Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 10:43:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qk7_4571/10_2023/6qk7_4571_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qk7_4571/10_2023/6qk7_4571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qk7_4571/10_2023/6qk7_4571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qk7_4571/10_2023/6qk7_4571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qk7_4571/10_2023/6qk7_4571_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qk7_4571/10_2023/6qk7_4571_updated.pdb" } resolution = 3.3 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= 0.005 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 Fe 4 7.16 5 S 95 5.16 5 C 13221 2.51 5 N 3506 2.21 5 O 3964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 1170": "NH1" <-> "NH2" Residue "A ARG 1171": "NH1" <-> "NH2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A ARG 1261": "NH1" <-> "NH2" Residue "A ARG 1265": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B ARG 759": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 393": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 472": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "D ARG 1170": "NH1" <-> "NH2" Residue "D ARG 1171": "NH1" <-> "NH2" Residue "D ARG 1261": "NH1" <-> "NH2" Residue "D ARG 1265": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20790 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9267 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 37, 'TRANS': 1123} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 6019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6019 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 24, 'TRANS': 724} Chain breaks: 2 Chain: "C" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3560 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1918 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 4, 'TRANS': 233} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'5AD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15392 SG CYS C 108 67.358 91.522 59.590 1.00 58.12 S ATOM 15467 SG CYS C 118 62.700 89.053 63.757 1.00 65.28 S ATOM 15492 SG CYS C 121 68.032 92.046 65.725 1.00 61.72 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU C 162 " occ=0.43 ... (7 atoms not shown) pdb=" OE2 GLU C 162 " occ=0.43 Time building chain proxies: 10.94, per 1000 atoms: 0.53 Number of scatterers: 20790 At special positions: 0 Unit cell: (179.55, 147.15, 170.1, 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) Fe 4 26.01 S 95 16.00 O 3964 8.00 N 3506 7.00 C 13221 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 - 3.50 Amino acid : False - 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: 8.19 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 108 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 121 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 118 " Number of angles added : 9 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 32 sheets defined 26.4% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.594A pdb=" N LYS A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.632A pdb=" N ALA A 747 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.752A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 4.329A pdb=" N LEU A 775 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 776 " --> pdb=" O ASP A 773 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 777 " --> pdb=" O ILE A 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 777' Processing helix chain 'A' and resid 780 through 785 removed outlier: 4.378A pdb=" N ILE A 784 " --> pdb=" O PRO A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 797 through 805 removed outlier: 3.929A pdb=" N LEU A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 removed outlier: 3.593A pdb=" N TYR A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 866 removed outlier: 3.560A pdb=" N ILE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 860 " --> pdb=" O ASN A 856 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 875 No H-bonds generated for 'chain 'A' and resid 872 through 875' Processing helix chain 'A' and resid 877 through 884 removed outlier: 3.865A pdb=" N ILE A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 882 " --> pdb=" O GLN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 898 removed outlier: 3.731A pdb=" N LEU A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.623A pdb=" N SER A 910 " --> pdb=" O GLU A 907 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS A 911 " --> pdb=" O LYS A 908 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A 913 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 928 Processing helix chain 'A' and resid 934 through 943 removed outlier: 3.954A pdb=" N LEU A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 957 removed outlier: 3.708A pdb=" N LEU A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) Proline residue: A 953 - end of helix Processing helix chain 'A' and resid 963 through 972 removed outlier: 3.706A pdb=" N PHE A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 971 " --> pdb=" O LYS A 967 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 985 removed outlier: 3.831A pdb=" N HIS A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1018 through 1034 removed outlier: 4.657A pdb=" N VAL A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A1024 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A1025 " --> pdb=" O GLN A1021 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A1029 " --> pdb=" O TYR A1025 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS A1030 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A1034 " --> pdb=" O LYS A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 removed outlier: 3.966A pdb=" N ALA A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 removed outlier: 3.528A pdb=" N GLN A1059 " --> pdb=" O MET A1055 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A1060 " --> pdb=" O GLY A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.530A pdb=" N MET A1068 " --> pdb=" O TRP A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1093 removed outlier: 3.683A pdb=" N VAL A1079 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A1080 " --> pdb=" O GLU A1077 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1082 " --> pdb=" O VAL A1079 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1083 " --> pdb=" O GLU A1080 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A1084 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A1087 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER A1088 " --> pdb=" O GLU A1085 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1092 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A1093 " --> pdb=" O LEU A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.834A pdb=" N ILE A1102 " --> pdb=" O ASP A1098 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A1105 " --> pdb=" O ASP A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1119 Processing helix chain 'A' and resid 1123 through 1132 removed outlier: 3.814A pdb=" N LEU A1128 " --> pdb=" O ASP A1124 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 3.540A pdb=" N LEU A1139 " --> pdb=" O ASP A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1171 removed outlier: 3.620A pdb=" N GLY A1148 " --> pdb=" O ASP A1144 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A1159 " --> pdb=" O ALA A1155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A1163 " --> pdb=" O ALA A1159 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1164 " --> pdb=" O ASP A1160 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1282 removed outlier: 3.675A pdb=" N GLN A1257 " --> pdb=" O TYR A1254 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A1260 " --> pdb=" O GLN A1257 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A1261 " --> pdb=" O SER A1258 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A1264 " --> pdb=" O ARG A1261 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A1265 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A1266 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A1267 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1269 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A1270 " --> pdb=" O ASN A1267 " (cutoff:3.500A) Proline residue: A1271 - end of helix removed outlier: 3.728A pdb=" N VAL A1274 " --> pdb=" O PRO A1271 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A1275 " --> pdb=" O ASP A1272 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A1278 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1280 " --> pdb=" O VAL A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1304 removed outlier: 3.559A pdb=" N LEU A1303 " --> pdb=" O VAL A1299 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 removed outlier: 4.084A pdb=" N MET B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.715A pdb=" N ARG B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 141 through 149 removed outlier: 3.723A pdb=" N ARG C 145 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 166 removed outlier: 3.581A pdb=" N LYS C 165 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 188 through 203 removed outlier: 4.194A pdb=" N ASP C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.874A pdb=" N ILE C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.067A pdb=" N ASP C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 273 through 286 removed outlier: 3.558A pdb=" N CYS C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 281 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.503A pdb=" N PHE C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 353 through 364 removed outlier: 4.094A pdb=" N ALA C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 508 through 522 removed outlier: 3.521A pdb=" N GLU C 517 " --> pdb=" O MET C 513 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 520 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 522 " --> pdb=" O ARG C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.511A pdb=" N GLY C 542 " --> pdb=" O ARG C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 538 through 542' Processing helix chain 'D' and resid 1007 through 1012 removed outlier: 3.565A pdb=" N ALA D1012 " --> pdb=" O LYS D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1033 removed outlier: 3.696A pdb=" N ASN D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1048 removed outlier: 3.582A pdb=" N ALA D1044 " --> pdb=" O ASP D1040 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET D1047 " --> pdb=" O VAL D1043 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1061 removed outlier: 4.069A pdb=" N GLY D1056 " --> pdb=" O LYS D1052 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA D1057 " --> pdb=" O GLU D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1074 removed outlier: 3.608A pdb=" N ILE D1070 " --> pdb=" O GLU D1066 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D1073 " --> pdb=" O SER D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1092 removed outlier: 3.773A pdb=" N ALA D1083 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D1084 " --> pdb=" O GLU D1080 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE D1092 " --> pdb=" O SER D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1105 removed outlier: 3.860A pdb=" N GLU D1105 " --> pdb=" O ASP D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1120 removed outlier: 3.568A pdb=" N ALA D1115 " --> pdb=" O LYS D1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 1123 through 1132 removed outlier: 3.621A pdb=" N ILE D1131 " --> pdb=" O SER D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1141 Processing helix chain 'D' and resid 1143 through 1168 removed outlier: 3.538A pdb=" N GLY D1152 " --> pdb=" O GLY D1148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D1165 " --> pdb=" O CYS D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1253 through 1282 removed outlier: 3.520A pdb=" N GLN D1257 " --> pdb=" O GLU D1253 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D1262 " --> pdb=" O SER D1258 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D1263 " --> pdb=" O VAL D1259 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D1264 " --> pdb=" O GLY D1260 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D1265 " --> pdb=" O ARG D1261 " (cutoff:3.500A) Proline residue: D1271 - end of helix removed outlier: 3.591A pdb=" N VAL D1274 " --> pdb=" O LYS D1270 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D1275 " --> pdb=" O PRO D1271 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D1276 " --> pdb=" O ASP D1272 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY D1279 " --> pdb=" O ARG D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1286 through 1309 removed outlier: 3.642A pdb=" N GLU D1298 " --> pdb=" O LYS D1294 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D1305 " --> pdb=" O ASP D1301 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN D1306 " --> pdb=" O LEU D1302 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D1307 " --> pdb=" O LEU D1303 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS D1308 " --> pdb=" O LYS D1304 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D1309 " --> pdb=" O ALA D1305 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 46 through 53 removed outlier: 6.982A pdb=" N VAL A 62 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A 50 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A 60 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A 52 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER A 58 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 73 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 86 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN A 75 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A 84 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 165 through 168 removed outlier: 3.565A pdb=" N VAL A 166 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 168 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 177 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.755A pdb=" N SER A 296 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 289 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU A 294 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 332 through 335 removed outlier: 4.501A pdb=" N VAL A 332 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.206A pdb=" N GLN A 391 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.738A pdb=" N PHE A 413 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 25 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 425 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR A 23 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS A 427 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 21 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 441 through 446 Processing sheet with id= I, first strand: chain 'A' and resid 478 through 480 removed outlier: 4.074A pdb=" N CYS A 516 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 499 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 514 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.254A pdb=" N LEU A 555 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 532 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP A 546 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 530 " --> pdb=" O ASP A 546 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 576 through 581 removed outlier: 6.717A pdb=" N GLU A 591 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 579 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 589 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS A 598 " --> pdb=" O TYR A 590 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN A 599 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU A 608 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 653 through 655 removed outlier: 3.650A pdb=" N GLU A 641 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 624 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 618 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 666 through 670 removed outlier: 4.386A pdb=" N SER A 666 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 676 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 709 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 736 through 739 removed outlier: 3.917A pdb=" N SER A 719 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN A 730 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU A 717 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.613A pdb=" N ALA B 31 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.543A pdb=" N ALA B 77 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 65 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 67 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE B 73 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 98 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS B 87 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N CYS B 96 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.979A pdb=" N GLY B 120 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 110 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER B 118 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA B 112 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B 125 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B 130 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 140 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 155 through 161 removed outlier: 3.610A pdb=" N SER B 157 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 182 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 179 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER B 181 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL B 194 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.675A pdb=" N GLY B 270 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 261 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.560A pdb=" N ALA B 299 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 297 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP B 289 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN B 295 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 321 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B 309 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N CYS B 319 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.536A pdb=" N LEU B 345 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 356 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 347 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP B 353 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 369 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET B 366 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 370 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 391 through 393 Processing sheet with id= W, first strand: chain 'B' and resid 444 through 447 removed outlier: 3.524A pdb=" N LEU B 554 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 552 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 466 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU B 550 " --> pdb=" O ASP B 466 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 588 through 591 removed outlier: 3.638A pdb=" N CYS B 563 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 642 through 644 removed outlier: 3.541A pdb=" N GLU B 643 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 613 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 656 through 661 removed outlier: 6.820A pdb=" N ALA B 673 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 659 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 671 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TRP B 661 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 669 " --> pdb=" O TRP B 661 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 670 " --> pdb=" O TRP B 682 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 674 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 696 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG B 683 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 694 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN B 685 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR B 692 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 704 through 709 removed outlier: 6.830A pdb=" N GLY B 723 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 707 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER B 721 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE B 709 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 719 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 718 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 731 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 743 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER B 733 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU B 741 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.811A pdb=" N ILE B 782 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 10 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR B 780 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 774 " --> pdb=" O ARG B 757 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 411 through 415 removed outlier: 4.170A pdb=" N SER B 433 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 413 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU B 431 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP B 415 " --> pdb=" O TRP B 429 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP B 429 " --> pdb=" O TRP B 415 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 97 through 102 removed outlier: 3.653A pdb=" N VAL C 99 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS C 223 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR C 176 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 225 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N LEU C 178 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N ILE C 227 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 229 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 252 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR C 231 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 254 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS C 289 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 254 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 291 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 256 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS C 293 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY C 323 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET C 294 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS C 325 " --> pdb=" O MET C 294 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG C 370 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE C 326 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR C 372 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 430 through 438 removed outlier: 4.228A pdb=" N GLY C 458 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 462 through 464 removed outlier: 6.483A pdb=" N LYS C 528 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL C 483 " --> pdb=" O LYS C 528 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER C 530 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 552 " --> pdb=" O ASP C 549 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1500 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: 8.55 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 8584 1.39 - 1.58: 12475 1.58 - 1.76: 0 1.76 - 1.95: 141 1.95 - 2.13: 12 Bond restraints: 21212 Sorted by residual: bond pdb=" S4 SF4 C 601 " pdb="FE2 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.118 0.162 3.00e-02 1.11e+03 2.92e+01 bond pdb=" S1 SF4 C 601 " pdb="FE2 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.118 0.162 3.00e-02 1.11e+03 2.91e+01 bond pdb=" S3 SF4 C 601 " pdb="FE2 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.119 0.161 3.00e-02 1.11e+03 2.89e+01 bond pdb=" S2 SF4 C 601 " pdb="FE1 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.119 0.161 3.00e-02 1.11e+03 2.89e+01 bond pdb=" S2 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.120 0.160 3.00e-02 1.11e+03 2.86e+01 ... (remaining 21207 not shown) Histogram of bond angle deviations from ideal: 87.34 - 97.08: 24 97.08 - 106.82: 502 106.82 - 116.56: 14250 116.56 - 126.30: 13637 126.30 - 136.05: 307 Bond angle restraints: 28720 Sorted by residual: angle pdb="FE2 SF4 C 601 " pdb=" S3 SF4 C 601 " pdb="FE4 SF4 C 601 " ideal model delta sigma weight residual 73.70 92.35 -18.65 1.50e+00 4.44e-01 1.55e+02 angle pdb="FE2 SF4 C 601 " pdb=" S1 SF4 C 601 " pdb="FE4 SF4 C 601 " ideal model delta sigma weight residual 73.70 92.10 -18.40 1.50e+00 4.44e-01 1.51e+02 angle pdb="FE1 SF4 C 601 " pdb=" S2 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 73.70 91.18 -17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb="FE2 SF4 C 601 " pdb=" S4 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 73.70 91.03 -17.33 1.50e+00 4.44e-01 1.33e+02 angle pdb="FE1 SF4 C 601 " pdb=" S4 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 73.70 91.00 -17.30 1.50e+00 4.44e-01 1.33e+02 ... (remaining 28715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 12012 15.87 - 31.74: 611 31.74 - 47.60: 122 47.60 - 63.47: 10 63.47 - 79.34: 16 Dihedral angle restraints: 12771 sinusoidal: 5175 harmonic: 7596 Sorted by residual: dihedral pdb=" CA LEU B 251 " pdb=" C LEU B 251 " pdb=" N THR B 252 " pdb=" CA THR B 252 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU A1086 " pdb=" C LEU A1086 " pdb=" N ILE A1087 " pdb=" CA ILE A1087 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ALA A 679 " pdb=" C ALA A 679 " pdb=" N GLN A 680 " pdb=" CA GLN A 680 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 12768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 3208 0.213 - 0.425: 6 0.425 - 0.638: 0 0.638 - 0.851: 0 0.851 - 1.063: 4 Chirality restraints: 3218 Sorted by residual: chirality pdb="FE2 SF4 C 601 " pdb=" S1 SF4 C 601 " pdb=" S3 SF4 C 601 " pdb=" S4 SF4 C 601 " both_signs ideal model delta sigma weight residual False 10.55 9.49 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb="FE1 SF4 C 601 " pdb=" S2 SF4 C 601 " pdb=" S3 SF4 C 601 " pdb=" S4 SF4 C 601 " both_signs ideal model delta sigma weight residual False -10.55 -9.54 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb="FE3 SF4 C 601 " pdb=" S1 SF4 C 601 " pdb=" S2 SF4 C 601 " pdb=" S4 SF4 C 601 " both_signs ideal model delta sigma weight residual False -10.55 -9.56 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 3215 not shown) Planarity restraints: 3679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 303 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C GLY A 303 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY A 303 " 0.020 2.00e-02 2.50e+03 pdb=" N MET A 304 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 108 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO C 109 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 750 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO B 751 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 751 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 751 " 0.034 5.00e-02 4.00e+02 ... (remaining 3676 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 163 2.57 - 3.16: 16333 3.16 - 3.74: 30206 3.74 - 4.32: 43054 4.32 - 4.90: 70353 Nonbonded interactions: 160109 Sorted by model distance: nonbonded pdb=" NE2 GLN A 307 " pdb=" O VAL A 357 " model vdw 1.993 2.520 nonbonded pdb=" OH TYR C 120 " pdb=" OE1 GLN C 257 " model vdw 2.102 2.440 nonbonded pdb=" N GLN A 307 " pdb=" OE1 GLN A 307 " model vdw 2.188 2.520 nonbonded pdb=" OG SER B 674 " pdb=" OD1 ASP B 676 " model vdw 2.199 2.440 nonbonded pdb=" O ILE B 749 " pdb=" OH TYR B 783 " model vdw 2.200 2.440 ... (remaining 160104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.730 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: 6.080 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 59.000 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.004 0.162 21212 Z= 0.297 Angle : 0.750 18.648 28720 Z= 0.453 Chirality : 0.057 1.063 3218 Planarity : 0.006 0.075 3679 Dihedral : 10.672 79.341 7861 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.44 % Allowed : 4.42 % Favored : 95.14 % 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: -4.70 (0.13), residues: 2564 helix: -3.81 (0.11), residues: 696 sheet: -2.07 (0.20), residues: 573 loop : -3.22 (0.13), residues: 1295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 223 average time/residue: 0.3722 time to fit residues: 124.5607 Evaluate side-chains 98 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 2.592 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2710 time to fit residues: 5.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 233 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 321 GLN A 563 GLN A 890 GLN C 524 HIS D1295 ASN D1345 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21212 Z= 0.250 Angle : 0.650 8.831 28720 Z= 0.346 Chirality : 0.046 0.190 3218 Planarity : 0.005 0.050 3679 Dihedral : 5.664 24.436 2820 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.06 % Allowed : 8.01 % Favored : 89.94 % 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: -3.70 (0.14), residues: 2564 helix: -2.30 (0.15), residues: 720 sheet: -1.68 (0.20), residues: 628 loop : -2.95 (0.15), residues: 1216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 99 time to evaluate : 2.712 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 21 residues processed: 142 average time/residue: 0.3390 time to fit residues: 76.3883 Evaluate side-chains 107 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 2.500 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.2017 time to fit residues: 11.0770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 233 optimal weight: 0.4980 chunk 252 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 231 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 956 GLN C 200 ASN C 375 GLN D1094 HIS D1295 ASN D1306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21212 Z= 0.223 Angle : 0.605 10.499 28720 Z= 0.319 Chirality : 0.045 0.184 3218 Planarity : 0.004 0.047 3679 Dihedral : 5.283 26.079 2820 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.40 % Allowed : 9.19 % Favored : 89.41 % 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: -2.87 (0.15), residues: 2564 helix: -1.26 (0.18), residues: 728 sheet: -1.31 (0.20), residues: 636 loop : -2.65 (0.16), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 2.595 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 119 average time/residue: 0.3444 time to fit residues: 65.5850 Evaluate side-chains 95 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 2.560 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1892 time to fit residues: 8.9185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 222 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS A 614 GLN A1022 ASN C 487 HIS D1059 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21212 Z= 0.335 Angle : 0.645 8.767 28720 Z= 0.341 Chirality : 0.046 0.183 3218 Planarity : 0.004 0.045 3679 Dihedral : 5.350 25.260 2820 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.23 % Favored : 91.73 % Rotamer: Outliers : 1.79 % Allowed : 10.32 % Favored : 87.88 % 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: -2.46 (0.16), residues: 2564 helix: -0.67 (0.19), residues: 731 sheet: -1.20 (0.21), residues: 645 loop : -2.51 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 2.525 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 126 average time/residue: 0.3334 time to fit residues: 67.7795 Evaluate side-chains 99 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 2.462 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2234 time to fit residues: 9.6050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 0.6980 chunk 141 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1059 GLN D1094 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21212 Z= 0.237 Angle : 0.608 10.571 28720 Z= 0.318 Chirality : 0.045 0.182 3218 Planarity : 0.004 0.046 3679 Dihedral : 5.149 26.026 2820 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.14 % Allowed : 11.02 % Favored : 87.84 % 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: -2.20 (0.16), residues: 2564 helix: -0.34 (0.19), residues: 733 sheet: -1.08 (0.21), residues: 636 loop : -2.40 (0.17), residues: 1195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 2.548 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 112 average time/residue: 0.3183 time to fit residues: 59.1778 Evaluate side-chains 95 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 2.455 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2183 time to fit residues: 8.9144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 248 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21212 Z= 0.339 Angle : 0.642 8.705 28720 Z= 0.338 Chirality : 0.046 0.189 3218 Planarity : 0.004 0.049 3679 Dihedral : 5.267 27.306 2820 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.78 % Favored : 91.19 % Rotamer: Outliers : 0.96 % Allowed : 11.77 % Favored : 87.27 % 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: -2.11 (0.16), residues: 2564 helix: -0.12 (0.19), residues: 737 sheet: -1.06 (0.21), residues: 634 loop : -2.43 (0.17), residues: 1193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 2.686 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 104 average time/residue: 0.3165 time to fit residues: 54.7534 Evaluate side-chains 91 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 2.491 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2005 time to fit residues: 7.0722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 20.0000 chunk 28 optimal weight: 0.0980 chunk 141 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN A1345 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21212 Z= 0.159 Angle : 0.575 11.529 28720 Z= 0.300 Chirality : 0.044 0.173 3218 Planarity : 0.003 0.049 3679 Dihedral : 4.916 27.335 2820 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.66 % Allowed : 12.20 % Favored : 87.14 % 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: -1.92 (0.16), residues: 2564 helix: 0.08 (0.20), residues: 740 sheet: -0.97 (0.21), residues: 640 loop : -2.35 (0.17), residues: 1184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 2.575 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 0.3283 time to fit residues: 53.7766 Evaluate side-chains 88 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 2.599 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1882 time to fit residues: 5.9772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 74 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21212 Z= 0.205 Angle : 0.572 9.577 28720 Z= 0.300 Chirality : 0.044 0.176 3218 Planarity : 0.003 0.048 3679 Dihedral : 4.846 26.404 2820 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.48 % Allowed : 12.69 % Favored : 86.83 % 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: -1.79 (0.17), residues: 2564 helix: 0.24 (0.20), residues: 741 sheet: -0.92 (0.21), residues: 640 loop : -2.30 (0.17), residues: 1183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 2.660 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.3448 time to fit residues: 52.8661 Evaluate side-chains 90 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 2.497 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1980 time to fit residues: 5.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 218 optimal weight: 0.3980 chunk 151 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21212 Z= 0.164 Angle : 0.569 12.439 28720 Z= 0.295 Chirality : 0.044 0.165 3218 Planarity : 0.003 0.048 3679 Dihedral : 4.753 26.645 2820 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.35 % Allowed : 12.95 % Favored : 86.70 % 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: -1.66 (0.17), residues: 2564 helix: 0.35 (0.20), residues: 741 sheet: -0.83 (0.21), residues: 643 loop : -2.24 (0.17), residues: 1180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 2.364 Fit side-chains TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.3263 time to fit residues: 50.2675 Evaluate side-chains 86 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 2.482 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1950 time to fit residues: 5.0973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 169 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 235 optimal weight: 0.0060 chunk 203 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21212 Z= 0.149 Angle : 0.564 11.319 28720 Z= 0.291 Chirality : 0.043 0.171 3218 Planarity : 0.003 0.048 3679 Dihedral : 4.624 26.789 2820 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.22 % Allowed : 13.30 % Favored : 86.48 % 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: -1.56 (0.17), residues: 2564 helix: 0.48 (0.20), residues: 741 sheet: -0.77 (0.21), residues: 643 loop : -2.20 (0.17), residues: 1180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 2.591 Fit side-chains TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.3571 time to fit residues: 53.9383 Evaluate side-chains 84 residues out of total 2286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 2.512 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2081 time to fit residues: 4.5594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.0060 chunk 204 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 179 optimal weight: 0.8980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066991 restraints weight = 54747.837| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.46 r_work: 0.2944 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21212 Z= 0.136 Angle : 0.563 11.463 28720 Z= 0.289 Chirality : 0.043 0.167 3218 Planarity : 0.003 0.052 3679 Dihedral : 4.507 26.868 2820 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.17 % Allowed : 13.39 % Favored : 86.44 % 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: -1.45 (0.17), residues: 2564 helix: 0.55 (0.20), residues: 741 sheet: -0.71 (0.21), residues: 644 loop : -2.13 (0.17), residues: 1179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.29 seconds wall clock time: 70 minutes 39.36 seconds (4239.36 seconds total)