Starting phenix.real_space_refine on Tue Aug 26 10:31:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asv_15622/08_2025/8asv_15622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asv_15622/08_2025/8asv_15622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asv_15622/08_2025/8asv_15622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asv_15622/08_2025/8asv_15622.map" model { file = "/net/cci-nas-00/data/ceres_data/8asv_15622/08_2025/8asv_15622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asv_15622/08_2025/8asv_15622.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 147 5.16 5 C 22720 2.51 5 N 6063 2.21 5 O 6855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35789 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 9844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1235, 9844 Classifications: {'peptide': 1235} Link IDs: {'PTRANS': 39, 'TRANS': 1195} Chain breaks: 1 Chain: "B" Number of atoms: 6286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6286 Classifications: {'peptide': 786} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 759} Chain: "C" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3730 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 442} Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2769 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "E" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1871 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2129 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "G" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2346 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 277} Chain breaks: 1 Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1865 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "I" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2129 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "J" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2812 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 331} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16336 SG CYS C 121 61.749 72.793 63.212 1.00 55.00 S ATOM 16236 SG CYS C 108 56.173 72.226 59.603 1.00 56.86 S ATOM 16311 SG CYS C 118 59.720 77.063 62.489 1.00 49.05 S Time building chain proxies: 9.09, per 1000 atoms: 0.25 Number of scatterers: 35789 At special positions: 0 Unit cell: (157.38, 165.12, 226.18, 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 147 16.00 O 6855 8.00 N 6063 7.00 C 22720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 118 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 121 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 108 " Number of angles added : 9 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8530 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 45 sheets defined 30.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.133A pdb=" N GLU A 132 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.791A pdb=" N VAL A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 removed outlier: 3.533A pdb=" N HIS A 768 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.529A pdb=" N ILE A 774 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 776 " --> pdb=" O ASP A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 794 removed outlier: 3.637A pdb=" N PHE A 783 " --> pdb=" O ALA A 779 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 818 through 822 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 841 through 848 removed outlier: 3.601A pdb=" N LYS A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 867 removed outlier: 3.579A pdb=" N LYS A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 886 removed outlier: 7.947A pdb=" N GLN A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 901 removed outlier: 3.814A pdb=" N GLU A 901 " --> pdb=" O LYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 919 removed outlier: 3.663A pdb=" N LEU A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 Processing helix chain 'A' and resid 934 through 942 Processing helix chain 'A' and resid 947 through 959 removed outlier: 4.114A pdb=" N TYR A 951 " --> pdb=" O ASP A 947 " (cutoff:3.500A) Proline residue: A 953 - end of helix Processing helix chain 'A' and resid 962 through 975 Processing helix chain 'A' and resid 976 through 988 removed outlier: 3.918A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 3.879A pdb=" N ILE A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1013 Processing helix chain 'A' and resid 1017 through 1035 removed outlier: 4.832A pdb=" N VAL A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1049 Processing helix chain 'A' and resid 1050 through 1061 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1078 through 1093 removed outlier: 4.455A pdb=" N GLU A1084 " --> pdb=" O GLU A1080 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A1093 " --> pdb=" O SER A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1101 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.762A pdb=" N TYR A1106 " --> pdb=" O ILE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1120 removed outlier: 4.520A pdb=" N LEU A1116 " --> pdb=" O GLU A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1133 Processing helix chain 'A' and resid 1137 through 1142 Processing helix chain 'A' and resid 1142 through 1171 Processing helix chain 'A' and resid 1253 through 1269 removed outlier: 3.525A pdb=" N GLN A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1283 Processing helix chain 'A' and resid 1285 through 1304 Processing helix chain 'B' and resid 469 through 479 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.863A pdb=" N GLU B 488 " --> pdb=" O GLU B 485 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 489 " --> pdb=" O LYS B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 485 through 489' Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.916A pdb=" N GLN B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.694A pdb=" N ALA C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 3.830A pdb=" N GLY C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.533A pdb=" N LEU C 186 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.910A pdb=" N ARG C 191 " --> pdb=" O PRO C 187 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.719A pdb=" N ALA C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 261 through 267 removed outlier: 4.060A pdb=" N ARG C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 4.215A pdb=" N VAL C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N CYS C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.547A pdb=" N PHE C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 343 removed outlier: 4.039A pdb=" N GLU C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.709A pdb=" N LEU C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 404 removed outlier: 3.543A pdb=" N LEU C 395 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.807A pdb=" N ARG C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 523 removed outlier: 3.559A pdb=" N LEU C 511 " --> pdb=" O GLY C 507 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 538 Processing helix chain 'D' and resid 1007 through 1013 Processing helix chain 'D' and resid 1017 through 1036 removed outlier: 3.534A pdb=" N GLN D1021 " --> pdb=" O ASP D1017 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS D1030 " --> pdb=" O ASN D1026 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N HIS D1031 " --> pdb=" O ILE D1027 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN D1036 " --> pdb=" O LEU D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1049 removed outlier: 3.787A pdb=" N ALA D1041 " --> pdb=" O MET D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1061 removed outlier: 3.698A pdb=" N GLY D1056 " --> pdb=" O LYS D1052 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D1061 " --> pdb=" O ALA D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1074 Processing helix chain 'D' and resid 1075 through 1078 Processing helix chain 'D' and resid 1079 through 1092 removed outlier: 4.263A pdb=" N ALA D1083 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D1085 " --> pdb=" O SER D1081 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D1086 " --> pdb=" O VAL D1082 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER D1089 " --> pdb=" O GLU D1085 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1108 removed outlier: 3.786A pdb=" N ALA D1099 " --> pdb=" O ARG D1095 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP D1108 " --> pdb=" O LEU D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1120 Processing helix chain 'D' and resid 1122 through 1133 Processing helix chain 'D' and resid 1137 through 1142 Processing helix chain 'D' and resid 1142 through 1159 Processing helix chain 'D' and resid 1159 through 1166 removed outlier: 3.992A pdb=" N GLY D1163 " --> pdb=" O ALA D1159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D1164 " --> pdb=" O ASP D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1253 through 1283 removed outlier: 4.385A pdb=" N GLN D1257 " --> pdb=" O GLU D1253 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU D1262 " --> pdb=" O SER D1258 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D1264 " --> pdb=" O GLY D1260 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG D1265 " --> pdb=" O ARG D1261 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D1266 " --> pdb=" O LEU D1262 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN D1267 " --> pdb=" O ILE D1263 " (cutoff:3.500A) Proline residue: D1271 - end of helix removed outlier: 3.783A pdb=" N ARG D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1287 through 1307 Processing helix chain 'D' and resid 1308 through 1310 No H-bonds generated for 'chain 'D' and resid 1308 through 1310' Processing helix chain 'E' and resid 7 through 17 Processing helix chain 'E' and resid 36 through 49 removed outlier: 3.747A pdb=" N GLN E 40 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 48 " --> pdb=" O HIS E 44 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 3.818A pdb=" N ILE E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 156 through 164 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.506A pdb=" N ASP F 25 " --> pdb=" O PHE F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 54 removed outlier: 4.174A pdb=" N ALA F 48 " --> pdb=" O TRP F 44 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 96 removed outlier: 3.687A pdb=" N LYS F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 121 through 137 Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 162 through 170 Processing helix chain 'F' and resid 170 through 177 Processing helix chain 'F' and resid 201 through 215 removed outlier: 3.810A pdb=" N PHE F 212 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS F 214 " --> pdb=" O SER F 210 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.660A pdb=" N GLU F 266 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 117 through 136 removed outlier: 4.175A pdb=" N ILE G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 122 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 264 through 279 removed outlier: 3.508A pdb=" N GLU G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 303 through 321 removed outlier: 4.039A pdb=" N ILE G 307 " --> pdb=" O GLU G 303 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 346 removed outlier: 3.865A pdb=" N ASN G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'G' and resid 387 through 393 removed outlier: 3.625A pdb=" N ARG G 392 " --> pdb=" O PHE G 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 17 Processing helix chain 'H' and resid 35 through 48 removed outlier: 3.643A pdb=" N SER H 48 " --> pdb=" O HIS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 90 removed outlier: 4.339A pdb=" N LYS H 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE H 88 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR H 90 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 142 through 146 removed outlier: 4.117A pdb=" N VAL H 146 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 165 removed outlier: 3.716A pdb=" N LEU H 160 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 190 Processing helix chain 'I' and resid 20 through 25 removed outlier: 3.518A pdb=" N GLN I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.749A pdb=" N ALA I 48 " --> pdb=" O TRP I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 96 Processing helix chain 'I' and resid 121 through 137 removed outlier: 4.127A pdb=" N PHE I 133 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 158 removed outlier: 3.919A pdb=" N SER I 156 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 178 removed outlier: 3.608A pdb=" N LEU I 166 " --> pdb=" O THR I 162 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Proline residue: I 173 - end of helix Processing helix chain 'I' and resid 201 through 215 removed outlier: 4.358A pdb=" N GLN I 205 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE I 207 " --> pdb=" O ASN I 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 97 Processing helix chain 'J' and resid 118 through 136 removed outlier: 4.073A pdb=" N LEU J 122 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS J 124 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 125 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA J 127 " --> pdb=" O GLY J 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY J 130 " --> pdb=" O PHE J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 163 removed outlier: 3.656A pdb=" N LYS J 162 " --> pdb=" O MET J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 234 Processing helix chain 'J' and resid 264 through 278 removed outlier: 3.703A pdb=" N SER J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 303 removed outlier: 3.772A pdb=" N GLU J 303 " --> pdb=" O LYS J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 321 Processing helix chain 'J' and resid 337 through 345 Processing helix chain 'J' and resid 361 through 369 Processing helix chain 'J' and resid 387 through 391 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29 removed outlier: 4.464A pdb=" N LEU A 21 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS A 427 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR A 23 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA A 425 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN A 25 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 413 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 50 removed outlier: 7.097A pdb=" N VAL A 62 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 50 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR A 60 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 86 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN A 75 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 84 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET A 77 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG A 82 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 102 removed outlier: 3.996A pdb=" N SER A 99 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 150 removed outlier: 3.559A pdb=" N ALA A 147 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 removed outlier: 3.908A pdb=" N THR A 252 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE A 285 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA A 297 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 287 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 310 removed outlier: 4.691A pdb=" N VAL A 332 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY A 345 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.597A pdb=" N ILE A 377 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU A 392 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 379 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 446 removed outlier: 4.026A pdb=" N ILE A 452 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG A 467 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 477 through 480 removed outlier: 3.967A pdb=" N ASP A 477 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 495 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 517 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 497 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 536 Processing sheet with id=AB2, first strand: chain 'A' and resid 576 through 581 removed outlier: 6.723A pdb=" N GLU A 591 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU A 579 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 589 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLN A 599 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU A 608 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AB4, first strand: chain 'A' and resid 621 through 625 Processing sheet with id=AB5, first strand: chain 'A' and resid 664 through 670 removed outlier: 6.563A pdb=" N THR A 677 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 667 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 675 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 669 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 716 through 721 removed outlier: 5.566A pdb=" N LEU A 717 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN A 730 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 435 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 433 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP C 442 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 458 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP C 450 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 456 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 485 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG C 463 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL C 483 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER C 481 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 5 through 11 removed outlier: 3.561A pdb=" N THR B 6 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 782 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 10 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR B 780 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 775 " --> pdb=" O SER B 779 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 34 removed outlier: 4.366A pdb=" N ALA B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.692A pdb=" N ALA B 77 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 65 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE B 67 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 73 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 83 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 98 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS B 87 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N CYS B 96 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR B 89 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 94 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.660A pdb=" N GLY B 120 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 110 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER B 118 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA B 112 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG B 130 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 140 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 153 through 160 removed outlier: 7.169A pdb=" N GLY B 171 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU B 156 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 169 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU B 158 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 167 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS B 160 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS B 165 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER B 181 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 194 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ILE B 183 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N CYS B 192 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.472A pdb=" N GLY B 224 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 208 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 222 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE B 210 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU B 220 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 275 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG B 234 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE B 273 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG B 236 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE B 271 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 288 removed outlier: 6.784A pdb=" N ALA B 299 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 297 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 305 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG B 322 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 307 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 348 removed outlier: 3.834A pdb=" N ILE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 411 through 417 removed outlier: 7.051A pdb=" N LEU B 411 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 428 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N TYR B 417 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ILE B 426 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 444 through 449 removed outlier: 6.831A pdb=" N ARG B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE B 453 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 462 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS B 553 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 464 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 514 through 515 Processing sheet with id=AD1, first strand: chain 'B' and resid 561 through 566 Processing sheet with id=AD2, first strand: chain 'B' and resid 609 through 614 removed outlier: 3.582A pdb=" N VAL B 624 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 613 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP B 630 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS B 647 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 632 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 656 through 660 removed outlier: 7.003A pdb=" N ALA B 673 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA B 659 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 671 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 679 " --> pdb=" O SER B 697 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B 697 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 681 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 704 through 709 removed outlier: 6.983A pdb=" N GLY B 723 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 707 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER B 721 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 709 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 719 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 729 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN B 744 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 731 " --> pdb=" O ILE B 742 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.340A pdb=" N ALA C 97 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 177 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 99 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET C 179 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 101 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 174 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY C 226 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU C 230 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 251 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 229 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU C 253 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.607A pdb=" N LEU C 324 " --> pdb=" O ARG C 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 331 through 332 removed outlier: 6.763A pdb=" N VAL C 331 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 73 through 74 removed outlier: 6.565A pdb=" N VAL E 56 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR E 134 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 25 " --> pdb=" O MET E 131 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA E 133 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E 167 " --> pdb=" O PHE E 24 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 103 through 107 removed outlier: 3.595A pdb=" N SER F 81 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 147 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA F 80 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU F 149 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN F 30 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE F 183 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE F 32 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER F 185 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE F 34 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE F 217 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 103 through 107 removed outlier: 3.595A pdb=" N SER F 81 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 147 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA F 80 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU F 149 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN F 30 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE F 183 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE F 32 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER F 185 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE F 34 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE F 217 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 222 " --> pdb=" O SER F 235 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER F 235 " --> pdb=" O ASN F 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AE3, first strand: chain 'G' and resid 256 through 259 removed outlier: 6.487A pdb=" N VAL G 151 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE G 259 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL G 153 " --> pdb=" O ILE G 259 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE G 152 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU G 154 " --> pdb=" O PRO G 289 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU G 291 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 326 " --> pdb=" O ARG G 285 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL G 287 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE G 328 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER G 330 " --> pdb=" O PRO G 289 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL G 108 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE G 331 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL G 110 " --> pdb=" O ILE G 331 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU G 109 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU G 354 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU G 111 " --> pdb=" O LEU G 354 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL G 351 " --> pdb=" O LEU G 384 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY G 379 " --> pdb=" O TRP G 402 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TRP G 402 " --> pdb=" O GLY G 379 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL G 381 " --> pdb=" O SER G 400 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 400 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 165 through 170 removed outlier: 5.683A pdb=" N THR G 245 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N TYR G 168 " --> pdb=" O ILE G 243 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE G 243 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLY G 170 " --> pdb=" O PHE G 241 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE G 241 " --> pdb=" O GLY G 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 55 through 58 removed outlier: 6.308A pdb=" N VAL H 104 " --> pdb=" O VAL H 132 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR H 134 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE H 106 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N HIS H 136 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 171 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU H 204 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE H 220 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN H 208 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU H 216 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 103 through 107 removed outlier: 4.044A pdb=" N VAL I 146 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU I 31 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LEU I 219 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE I 33 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU I 221 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR I 35 " --> pdb=" O LEU I 221 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 85 through 86 removed outlier: 3.617A pdb=" N THR J 86 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 256 through 258 removed outlier: 5.946A pdb=" N HIS J 150 " --> pdb=" O ARG J 285 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL J 287 " --> pdb=" O HIS J 150 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE J 152 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER J 330 " --> pdb=" O ILE J 288 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL J 108 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE J 331 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL J 110 " --> pdb=" O ILE J 331 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE J 352 " --> pdb=" O SER J 107 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU J 109 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU J 354 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU J 111 " --> pdb=" O LEU J 354 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL J 351 " --> pdb=" O LEU J 384 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 402 through 405 1226 hydrogen bonds defined for protein. 3393 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: 9.52 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 15518 1.44 - 1.65: 20758 1.65 - 1.86: 231 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 36519 Sorted by residual: bond pdb=" C VAL C 493 " pdb=" N PRO C 494 " ideal model delta sigma weight residual 1.329 1.360 -0.031 1.22e-02 6.72e+03 6.26e+00 bond pdb=" CA ILE G 252 " pdb=" C ILE G 252 " ideal model delta sigma weight residual 1.524 1.504 0.020 8.60e-03 1.35e+04 5.40e+00 bond pdb=" C MET G 248 " pdb=" O MET G 248 " ideal model delta sigma weight residual 1.244 1.227 0.017 9.30e-03 1.16e+04 3.22e+00 bond pdb=" CA ASN A 992 " pdb=" C ASN A 992 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.21e-02 6.83e+03 2.58e+00 bond pdb=" C PRO J 338 " pdb=" N PRO J 339 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 ... (remaining 36514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 48787 2.35 - 4.69: 608 4.69 - 7.04: 60 7.04 - 9.39: 7 9.39 - 11.73: 3 Bond angle restraints: 49465 Sorted by residual: angle pdb=" N VAL J 75 " pdb=" CA VAL J 75 " pdb=" C VAL J 75 " ideal model delta sigma weight residual 111.91 107.08 4.83 8.90e-01 1.26e+00 2.94e+01 angle pdb=" N SER F 64 " pdb=" CA SER F 64 " pdb=" C SER F 64 " ideal model delta sigma weight residual 108.19 114.36 -6.17 1.29e+00 6.01e-01 2.29e+01 angle pdb=" C SER D1314 " pdb=" CA SER D1314 " pdb=" CB SER D1314 " ideal model delta sigma weight residual 116.63 111.18 5.45 1.16e+00 7.43e-01 2.21e+01 angle pdb=" N ASN I 102 " pdb=" CA ASN I 102 " pdb=" C ASN I 102 " ideal model delta sigma weight residual 112.97 108.00 4.97 1.06e+00 8.90e-01 2.19e+01 angle pdb=" N TYR A1038 " pdb=" CA TYR A1038 " pdb=" C TYR A1038 " ideal model delta sigma weight residual 110.97 115.43 -4.46 1.09e+00 8.42e-01 1.68e+01 ... (remaining 49460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 19733 17.79 - 35.59: 2001 35.59 - 53.38: 293 53.38 - 71.17: 73 71.17 - 88.96: 63 Dihedral angle restraints: 22163 sinusoidal: 8997 harmonic: 13166 Sorted by residual: dihedral pdb=" CA ASN J 191 " pdb=" C ASN J 191 " pdb=" N LEU J 192 " pdb=" CA LEU J 192 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA LYS I 225 " pdb=" C LYS I 225 " pdb=" N THR I 226 " pdb=" CA THR I 226 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 528 " pdb=" C ASP B 528 " pdb=" N PRO B 529 " pdb=" CA PRO B 529 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 22160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3882 0.040 - 0.081: 1254 0.081 - 0.121: 393 0.121 - 0.162: 60 0.162 - 0.202: 6 Chirality restraints: 5595 Sorted by residual: chirality pdb=" CB ILE F 217 " pdb=" CA ILE F 217 " pdb=" CG1 ILE F 217 " pdb=" CG2 ILE F 217 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU C 308 " pdb=" N GLU C 308 " pdb=" C GLU C 308 " pdb=" CB GLU C 308 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA PHE B 355 " pdb=" N PHE B 355 " pdb=" C PHE B 355 " pdb=" CB PHE B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 5592 not shown) Planarity restraints: 6353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 831 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C MET A 831 " 0.038 2.00e-02 2.50e+03 pdb=" O MET A 831 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 832 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1296 " -0.010 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE A1296 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A1296 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A1296 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A1296 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1296 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A1296 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 386 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO J 387 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO J 387 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 387 " 0.028 5.00e-02 4.00e+02 ... (remaining 6350 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 929 2.68 - 3.24: 35379 3.24 - 3.79: 52780 3.79 - 4.35: 71598 4.35 - 4.90: 115946 Nonbonded interactions: 276632 Sorted by model distance: nonbonded pdb=" OG1 THR I 35 " pdb=" OD1 ASN I 220 " model vdw 2.128 3.040 nonbonded pdb=" OE1 GLU E 41 " pdb=" OH TYR E 229 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR B 369 " pdb=" O ILE B 374 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR A 592 " pdb=" OD1 ASP A 594 " model vdw 2.171 3.040 nonbonded pdb=" O ASP A 185 " pdb=" NH2 ARG A 286 " model vdw 2.171 3.120 ... (remaining 276627 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 'E' and resid 2 through 232) selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 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: 0.040 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 43.000 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 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 0.036 36522 Z= 0.140 Angle : 0.719 35.072 49474 Z= 0.399 Chirality : 0.044 0.202 5595 Planarity : 0.004 0.050 6353 Dihedral : 15.093 88.964 13633 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.00 % Favored : 90.93 % Rotamer: Outliers : 0.02 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.12), residues: 4454 helix: -0.53 (0.15), residues: 1163 sheet: -0.64 (0.17), residues: 1020 loop : -2.32 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 209 TYR 0.024 0.001 TYR G 237 PHE 0.037 0.001 PHE A1296 TRP 0.020 0.001 TRP A1064 HIS 0.005 0.001 HIS D1345 Details of bonding type rmsd covalent geometry : bond 0.00262 (36519) covalent geometry : angle 0.67988 (49465) hydrogen bonds : bond 0.16451 ( 1214) hydrogen bonds : angle 7.01876 ( 3393) metal coordination : bond 0.00958 ( 3) metal coordination : angle 17.46236 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.7922 (mp10) cc_final: 0.7498 (mp10) REVERT: A 993 VAL cc_start: 0.5235 (OUTLIER) cc_final: 0.5030 (m) REVERT: A 1285 MET cc_start: 0.4030 (mtp) cc_final: 0.3700 (mmm) REVERT: C 234 ASP cc_start: 0.8127 (t70) cc_final: 0.7907 (t0) REVERT: C 400 MET cc_start: 0.7332 (mpp) cc_final: 0.7012 (mpp) REVERT: H 78 MET cc_start: 0.7242 (ppp) cc_final: 0.6700 (ppp) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.2132 time to fit residues: 95.3423 Evaluate side-chains 198 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 83 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN F 205 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN I 37 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.082253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067811 restraints weight = 199223.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067728 restraints weight = 145542.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067863 restraints weight = 119393.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.068213 restraints weight = 107108.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068308 restraints weight = 93729.391| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36522 Z= 0.195 Angle : 0.720 41.066 49474 Z= 0.360 Chirality : 0.046 0.177 5595 Planarity : 0.005 0.069 6353 Dihedral : 5.857 31.753 4853 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.75 % Favored : 89.18 % Rotamer: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.12), residues: 4454 helix: -0.62 (0.15), residues: 1190 sheet: -0.75 (0.17), residues: 1017 loop : -2.50 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1261 TYR 0.023 0.002 TYR G 237 PHE 0.027 0.002 PHE A1296 TRP 0.012 0.002 TRP A 310 HIS 0.007 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00441 (36519) covalent geometry : angle 0.67165 (49465) hydrogen bonds : bond 0.05072 ( 1214) hydrogen bonds : angle 5.78148 ( 3393) metal coordination : bond 0.02200 ( 3) metal coordination : angle 19.27549 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 246 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6274 (pp30) REVERT: A 605 GLN cc_start: 0.8014 (mp10) cc_final: 0.7433 (mp10) REVERT: C 234 ASP cc_start: 0.8021 (t70) cc_final: 0.7796 (t0) REVERT: D 1104 LEU cc_start: 0.7014 (tt) cc_final: 0.6698 (mt) REVERT: G 175 MET cc_start: 0.1733 (mpp) cc_final: 0.1441 (mpp) outliers start: 5 outliers final: 1 residues processed: 251 average time/residue: 0.2101 time to fit residues: 91.7045 Evaluate side-chains 178 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 244 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 407 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 334 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN D1164 GLN D1168 GLN ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN F 205 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN J 190 GLN J 193 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.082939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069589 restraints weight = 198265.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069344 restraints weight = 172452.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069834 restraints weight = 137457.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069957 restraints weight = 119869.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.070107 restraints weight = 109683.428| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36522 Z= 0.165 Angle : 0.698 36.981 49474 Z= 0.345 Chirality : 0.046 0.276 5595 Planarity : 0.005 0.056 6353 Dihedral : 5.831 30.665 4853 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.95 % Favored : 90.01 % Rotamer: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.12), residues: 4454 helix: -0.60 (0.15), residues: 1195 sheet: -0.77 (0.16), residues: 1019 loop : -2.49 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 376 TYR 0.021 0.002 TYR G 237 PHE 0.026 0.002 PHE A1151 TRP 0.030 0.002 TRP B 283 HIS 0.006 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00370 (36519) covalent geometry : angle 0.64503 (49465) hydrogen bonds : bond 0.04494 ( 1214) hydrogen bonds : angle 5.56321 ( 3393) metal coordination : bond 0.02704 ( 3) metal coordination : angle 19.70598 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.5819 (tm-30) cc_final: 0.5048 (pm20) REVERT: A 605 GLN cc_start: 0.8049 (mp10) cc_final: 0.7543 (mp10) REVERT: C 400 MET cc_start: 0.8086 (mpp) cc_final: 0.7226 (mpp) REVERT: F 216 MET cc_start: 0.8724 (pmm) cc_final: 0.8456 (pmm) REVERT: G 395 MET cc_start: 0.7466 (tpt) cc_final: 0.6699 (tpt) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.2198 time to fit residues: 95.5214 Evaluate side-chains 177 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 417 optimal weight: 10.0000 chunk 367 optimal weight: 0.7980 chunk 334 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 98 GLN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.083295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069861 restraints weight = 199372.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.069647 restraints weight = 170914.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.069940 restraints weight = 141423.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.070230 restraints weight = 125583.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070317 restraints weight = 111966.436| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36522 Z= 0.145 Angle : 0.671 37.903 49474 Z= 0.332 Chirality : 0.045 0.197 5595 Planarity : 0.004 0.055 6353 Dihedral : 5.717 30.465 4853 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.65 % Favored : 90.30 % Rotamer: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.12), residues: 4454 helix: -0.56 (0.15), residues: 1204 sheet: -0.77 (0.17), residues: 1026 loop : -2.42 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1235 TYR 0.021 0.001 TYR G 237 PHE 0.023 0.002 PHE A1151 TRP 0.017 0.001 TRP B 633 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd covalent geometry : bond 0.00326 (36519) covalent geometry : angle 0.62067 (49465) hydrogen bonds : bond 0.04149 ( 1214) hydrogen bonds : angle 5.41789 ( 3393) metal coordination : bond 0.01175 ( 3) metal coordination : angle 18.97851 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8749 (mm) cc_final: 0.8483 (mm) REVERT: A 605 GLN cc_start: 0.8024 (mp10) cc_final: 0.7527 (mp10) REVERT: D 1345 HIS cc_start: 0.5352 (m90) cc_final: 0.5067 (t-170) REVERT: F 216 MET cc_start: 0.8757 (pmm) cc_final: 0.8468 (pmm) REVERT: G 175 MET cc_start: 0.2267 (mpp) cc_final: 0.2038 (mpp) REVERT: I 103 TYR cc_start: 0.6780 (t80) cc_final: 0.6334 (t80) outliers start: 1 outliers final: 1 residues processed: 257 average time/residue: 0.2094 time to fit residues: 93.2840 Evaluate side-chains 184 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 254 optimal weight: 0.0870 chunk 128 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 405 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 304 optimal weight: 0.6980 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS A 474 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1290 HIS F 205 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.083505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.069706 restraints weight = 199506.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069370 restraints weight = 171025.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.069477 restraints weight = 143219.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.069609 restraints weight = 135301.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.069677 restraints weight = 123751.772| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36522 Z= 0.140 Angle : 0.668 37.848 49474 Z= 0.330 Chirality : 0.045 0.186 5595 Planarity : 0.004 0.065 6353 Dihedral : 5.675 30.326 4853 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.63 % Favored : 90.32 % Rotamer: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.12), residues: 4454 helix: -0.51 (0.15), residues: 1202 sheet: -0.69 (0.17), residues: 1023 loop : -2.41 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 145 TYR 0.025 0.001 TYR G 237 PHE 0.016 0.002 PHE B 670 TRP 0.014 0.001 TRP B 633 HIS 0.008 0.001 HIS J 382 Details of bonding type rmsd covalent geometry : bond 0.00315 (36519) covalent geometry : angle 0.61947 (49465) hydrogen bonds : bond 0.04032 ( 1214) hydrogen bonds : angle 5.33925 ( 3393) metal coordination : bond 0.01335 ( 3) metal coordination : angle 18.48314 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8013 (mp10) cc_final: 0.7518 (mp10) REVERT: C 258 SER cc_start: 0.8602 (t) cc_final: 0.8389 (p) REVERT: C 400 MET cc_start: 0.8059 (mpp) cc_final: 0.7189 (mpp) REVERT: D 1345 HIS cc_start: 0.5539 (m90) cc_final: 0.5200 (t-170) REVERT: F 216 MET cc_start: 0.8825 (pmm) cc_final: 0.8517 (pmm) REVERT: G 175 MET cc_start: 0.2263 (mpp) cc_final: 0.2036 (mpp) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1952 time to fit residues: 87.2200 Evaluate side-chains 187 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 117 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 279 optimal weight: 0.7980 chunk 401 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 chunk 271 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS F 205 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 98 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.069533 restraints weight = 205822.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.069362 restraints weight = 187512.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069803 restraints weight = 148536.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069956 restraints weight = 129715.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.070074 restraints weight = 117590.286| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36522 Z= 0.155 Angle : 0.685 38.885 49474 Z= 0.338 Chirality : 0.046 0.195 5595 Planarity : 0.004 0.061 6353 Dihedral : 5.753 30.596 4853 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.17 % Favored : 89.76 % Rotamer: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.12), residues: 4454 helix: -0.55 (0.15), residues: 1209 sheet: -0.77 (0.17), residues: 1027 loop : -2.43 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1320 TYR 0.029 0.002 TYR D1014 PHE 0.017 0.002 PHE B 670 TRP 0.015 0.002 TRP B 633 HIS 0.006 0.001 HIS J 382 Details of bonding type rmsd covalent geometry : bond 0.00351 (36519) covalent geometry : angle 0.63681 (49465) hydrogen bonds : bond 0.04141 ( 1214) hydrogen bonds : angle 5.34274 ( 3393) metal coordination : bond 0.01471 ( 3) metal coordination : angle 18.74049 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8654 (mm) cc_final: 0.8406 (mm) REVERT: A 605 GLN cc_start: 0.7947 (mp10) cc_final: 0.7485 (mp10) REVERT: C 400 MET cc_start: 0.7869 (mpp) cc_final: 0.7127 (mpp) REVERT: H 42 PHE cc_start: 0.7118 (m-80) cc_final: 0.5607 (t80) REVERT: I 103 TYR cc_start: 0.6918 (t80) cc_final: 0.6437 (t80) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.1942 time to fit residues: 82.7843 Evaluate side-chains 183 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 8 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 277 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 2 optimal weight: 0.0050 chunk 23 optimal weight: 0.2980 overall best weight: 1.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 484 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN F 205 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 HIS ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.083522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.070158 restraints weight = 200542.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069767 restraints weight = 170981.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.070103 restraints weight = 142618.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.070218 restraints weight = 127884.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070271 restraints weight = 123492.576| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36522 Z= 0.129 Angle : 0.654 36.729 49474 Z= 0.322 Chirality : 0.045 0.189 5595 Planarity : 0.004 0.055 6353 Dihedral : 5.570 29.874 4853 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.12 % Favored : 90.84 % Rotamer: Outliers : 0.02 % Allowed : 1.75 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.12), residues: 4454 helix: -0.40 (0.15), residues: 1206 sheet: -0.64 (0.17), residues: 1013 loop : -2.37 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1320 TYR 0.018 0.001 TYR E 218 PHE 0.017 0.001 PHE B 670 TRP 0.012 0.001 TRP B 367 HIS 0.007 0.001 HIS J 382 Details of bonding type rmsd covalent geometry : bond 0.00291 (36519) covalent geometry : angle 0.60668 (49465) hydrogen bonds : bond 0.03813 ( 1214) hydrogen bonds : angle 5.21343 ( 3393) metal coordination : bond 0.01232 ( 3) metal coordination : angle 18.02203 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.7974 (mp10) cc_final: 0.7563 (mp10) REVERT: C 258 SER cc_start: 0.8420 (t) cc_final: 0.8216 (p) REVERT: C 400 MET cc_start: 0.7794 (mpp) cc_final: 0.7195 (mpp) REVERT: J 307 ILE cc_start: 0.9120 (pt) cc_final: 0.8867 (pt) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1855 time to fit residues: 81.4781 Evaluate side-chains 183 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 243 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 266 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 426 optimal weight: 0.8980 chunk 291 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 484 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 98 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN J 193 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.081797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067930 restraints weight = 207720.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.067156 restraints weight = 156681.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067385 restraints weight = 128081.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067705 restraints weight = 115262.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067733 restraints weight = 103276.290| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36522 Z= 0.228 Angle : 0.780 39.852 49474 Z= 0.387 Chirality : 0.048 0.236 5595 Planarity : 0.005 0.058 6353 Dihedral : 6.133 32.526 4853 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.65 % Favored : 88.28 % Rotamer: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.12), residues: 4454 helix: -0.71 (0.15), residues: 1208 sheet: -0.86 (0.17), residues: 1006 loop : -2.59 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1095 TYR 0.026 0.002 TYR E 218 PHE 0.022 0.002 PHE B 453 TRP 0.018 0.002 TRP B 633 HIS 0.009 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00523 (36519) covalent geometry : angle 0.72890 (49465) hydrogen bonds : bond 0.04778 ( 1214) hydrogen bonds : angle 5.58155 ( 3393) metal coordination : bond 0.00950 ( 3) metal coordination : angle 20.69270 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7107 (tpt) cc_final: 0.6836 (mmm) REVERT: A 317 ILE cc_start: 0.8810 (mm) cc_final: 0.8453 (mm) REVERT: A 412 MET cc_start: 0.8024 (tpp) cc_final: 0.7599 (tpp) REVERT: A 605 GLN cc_start: 0.8031 (mp10) cc_final: 0.7753 (mp10) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.1963 time to fit residues: 80.6708 Evaluate side-chains 176 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 380 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 390 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 219 GLN F 21 HIS F 94 ASN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN G 150 HIS H 44 HIS ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.081534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.068052 restraints weight = 201073.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067291 restraints weight = 161694.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.067505 restraints weight = 137818.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067717 restraints weight = 123532.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067840 restraints weight = 113127.416| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36522 Z= 0.217 Angle : 0.775 39.460 49474 Z= 0.387 Chirality : 0.048 0.243 5595 Planarity : 0.005 0.058 6353 Dihedral : 6.291 32.144 4853 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.54 % Favored : 88.41 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.12), residues: 4454 helix: -0.81 (0.14), residues: 1196 sheet: -0.91 (0.17), residues: 988 loop : -2.62 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1265 TYR 0.032 0.002 TYR C 120 PHE 0.021 0.002 PHE F 82 TRP 0.020 0.002 TRP B 367 HIS 0.008 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00500 (36519) covalent geometry : angle 0.72982 (49465) hydrogen bonds : bond 0.04771 ( 1214) hydrogen bonds : angle 5.64566 ( 3393) metal coordination : bond 0.01117 ( 3) metal coordination : angle 19.38963 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8022 (tpp) cc_final: 0.7591 (tpp) REVERT: A 605 GLN cc_start: 0.8078 (mp10) cc_final: 0.7811 (mp10) REVERT: A 1068 MET cc_start: 0.6991 (mpp) cc_final: 0.6728 (mtt) REVERT: C 400 MET cc_start: 0.7918 (mpp) cc_final: 0.7053 (mpp) REVERT: E 164 MET cc_start: 0.6735 (ttm) cc_final: 0.6511 (ttm) REVERT: E 218 TYR cc_start: 0.7364 (m-80) cc_final: 0.6981 (m-80) REVERT: H 10 ILE cc_start: 0.8257 (mm) cc_final: 0.8016 (mm) REVERT: I 103 TYR cc_start: 0.7084 (t80) cc_final: 0.6614 (t80) outliers start: 2 outliers final: 0 residues processed: 238 average time/residue: 0.2033 time to fit residues: 83.2318 Evaluate side-chains 181 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 383 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 437 optimal weight: 9.9990 chunk 440 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 484 ASN ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** G 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.083484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.070529 restraints weight = 200353.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.069975 restraints weight = 173514.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.070332 restraints weight = 144875.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.070465 restraints weight = 129381.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070634 restraints weight = 118078.121| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36522 Z= 0.122 Angle : 0.681 35.661 49474 Z= 0.334 Chirality : 0.046 0.210 5595 Planarity : 0.004 0.054 6353 Dihedral : 5.758 29.437 4853 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.30 % Favored : 90.66 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.12), residues: 4454 helix: -0.50 (0.15), residues: 1199 sheet: -0.75 (0.17), residues: 1003 loop : -2.41 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1095 TYR 0.024 0.001 TYR D1025 PHE 0.022 0.002 PHE A1151 TRP 0.018 0.002 TRP C 442 HIS 0.007 0.001 HIS G 312 Details of bonding type rmsd covalent geometry : bond 0.00271 (36519) covalent geometry : angle 0.63299 (49465) hydrogen bonds : bond 0.03822 ( 1214) hydrogen bonds : angle 5.29493 ( 3393) metal coordination : bond 0.01059 ( 3) metal coordination : angle 18.54375 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8660 (mm) cc_final: 0.8290 (mm) REVERT: A 605 GLN cc_start: 0.8077 (mp10) cc_final: 0.7626 (mp10) REVERT: E 218 TYR cc_start: 0.7323 (m-80) cc_final: 0.6934 (m-80) REVERT: J 307 ILE cc_start: 0.9122 (pt) cc_final: 0.8887 (pt) outliers start: 2 outliers final: 0 residues processed: 254 average time/residue: 0.1966 time to fit residues: 85.3095 Evaluate side-chains 183 residues out of total 4010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 432 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 365 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 324 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 219 GLN F 205 GLN G 129 GLN G 133 HIS G 150 HIS I 37 GLN ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.084381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.071137 restraints weight = 198731.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.070777 restraints weight = 170510.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.071216 restraints weight = 139641.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.071334 restraints weight = 121576.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.071391 restraints weight = 114754.565| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36522 Z= 0.107 Angle : 0.653 34.798 49474 Z= 0.317 Chirality : 0.045 0.206 5595 Planarity : 0.004 0.051 6353 Dihedral : 5.375 28.734 4853 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 0.07 % Allowed : 0.25 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.12), residues: 4454 helix: -0.29 (0.15), residues: 1209 sheet: -0.66 (0.17), residues: 1029 loop : -2.28 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 367 TYR 0.030 0.001 TYR G 237 PHE 0.022 0.001 PHE A1151 TRP 0.014 0.001 TRP C 442 HIS 0.006 0.001 HIS J 382 Details of bonding type rmsd covalent geometry : bond 0.00236 (36519) covalent geometry : angle 0.60501 (49465) hydrogen bonds : bond 0.03489 ( 1214) hydrogen bonds : angle 5.08036 ( 3393) metal coordination : bond 0.00920 ( 3) metal coordination : angle 18.31641 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5113.86 seconds wall clock time: 90 minutes 14.84 seconds (5414.84 seconds total)