Starting phenix.real_space_refine on Sun Sep 29 08:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/09_2024/8ga8_29892.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/09_2024/8ga8_29892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/09_2024/8ga8_29892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/09_2024/8ga8_29892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/09_2024/8ga8_29892.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga8_29892/09_2024/8ga8_29892.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Zn 2 6.06 5 S 95 5.16 5 C 14023 2.51 5 N 3795 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22011 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1206 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "A" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4417 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain breaks: 5 Chain: "J" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 767 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1052 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "M" Number of atoms: 1832 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 4 bond proxies already assigned to first conformer: 1839 Chain: "G" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 838 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain breaks: 1 Chain: "B" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3039 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "E" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3031 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain: "K" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1587 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4240 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 12, 'TRANS': 490} Chain breaks: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AILE M 169 " occ=0.51 ... (14 atoms not shown) pdb=" CD1BILE M 169 " occ=0.49 Time building chain proxies: 13.19, per 1000 atoms: 0.60 Number of scatterers: 22011 At special positions: 0 Unit cell: (104.076, 156.94, 199.892, 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) Zn 2 29.99 S 95 16.00 O 4096 8.00 N 3795 7.00 C 14023 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: 5.57 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 188 " 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 11 sheets defined 61.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'H' and resid 11 through 35 removed outlier: 4.057A pdb=" N ARG H 17 " --> pdb=" O ARG H 13 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 56 removed outlier: 3.855A pdb=" N GLN H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 117 Processing helix chain 'H' and resid 300 through 316 removed outlier: 3.873A pdb=" N GLU H 306 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.647A pdb=" N GLU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 707 Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 759 through 764 removed outlier: 4.285A pdb=" N PHE A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.920A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 777 " --> pdb=" O MET A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 777' Processing helix chain 'A' and resid 803 through 839 removed outlier: 3.677A pdb=" N THR A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 841 No H-bonds generated for 'chain 'A' and resid 840 through 841' Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 861 through 871 removed outlier: 3.587A pdb=" N VAL A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 867 " --> pdb=" O TYR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.778A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 922 Proline residue: A 892 - end of helix removed outlier: 3.990A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 929 removed outlier: 3.636A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 3.524A pdb=" N LEU A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 961 removed outlier: 3.689A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 955 " --> pdb=" O GLU A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 removed outlier: 4.374A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.795A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1066 through 1070' Processing helix chain 'A' and resid 1070 through 1082 Processing helix chain 'A' and resid 1141 through 1163 removed outlier: 4.265A pdb=" N PHE A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A1161 " --> pdb=" O ARG A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.811A pdb=" N LYS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1216 removed outlier: 3.869A pdb=" N ARG A1209 " --> pdb=" O LYS A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1233 removed outlier: 3.715A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1274 removed outlier: 3.590A pdb=" N ASN A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.744A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 120 removed outlier: 3.538A pdb=" N LEU J 112 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 removed outlier: 3.971A pdb=" N GLY J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 141 Processing helix chain 'J' and resid 142 through 148 Processing helix chain 'J' and resid 158 through 173 removed outlier: 3.732A pdb=" N LEU J 162 " --> pdb=" O HIS J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 191 Proline residue: J 182 - end of helix Processing helix chain 'L' and resid 13 through 39 Proline residue: L 22 - end of helix removed outlier: 3.648A pdb=" N CYS L 39 " --> pdb=" O ILE L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 54 Processing helix chain 'L' and resid 61 through 114 Proline residue: L 81 - end of helix removed outlier: 4.174A pdb=" N ASN L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 152 removed outlier: 3.554A pdb=" N GLU L 136 " --> pdb=" O HIS L 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER L 150 " --> pdb=" O ASN L 146 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN L 151 " --> pdb=" O SER L 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 4.240A pdb=" N GLU M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS M 37 " --> pdb=" O ILE M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 162 through 166 Processing helix chain 'M' and resid 180 through 186 Processing helix chain 'M' and resid 188 through 217 removed outlier: 3.773A pdb=" N SER M 207 " --> pdb=" O LYS M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 removed outlier: 3.624A pdb=" N ASN M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 384 removed outlier: 3.518A pdb=" N LEU M 384 " --> pdb=" O SER M 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 298 removed outlier: 3.620A pdb=" N ASP G 297 " --> pdb=" O ARG G 293 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE G 298 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 404 removed outlier: 3.577A pdb=" N PHE G 400 " --> pdb=" O ILE G 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.893A pdb=" N ASN B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 42 through 55 removed outlier: 4.358A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.554A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 61 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.930A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.909A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 42 through 56 removed outlier: 3.731A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 79 through 89 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 115 through 136 Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.673A pdb=" N LEU E 168 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 196 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 243 through 262 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.911A pdb=" N CYS E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL E 295 " --> pdb=" O HIS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 330 removed outlier: 3.642A pdb=" N ASN E 330 " --> pdb=" O THR E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 365 through 381 Processing helix chain 'K' and resid 70 through 80 Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 144 through 153 removed outlier: 3.624A pdb=" N ASN K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 176 through 184 Processing helix chain 'D' and resid 662 through 677 Processing helix chain 'D' and resid 678 through 694 Processing helix chain 'D' and resid 698 through 710 removed outlier: 3.869A pdb=" N PHE D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 709 " --> pdb=" O LYS D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 760 through 764 removed outlier: 3.539A pdb=" N THR D 763 " --> pdb=" O LYS D 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 764 " --> pdb=" O SER D 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 760 through 764' Processing helix chain 'D' and resid 771 through 778 Processing helix chain 'D' and resid 801 through 841 removed outlier: 4.002A pdb=" N ASN D 840 " --> pdb=" O ASN D 836 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 841 " --> pdb=" O LYS D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 848 removed outlier: 3.523A pdb=" N ASN D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.775A pdb=" N LYS D 865 " --> pdb=" O THR D 861 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 886 removed outlier: 4.444A pdb=" N PHE D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 878 " --> pdb=" O GLU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 924 Proline residue: D 892 - end of helix removed outlier: 3.515A pdb=" N GLU D 903 " --> pdb=" O LYS D 899 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 914 " --> pdb=" O ARG D 910 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 943 removed outlier: 3.940A pdb=" N LYS D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 960 removed outlier: 3.602A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 949 " --> pdb=" O THR D 945 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 999 removed outlier: 4.379A pdb=" N TYR D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1023 removed outlier: 3.504A pdb=" N ARG D1009 " --> pdb=" O PRO D1005 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D1012 " --> pdb=" O GLU D1008 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D1014 " --> pdb=" O LEU D1010 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS D1015 " --> pdb=" O LYS D1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1070 Processing helix chain 'D' and resid 1141 through 1160 removed outlier: 3.718A pdb=" N ARG D1157 " --> pdb=" O THR D1153 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D1158 " --> pdb=" O ILE D1154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1163 No H-bonds generated for 'chain 'D' and resid 1161 through 1163' Processing helix chain 'D' and resid 1164 through 1173 removed outlier: 4.000A pdb=" N ASN D1173 " --> pdb=" O THR D1169 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1216 removed outlier: 3.682A pdb=" N ARG D1213 " --> pdb=" O ARG D1209 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D1214 " --> pdb=" O LEU D1210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D1215 " --> pdb=" O SER D1211 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN D1216 " --> pdb=" O ARG D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1232 removed outlier: 4.271A pdb=" N PHE D1224 " --> pdb=" O GLU D1220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D1225 " --> pdb=" O HIS D1221 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D1226 " --> pdb=" O GLN D1222 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D1228 " --> pdb=" O PHE D1224 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D1229 " --> pdb=" O GLU D1225 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D1231 " --> pdb=" O SER D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1241 through 1259 removed outlier: 3.568A pdb=" N ASP D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1259 through 1274 Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.718A pdb=" N ILE D1284 " --> pdb=" O ALA D1280 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS D1293 " --> pdb=" O GLN D1289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 751 removed outlier: 4.268A pdb=" N TYR A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AA3, first strand: chain 'M' and resid 89 through 90 removed outlier: 4.001A pdb=" N GLN M 89 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 206 removed outlier: 6.758A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 62 through 64 removed outlier: 6.732A pdb=" N VAL E 21 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR E 64 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR E 23 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 142 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU E 181 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN E 270 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE E 183 " --> pdb=" O GLN E 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 90 through 91 removed outlier: 6.267A pdb=" N LEU K 90 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP K 225 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE K 272 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 227 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE K 270 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU K 229 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 90 through 91 removed outlier: 6.267A pdb=" N LEU K 90 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP K 225 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE K 272 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 227 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE K 270 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU K 229 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 243 through 244 Processing sheet with id=AB1, first strand: chain 'D' and resid 755 through 757 Processing sheet with id=AB2, first strand: chain 'D' and resid 975 through 978 removed outlier: 3.794A pdb=" N LEU D 975 " --> pdb=" O ILE D1314 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D1314 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE D1301 " --> pdb=" O ALA D1140 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D1140 " --> pdb=" O PHE D1301 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3450 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: 6.33 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5886 1.33 - 1.45: 4045 1.45 - 1.57: 12394 1.57 - 1.69: 1 1.69 - 1.81: 155 Bond restraints: 22481 Sorted by residual: bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 1.503 1.553 -0.050 3.40e-02 8.65e+02 2.17e+00 bond pdb=" CB GLN D1222 " pdb=" CG GLN D1222 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB GLU A 843 " pdb=" CG GLU A 843 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 22476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 30012 2.20 - 4.40: 244 4.40 - 6.61: 44 6.61 - 8.81: 15 8.81 - 11.01: 2 Bond angle restraints: 30317 Sorted by residual: angle pdb=" CA PRO B 111 " pdb=" N PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 112.00 103.47 8.53 1.40e+00 5.10e-01 3.71e+01 angle pdb=" CA GLU M 36 " pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA PRO B 253 " pdb=" N PRO B 253 " pdb=" CD PRO B 253 " ideal model delta sigma weight residual 112.00 107.05 4.95 1.40e+00 5.10e-01 1.25e+01 angle pdb=" N PHE D1017 " pdb=" CA PHE D1017 " pdb=" CB PHE D1017 " ideal model delta sigma weight residual 110.16 115.18 -5.02 1.48e+00 4.57e-01 1.15e+01 angle pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " pdb=" CD GLU M 36 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 ... (remaining 30312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11394 17.97 - 35.94: 1702 35.94 - 53.91: 406 53.91 - 71.88: 62 71.88 - 89.85: 21 Dihedral angle restraints: 13585 sinusoidal: 5698 harmonic: 7887 Sorted by residual: dihedral pdb=" CA TYR B 346 " pdb=" C TYR B 346 " pdb=" N TYR B 347 " pdb=" CA TYR B 347 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR E 313 " pdb=" C TYR E 313 " pdb=" N THR E 314 " pdb=" CA THR E 314 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 695 " pdb=" CB ASP A 695 " pdb=" CG ASP A 695 " pdb=" OD1 ASP A 695 " ideal model delta sinusoidal sigma weight residual -30.00 -89.77 59.77 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 13582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2427 0.040 - 0.079: 685 0.079 - 0.119: 152 0.119 - 0.158: 15 0.158 - 0.198: 3 Chirality restraints: 3282 Sorted by residual: chirality pdb=" CA MET L 80 " pdb=" N MET L 80 " pdb=" C MET L 80 " pdb=" CB MET L 80 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA PHE A1180 " pdb=" N PHE A1180 " pdb=" C PHE A1180 " pdb=" CB PHE A1180 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLU L 105 " pdb=" N GLU L 105 " pdb=" C GLU L 105 " pdb=" CB GLU L 105 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 3279 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 252 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 253 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 110 " 0.049 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO B 111 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 90 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO B 91 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " 0.028 5.00e-02 4.00e+02 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 264 2.60 - 3.18: 19004 3.18 - 3.75: 36049 3.75 - 4.33: 45415 4.33 - 4.90: 75987 Nonbonded interactions: 176719 Sorted by model distance: nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.028 2.230 nonbonded pdb=" OD1 ASP E 186 " pdb="ZN ZN E 501 " model vdw 2.031 2.230 nonbonded pdb=" OD2 ASP E 274 " pdb="ZN ZN E 501 " model vdw 2.035 2.230 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B 501 " model vdw 2.041 2.230 nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.074 2.230 ... (remaining 176714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 659 through 724 or resid 749 through 787 or resid 799 thro \ ugh 1070 or resid 1075 or resid 1079 through 1080 or resid 1135 through 1174 or \ resid 1203 through 1317)) selection = (chain 'D' and (resid 659 through 724 or resid 749 through 787 or resid 799 thro \ ugh 961 or resid 975 through 1070 or resid 1131 or resid 1133 through 1317)) } ncs_group { reference = (chain 'B' and (resid 2 through 383 or resid 501)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 52.340 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 22481 Z= 0.166 Angle : 0.540 11.010 30317 Z= 0.281 Chirality : 0.038 0.198 3282 Planarity : 0.004 0.109 3894 Dihedral : 17.426 89.848 8481 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.33 % Allowed : 29.89 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2622 helix: 1.76 (0.13), residues: 1496 sheet: -0.52 (0.39), residues: 204 loop : -0.90 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 PHE 0.019 0.001 PHE H 19 TYR 0.021 0.001 TYR B 58 ARG 0.006 0.000 ARG D1229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.6086 (tmm) cc_final: 0.5029 (tmm) REVERT: D 1222 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 1226 GLU cc_start: 0.8132 (pp20) cc_final: 0.7926 (pp20) outliers start: 8 outliers final: 5 residues processed: 243 average time/residue: 0.3413 time to fit residues: 130.4515 Evaluate side-chains 231 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 928 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 54 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22481 Z= 0.192 Angle : 0.521 10.948 30317 Z= 0.270 Chirality : 0.039 0.147 3282 Planarity : 0.004 0.069 3894 Dihedral : 4.090 48.010 2954 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.00 % Allowed : 27.14 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2622 helix: 1.75 (0.13), residues: 1502 sheet: -0.66 (0.38), residues: 203 loop : -0.90 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 PHE 0.040 0.001 PHE D1017 TYR 0.035 0.001 TYR M 211 ARG 0.005 0.000 ARG M 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 256 time to evaluate : 2.478 Fit side-chains revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8579 (t70) cc_final: 0.8246 (t70) REVERT: A 841 MET cc_start: 0.6339 (tmm) cc_final: 0.5444 (ppp) REVERT: A 1169 THR cc_start: 0.8640 (t) cc_final: 0.8411 (m) REVERT: L 131 MET cc_start: 0.7446 (tpp) cc_final: 0.6956 (tmm) REVERT: L 134 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.6758 (t70) REVERT: B 330 ASN cc_start: 0.8871 (m110) cc_final: 0.8651 (m-40) REVERT: B 375 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8055 (t0) REVERT: E 207 SER cc_start: 0.7866 (t) cc_final: 0.7423 (p) REVERT: D 818 ASP cc_start: 0.7435 (t0) cc_final: 0.7159 (t0) REVERT: D 928 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6518 (mm) REVERT: D 956 LYS cc_start: 0.8249 (tptt) cc_final: 0.7916 (tptt) REVERT: D 1257 MET cc_start: 0.7850 (tmm) cc_final: 0.7550 (tmm) outliers start: 71 outliers final: 38 residues processed: 310 average time/residue: 0.3105 time to fit residues: 153.4753 Evaluate side-chains 275 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 132 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 213 optimal weight: 0.0570 chunk 237 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1206 GLN L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22481 Z= 0.156 Angle : 0.499 9.543 30317 Z= 0.257 Chirality : 0.038 0.162 3282 Planarity : 0.003 0.055 3894 Dihedral : 4.010 48.818 2951 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 26.89 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2622 helix: 1.81 (0.13), residues: 1503 sheet: -0.68 (0.38), residues: 203 loop : -0.83 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 PHE 0.030 0.001 PHE H 19 TYR 0.030 0.001 TYR M 211 ARG 0.006 0.000 ARG D1229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 258 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 314 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6311 (tt) REVERT: A 762 ASP cc_start: 0.8568 (t70) cc_final: 0.8239 (t70) REVERT: A 841 MET cc_start: 0.6297 (tmm) cc_final: 0.5546 (ppp) REVERT: L 131 MET cc_start: 0.7477 (tpp) cc_final: 0.7194 (tmm) REVERT: L 134 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.6719 (t70) REVERT: M 88 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: B 270 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: B 330 ASN cc_start: 0.8879 (m110) cc_final: 0.8614 (m-40) REVERT: B 375 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7896 (t0) REVERT: E 207 SER cc_start: 0.7855 (t) cc_final: 0.7404 (p) REVERT: K 102 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: K 152 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.6293 (t80) REVERT: D 818 ASP cc_start: 0.7539 (t0) cc_final: 0.7182 (t0) REVERT: D 956 LYS cc_start: 0.8222 (tptt) cc_final: 0.7903 (tptt) REVERT: D 1159 LEU cc_start: 0.7704 (mp) cc_final: 0.7335 (mp) REVERT: D 1204 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.5929 (t80) REVERT: D 1257 MET cc_start: 0.7817 (tmm) cc_final: 0.7509 (tmm) outliers start: 79 outliers final: 44 residues processed: 317 average time/residue: 0.3208 time to fit residues: 161.7901 Evaluate side-chains 284 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1239 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 236 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 227 optimal weight: 0.0170 chunk 68 optimal weight: 0.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22481 Z= 0.256 Angle : 0.561 9.705 30317 Z= 0.292 Chirality : 0.040 0.189 3282 Planarity : 0.004 0.051 3894 Dihedral : 4.268 51.108 2949 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.35 % Allowed : 25.16 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2622 helix: 1.53 (0.13), residues: 1508 sheet: -0.85 (0.37), residues: 203 loop : -0.94 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 775 HIS 0.010 0.001 HIS H 106 PHE 0.039 0.002 PHE D1017 TYR 0.027 0.002 TYR M 211 ARG 0.006 0.000 ARG D1229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 241 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7764 (tp) REVERT: H 314 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6590 (tt) REVERT: A 762 ASP cc_start: 0.8420 (t70) cc_final: 0.8018 (t70) REVERT: A 838 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5757 (mt) REVERT: A 841 MET cc_start: 0.6360 (tmm) cc_final: 0.5381 (ppp) REVERT: L 131 MET cc_start: 0.7537 (tpp) cc_final: 0.7253 (tmm) REVERT: L 134 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6151 (t70) REVERT: L 137 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5301 (mp) REVERT: B 270 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: B 375 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7084 (m-40) REVERT: E 230 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6448 (ttmt) REVERT: K 152 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.6367 (t80) REVERT: D 818 ASP cc_start: 0.7469 (t0) cc_final: 0.7174 (t0) REVERT: D 993 ASP cc_start: 0.6727 (m-30) cc_final: 0.6494 (m-30) REVERT: D 1257 MET cc_start: 0.7820 (tmm) cc_final: 0.7437 (tmm) REVERT: D 1300 MET cc_start: 0.6531 (mpp) cc_final: 0.6251 (mpp) outliers start: 128 outliers final: 94 residues processed: 339 average time/residue: 0.3365 time to fit residues: 183.3536 Evaluate side-chains 330 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 227 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1024 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1239 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1312 VAL Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 211 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 216 optimal weight: 0.0980 chunk 175 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 228 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS M 352 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22481 Z= 0.150 Angle : 0.507 10.281 30317 Z= 0.258 Chirality : 0.038 0.148 3282 Planarity : 0.003 0.043 3894 Dihedral : 4.051 51.147 2949 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.44 % Allowed : 26.60 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2622 helix: 1.75 (0.13), residues: 1505 sheet: -0.71 (0.38), residues: 203 loop : -0.87 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1151 HIS 0.006 0.001 HIS A1311 PHE 0.020 0.001 PHE H 19 TYR 0.025 0.001 TYR M 211 ARG 0.006 0.000 ARG D1229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 258 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 314 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6547 (tt) REVERT: A 762 ASP cc_start: 0.8647 (t70) cc_final: 0.8215 (t0) REVERT: A 838 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5623 (mt) REVERT: A 841 MET cc_start: 0.6263 (tmm) cc_final: 0.5311 (ppp) REVERT: L 131 MET cc_start: 0.7512 (tpp) cc_final: 0.7259 (tmm) REVERT: L 134 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.6573 (t70) REVERT: M 166 LEU cc_start: 0.7592 (tt) cc_final: 0.6997 (pp) REVERT: B 270 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: B 351 TYR cc_start: 0.6412 (m-80) cc_final: 0.6179 (m-80) REVERT: E 55 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5864 (t80) REVERT: E 160 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8685 (m-80) REVERT: E 316 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5842 (mtm-85) REVERT: K 152 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6308 (t80) REVERT: D 818 ASP cc_start: 0.7681 (t0) cc_final: 0.7340 (t0) REVERT: D 956 LYS cc_start: 0.8218 (tptt) cc_final: 0.7924 (tptt) REVERT: D 993 ASP cc_start: 0.6676 (m-30) cc_final: 0.6437 (m-30) REVERT: D 1159 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7625 (mp) REVERT: D 1204 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.5712 (t80) REVERT: D 1261 LYS cc_start: 0.4380 (tptt) cc_final: 0.4090 (tptt) outliers start: 106 outliers final: 63 residues processed: 340 average time/residue: 0.3338 time to fit residues: 179.9140 Evaluate side-chains 310 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 237 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1239 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 85 optimal weight: 0.7980 chunk 228 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22481 Z= 0.160 Angle : 0.514 10.164 30317 Z= 0.261 Chirality : 0.038 0.165 3282 Planarity : 0.003 0.043 3894 Dihedral : 4.019 51.895 2949 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.32 % Allowed : 26.85 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2622 helix: 1.77 (0.13), residues: 1505 sheet: -0.68 (0.38), residues: 203 loop : -0.80 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1151 HIS 0.005 0.001 HIS A1311 PHE 0.018 0.001 PHE A1180 TYR 0.024 0.001 TYR M 211 ARG 0.005 0.000 ARG D1229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 247 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8734 (t70) cc_final: 0.8279 (t0) REVERT: A 838 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5523 (mt) REVERT: A 841 MET cc_start: 0.6095 (tmm) cc_final: 0.5142 (ppp) REVERT: A 1294 MET cc_start: 0.6127 (mtp) cc_final: 0.5624 (ptm) REVERT: L 131 MET cc_start: 0.7578 (tpp) cc_final: 0.7274 (tmm) REVERT: L 134 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.6385 (t70) REVERT: L 137 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5145 (mp) REVERT: B 270 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: B 351 TYR cc_start: 0.6460 (m-80) cc_final: 0.6200 (m-80) REVERT: B 375 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7028 (m-40) REVERT: E 55 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.5920 (t80) REVERT: E 160 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: E 316 ARG cc_start: 0.6353 (OUTLIER) cc_final: 0.5813 (mtm-85) REVERT: K 102 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5868 (tt0) REVERT: D 818 ASP cc_start: 0.7671 (t0) cc_final: 0.7391 (t0) REVERT: D 956 LYS cc_start: 0.8253 (tptt) cc_final: 0.7943 (tptt) REVERT: D 993 ASP cc_start: 0.6686 (m-30) cc_final: 0.6437 (m-30) REVERT: D 1159 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7662 (mp) REVERT: D 1204 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5652 (t80) REVERT: D 1257 MET cc_start: 0.8194 (tmm) cc_final: 0.7913 (tmm) REVERT: D 1261 LYS cc_start: 0.4582 (tptt) cc_final: 0.4146 (tptt) REVERT: D 1266 MET cc_start: 0.6720 (tmm) cc_final: 0.6443 (ptt) outliers start: 103 outliers final: 74 residues processed: 328 average time/residue: 0.3190 time to fit residues: 166.9318 Evaluate side-chains 319 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 234 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 245 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 214 optimal weight: 0.2980 chunk 142 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22481 Z= 0.168 Angle : 0.520 11.365 30317 Z= 0.263 Chirality : 0.038 0.161 3282 Planarity : 0.003 0.049 3894 Dihedral : 3.855 50.205 2947 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.52 % Allowed : 26.93 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2622 helix: 1.78 (0.13), residues: 1506 sheet: -0.72 (0.38), residues: 203 loop : -0.80 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1151 HIS 0.006 0.001 HIS A1311 PHE 0.016 0.001 PHE B 77 TYR 0.023 0.001 TYR M 211 ARG 0.006 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 238 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8751 (t70) cc_final: 0.8290 (t0) REVERT: A 838 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5576 (mt) REVERT: A 841 MET cc_start: 0.6120 (tmm) cc_final: 0.5193 (ppp) REVERT: A 1294 MET cc_start: 0.6102 (mtp) cc_final: 0.5429 (ptm) REVERT: L 131 MET cc_start: 0.7578 (tpp) cc_final: 0.7282 (tmm) REVERT: L 134 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.6429 (t70) REVERT: L 137 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.5178 (mp) REVERT: M 166 LEU cc_start: 0.7551 (tt) cc_final: 0.7035 (pp) REVERT: B 270 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: B 375 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7043 (m-40) REVERT: E 55 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.5927 (t80) REVERT: E 160 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: E 230 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6362 (ttmt) REVERT: K 102 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5864 (tt0) REVERT: D 818 ASP cc_start: 0.7681 (t0) cc_final: 0.7401 (t0) REVERT: D 993 ASP cc_start: 0.6687 (m-30) cc_final: 0.6442 (m-30) REVERT: D 1159 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7675 (mp) REVERT: D 1204 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.5430 (t80) REVERT: D 1266 MET cc_start: 0.6786 (tmm) cc_final: 0.6430 (ptt) REVERT: D 1300 MET cc_start: 0.5794 (mpp) cc_final: 0.5267 (mpp) outliers start: 108 outliers final: 83 residues processed: 325 average time/residue: 0.3124 time to fit residues: 162.8330 Evaluate side-chains 327 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 233 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 199 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22481 Z= 0.170 Angle : 0.527 12.504 30317 Z= 0.266 Chirality : 0.038 0.156 3282 Planarity : 0.003 0.050 3894 Dihedral : 3.850 51.198 2945 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.48 % Allowed : 27.18 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2622 helix: 1.76 (0.13), residues: 1507 sheet: -0.74 (0.38), residues: 203 loop : -0.81 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1151 HIS 0.006 0.001 HIS A1311 PHE 0.043 0.001 PHE H 19 TYR 0.022 0.001 TYR M 211 ARG 0.006 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 241 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8761 (t70) cc_final: 0.8290 (t0) REVERT: A 841 MET cc_start: 0.6071 (tmm) cc_final: 0.5274 (ppp) REVERT: A 1294 MET cc_start: 0.6069 (mtp) cc_final: 0.5533 (ptm) REVERT: L 131 MET cc_start: 0.7795 (tpp) cc_final: 0.7434 (tmm) REVERT: L 134 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6431 (t70) REVERT: L 137 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5173 (mp) REVERT: B 270 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: B 375 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7071 (m-40) REVERT: E 55 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5918 (t80) REVERT: E 160 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: E 176 TYR cc_start: 0.6440 (m-80) cc_final: 0.5935 (m-80) REVERT: E 230 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6379 (ttmt) REVERT: K 102 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5875 (tt0) REVERT: D 818 ASP cc_start: 0.7679 (t0) cc_final: 0.7412 (t0) REVERT: D 956 LYS cc_start: 0.8326 (tptt) cc_final: 0.8016 (tptt) REVERT: D 993 ASP cc_start: 0.6688 (m-30) cc_final: 0.6470 (m-30) REVERT: D 1159 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7677 (mp) REVERT: D 1204 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.5416 (t80) REVERT: D 1261 LYS cc_start: 0.3872 (tptt) cc_final: 0.3550 (tptt) REVERT: D 1266 MET cc_start: 0.6784 (tmm) cc_final: 0.6441 (ptt) REVERT: D 1300 MET cc_start: 0.5755 (mpp) cc_final: 0.5255 (mpp) outliers start: 107 outliers final: 84 residues processed: 326 average time/residue: 0.3207 time to fit residues: 167.0185 Evaluate side-chains 329 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 235 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 242 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 235 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22481 Z= 0.166 Angle : 0.532 13.240 30317 Z= 0.268 Chirality : 0.038 0.159 3282 Planarity : 0.003 0.050 3894 Dihedral : 3.851 52.090 2945 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.40 % Allowed : 27.10 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2622 helix: 1.77 (0.13), residues: 1507 sheet: -0.74 (0.37), residues: 207 loop : -0.78 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1151 HIS 0.007 0.001 HIS A1311 PHE 0.046 0.001 PHE H 19 TYR 0.021 0.001 TYR M 211 ARG 0.007 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 240 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8757 (t70) cc_final: 0.8312 (t70) REVERT: A 841 MET cc_start: 0.6097 (tmm) cc_final: 0.5339 (ppp) REVERT: A 1294 MET cc_start: 0.6075 (mtp) cc_final: 0.5524 (ptm) REVERT: L 131 MET cc_start: 0.7734 (tpp) cc_final: 0.7336 (tmm) REVERT: L 134 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6142 (t70) REVERT: M 166 LEU cc_start: 0.7530 (tt) cc_final: 0.7049 (pp) REVERT: B 270 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: B 375 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7072 (m-40) REVERT: E 160 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: E 176 TYR cc_start: 0.6443 (m-80) cc_final: 0.5927 (m-80) REVERT: E 230 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6339 (ttmt) REVERT: K 102 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5849 (tt0) REVERT: D 818 ASP cc_start: 0.7684 (t0) cc_final: 0.7414 (t0) REVERT: D 956 LYS cc_start: 0.8244 (tptt) cc_final: 0.7953 (tptt) REVERT: D 1159 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 1204 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.5412 (t80) REVERT: D 1261 LYS cc_start: 0.3864 (tptt) cc_final: 0.3562 (tptt) REVERT: D 1266 MET cc_start: 0.6771 (tmm) cc_final: 0.6430 (ptt) REVERT: D 1300 MET cc_start: 0.5719 (mpp) cc_final: 0.5224 (mpp) outliers start: 105 outliers final: 91 residues processed: 326 average time/residue: 0.3284 time to fit residues: 171.4176 Evaluate side-chains 328 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 229 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 118 optimal weight: 0.0470 chunk 173 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 208 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 0.0770 chunk 165 optimal weight: 0.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22481 Z= 0.142 Angle : 0.528 13.533 30317 Z= 0.264 Chirality : 0.038 0.255 3282 Planarity : 0.003 0.053 3894 Dihedral : 3.751 54.134 2945 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.54 % Allowed : 28.17 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2622 helix: 1.86 (0.13), residues: 1509 sheet: -0.66 (0.38), residues: 207 loop : -0.71 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1151 HIS 0.005 0.001 HIS A1311 PHE 0.044 0.001 PHE H 19 TYR 0.022 0.001 TYR M 211 ARG 0.006 0.000 ARG A 757 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 252 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8747 (t70) cc_final: 0.8277 (t70) REVERT: A 841 MET cc_start: 0.5803 (tmm) cc_final: 0.4905 (ppp) REVERT: A 883 LEU cc_start: 0.8167 (tp) cc_final: 0.7956 (tp) REVERT: A 1294 MET cc_start: 0.5957 (mtp) cc_final: 0.5457 (ptm) REVERT: L 131 MET cc_start: 0.7733 (tpp) cc_final: 0.7354 (tmm) REVERT: L 134 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6572 (t70) REVERT: L 137 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5070 (mp) REVERT: M 166 LEU cc_start: 0.7449 (tt) cc_final: 0.7048 (pp) REVERT: B 315 MET cc_start: 0.6959 (mtp) cc_final: 0.6726 (mtp) REVERT: B 330 ASN cc_start: 0.8791 (m110) cc_final: 0.8448 (m110) REVERT: E 55 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.5993 (t80) REVERT: E 160 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: E 176 TYR cc_start: 0.6179 (m-80) cc_final: 0.5230 (m-80) REVERT: E 316 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5894 (mtm-85) REVERT: K 102 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5731 (tt0) REVERT: D 818 ASP cc_start: 0.7561 (t0) cc_final: 0.7334 (t0) REVERT: D 956 LYS cc_start: 0.8192 (tptt) cc_final: 0.7916 (tptt) REVERT: D 1159 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 1204 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.5342 (t80) REVERT: D 1261 LYS cc_start: 0.3805 (tptt) cc_final: 0.3523 (tptt) REVERT: D 1266 MET cc_start: 0.6733 (tmm) cc_final: 0.6404 (ptt) REVERT: D 1300 MET cc_start: 0.5966 (mpp) cc_final: 0.5623 (mpp) REVERT: D 1313 SER cc_start: 0.7278 (OUTLIER) cc_final: 0.6818 (t) outliers start: 84 outliers final: 70 residues processed: 319 average time/residue: 0.3221 time to fit residues: 161.9661 Evaluate side-chains 315 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 236 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1313 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 192 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 208 optimal weight: 0.2980 chunk 87 optimal weight: 0.1980 chunk 214 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS M 230 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.143565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122895 restraints weight = 69633.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.125751 restraints weight = 38082.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.126618 restraints weight = 22631.735| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22481 Z= 0.147 Angle : 0.533 13.633 30317 Z= 0.266 Chirality : 0.038 0.159 3282 Planarity : 0.003 0.053 3894 Dihedral : 3.707 55.186 2945 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.62 % Allowed : 28.08 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.17), residues: 2622 helix: 1.86 (0.13), residues: 1515 sheet: -0.98 (0.36), residues: 219 loop : -0.60 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1151 HIS 0.005 0.001 HIS A1311 PHE 0.043 0.001 PHE H 19 TYR 0.022 0.001 TYR M 211 ARG 0.006 0.000 ARG A 757 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4180.62 seconds wall clock time: 76 minutes 22.58 seconds (4582.58 seconds total)