP cc_start: 0.7836 (t0) cc_final: 0.7536 (t0) REVERT: F 929 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8367 (mtmm) REVERT: F 931 LEU cc_start: 0.9263 (tp) cc_final: 0.8984 (tp) REVERT: F 976 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: F 1054 GLU cc_start: 0.8013 (mp0) cc_final: 0.7622 (mt-10) REVERT: G 128 TRP cc_start: 0.7080 (p90) cc_final: 0.6791 (p90) REVERT: G 156 TRP cc_start: 0.8095 (m-10) cc_final: 0.7691 (m-90) REVERT: G 184 LYS cc_start: 0.7985 (tttt) cc_final: 0.7744 (ttpp) REVERT: G 219 GLU cc_start: 0.7967 (pm20) cc_final: 0.7434 (tt0) REVERT: G 270 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: G 789 GLU cc_start: 0.6805 (tt0) cc_final: 0.6406 (tt0) REVERT: G 794 ASN cc_start: 0.8145 (t0) cc_final: 0.7944 (t0) REVERT: G 893 ARG cc_start: 0.6666 (ptt180) cc_final: 0.6216 (mtp-110) REVERT: G 943 GLU cc_start: 0.6759 (mp0) cc_final: 0.6540 (mp0) REVERT: H 45 LEU cc_start: 0.8713 (mp) cc_final: 0.8228 (tp) REVERT: H 146 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6203 (tm-30) REVERT: H 220 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7146 (tm-30) REVERT: H 233 GLN cc_start: 0.7024 (pp30) cc_final: 0.6568 (pp30) REVERT: I 215 ASP cc_start: 0.7322 (p0) cc_final: 0.7049 (p0) REVERT: J 134 ARG cc_start: 0.7006 (mtm180) cc_final: 0.6452 (mtm180) REVERT: J 196 ARG cc_start: 0.7598 (tmt-80) cc_final: 0.7366 (tpt90) REVERT: J 200 ARG cc_start: 0.8362 (mmm160) cc_final: 0.8142 (mmm160) REVERT: J 201 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7459 (ttt90) REVERT: J 203 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7664 (mt-10) REVERT: J 409 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6172 (p0) REVERT: J 452 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7022 (mtp) outliers start: 179 outliers final: 145 residues processed: 955 average time/residue: 0.1918 time to fit residues: 292.1122 Evaluate side-chains 986 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 826 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 863 ILE Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 THR Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 210 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 284 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 295 optimal weight: 0.3980 chunk 251 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 74 GLN E 396 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 396 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129467 restraints weight = 53433.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128059 restraints weight = 28946.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128772 restraints weight = 25549.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129602 restraints weight = 19890.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129746 restraints weight = 17859.850| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33972 Z= 0.153 Angle : 0.720 14.359 45964 Z= 0.358 Chirality : 0.043 0.255 5146 Planarity : 0.005 0.078 6034 Dihedral : 6.784 164.841 4640 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.27 % Rotamer: Outliers : 4.64 % Allowed : 30.07 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.13), residues: 4136 helix: 1.50 (0.11), residues: 2386 sheet: -1.00 (0.23), residues: 488 loop : -1.44 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 843 TYR 0.034 0.002 TYR G 187 PHE 0.023 0.002 PHE B 844 TRP 0.020 0.001 TRP I 115 HIS 0.007 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00347 (33972) covalent geometry : angle 0.71973 (45964) hydrogen bonds : bond 0.04145 ( 1985) hydrogen bonds : angle 4.61167 ( 5820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 841 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 271 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8171 (mtmt) REVERT: A 793 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 976 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6499 (tp30) REVERT: A 1056 ARG cc_start: 0.7472 (tpp80) cc_final: 0.7248 (tpp80) REVERT: B 17 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7856 (tpp80) REVERT: B 144 LEU cc_start: 0.7653 (mp) cc_final: 0.6949 (pp) REVERT: B 184 LYS cc_start: 0.7854 (tttt) cc_final: 0.7491 (ttpp) REVERT: B 219 GLU cc_start: 0.8022 (pm20) cc_final: 0.7457 (tt0) REVERT: B 237 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7277 (mm-30) REVERT: B 821 ASP cc_start: 0.7114 (t0) cc_final: 0.6762 (t0) REVERT: B 961 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 233 GLN cc_start: 0.6946 (pp30) cc_final: 0.6494 (pp30) REVERT: D 103 LYS cc_start: 0.8853 (pttm) cc_final: 0.8127 (pttm) REVERT: E 136 ILE cc_start: 0.8803 (pt) cc_final: 0.8570 (pt) REVERT: E 227 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7756 (mm) REVERT: E 263 MET cc_start: 0.7657 (mmt) cc_final: 0.7091 (mtt) REVERT: E 376 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: E 461 ILE cc_start: 0.7600 (pt) cc_final: 0.7267 (mp) REVERT: E 494 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5532 (t70) REVERT: F 267 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7843 (tt) REVERT: F 271 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8052 (mtmt) REVERT: F 921 ASP cc_start: 0.7780 (t0) cc_final: 0.7563 (t0) REVERT: F 929 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: F 931 LEU cc_start: 0.9240 (tp) cc_final: 0.8969 (tp) REVERT: F 976 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6461 (tp30) REVERT: F 1054 GLU cc_start: 0.7987 (mp0) cc_final: 0.7612 (mt-10) REVERT: G 128 TRP cc_start: 0.7030 (p90) cc_final: 0.6761 (p90) REVERT: G 156 TRP cc_start: 0.8115 (m-10) cc_final: 0.7678 (m-90) REVERT: G 190 ARG cc_start: 0.7691 (tpt-90) cc_final: 0.7466 (mmm160) REVERT: G 219 GLU cc_start: 0.7984 (pm20) cc_final: 0.7368 (tt0) REVERT: G 269 TRP cc_start: 0.7306 (t-100) cc_final: 0.6889 (t-100) REVERT: G 789 GLU cc_start: 0.6706 (tt0) cc_final: 0.6329 (tt0) REVERT: G 893 ARG cc_start: 0.6691 (ptt180) cc_final: 0.6282 (mtp-110) REVERT: H 45 LEU cc_start: 0.8678 (mp) cc_final: 0.8247 (tp) REVERT: H 146 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6221 (tm-30) REVERT: H 220 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7157 (tm-30) REVERT: H 233 GLN cc_start: 0.6975 (pp30) cc_final: 0.6538 (pp30) REVERT: I 103 LYS cc_start: 0.8534 (pttm) cc_final: 0.8257 (pttm) REVERT: I 215 ASP cc_start: 0.7388 (p0) cc_final: 0.7088 (p0) REVERT: J 196 ARG cc_start: 0.7579 (tmt-80) cc_final: 0.7328 (tpt90) REVERT: J 200 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7990 (mmm160) REVERT: J 201 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7516 (ttt90) REVERT: J 263 MET cc_start: 0.8171 (mmt) cc_final: 0.7938 (mmt) REVERT: J 289 ARG cc_start: 0.6834 (ttp-110) cc_final: 0.6620 (ttp-110) REVERT: J 409 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6117 (p0) REVERT: J 452 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6946 (mtp) outliers start: 165 outliers final: 143 residues processed: 942 average time/residue: 0.2028 time to fit residues: 304.2331 Evaluate side-chains 964 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 808 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1053 LYS Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 863 ILE Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 THR Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 311 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 338 optimal weight: 0.9990 chunk 384 optimal weight: 0.0970 chunk 392 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 348 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN E 11 ASN E 396 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS I 126 ASN J 396 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129214 restraints weight = 53229.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127934 restraints weight = 29252.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128738 restraints weight = 25712.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129616 restraints weight = 19820.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129726 restraints weight = 17772.429| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33972 Z= 0.146 Angle : 0.718 13.875 45964 Z= 0.356 Chirality : 0.042 0.250 5146 Planarity : 0.004 0.070 6034 Dihedral : 6.705 171.650 4640 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer: Outliers : 4.44 % Allowed : 30.49 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.13), residues: 4136 helix: 1.52 (0.11), residues: 2388 sheet: -0.97 (0.23), residues: 488 loop : -1.40 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 843 TYR 0.039 0.002 TYR G 187 PHE 0.024 0.001 PHE E 480 TRP 0.022 0.001 TRP G 143 HIS 0.008 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00332 (33972) covalent geometry : angle 0.71819 (45964) hydrogen bonds : bond 0.04083 ( 1985) hydrogen bonds : angle 4.61387 ( 5820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6578.41 seconds wall clock time: 113 minutes 58.27 seconds (6838.27 seconds total)