Starting phenix.real_space_refine on Fri Dec 8 16:23:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pea_13350/12_2023/7pea_13350_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pea_13350/12_2023/7pea_13350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pea_13350/12_2023/7pea_13350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pea_13350/12_2023/7pea_13350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pea_13350/12_2023/7pea_13350_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pea_13350/12_2023/7pea_13350_updated.pdb" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 384 5.16 5 C 37098 2.51 5 N 10164 2.21 5 O 10594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 58252 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 17454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17454 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 56, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "F" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 17454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17454 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 56, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.14, per 1000 atoms: 0.38 Number of scatterers: 58252 At special positions: 0 Unit cell: (275.776, 224.624, 152.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 384 16.00 P 12 15.00 O 10594 8.00 N 10164 7.00 C 37098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.16 Conformation dependent library (CDL) restraints added in 7.7 seconds 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 316 helices and 48 sheets defined 58.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.15 Creating SS restraints... Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.828A pdb=" N UNK B 52 " --> pdb=" O UNK B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 83 through 97 removed outlier: 3.538A pdb=" N SER B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 116 removed outlier: 4.234A pdb=" N ASN B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.585A pdb=" N ALA B 142 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 146 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 149 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 150 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 180 through 186 removed outlier: 3.521A pdb=" N GLN B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLN B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.747A pdb=" N VAL B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 removed outlier: 3.742A pdb=" N VAL B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 262 through 275 removed outlier: 3.575A pdb=" N LEU B 266 " --> pdb=" O HIS B 262 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.765A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 362 through 370 removed outlier: 3.603A pdb=" N UNK B 369 " --> pdb=" O UNK B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 387 through 402 Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 410 through 425 removed outlier: 3.689A pdb=" N HIS B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.628A pdb=" N GLN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 465 removed outlier: 3.583A pdb=" N VAL B 450 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Proline residue: B 453 - end of helix removed outlier: 3.902A pdb=" N LEU B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 457 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 463 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.574A pdb=" N THR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 532 through 548 Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 601 through 611 removed outlier: 3.735A pdb=" N ASP B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 629 Processing helix chain 'B' and resid 646 through 665 Processing helix chain 'B' and resid 669 through 678 Processing helix chain 'B' and resid 681 through 687 removed outlier: 4.584A pdb=" N ALA B 685 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 687 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 701 removed outlier: 3.564A pdb=" N VAL B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 719 Processing helix chain 'B' and resid 723 through 742 Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 747 through 763 Processing helix chain 'B' and resid 765 through 783 Proline residue: B 770 - end of helix removed outlier: 5.318A pdb=" N GLU B 773 " --> pdb=" O ARG B 769 " (cutoff:3.500A) Proline residue: B 774 - end of helix Processing helix chain 'B' and resid 792 through 809 removed outlier: 3.858A pdb=" N GLN B 807 " --> pdb=" O GLY B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 828 removed outlier: 4.726A pdb=" N ASP B 818 " --> pdb=" O LYS B 815 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 821 " --> pdb=" O ASP B 818 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 828 " --> pdb=" O MET B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 851 Processing helix chain 'B' and resid 856 through 860 Processing helix chain 'B' and resid 862 through 874 removed outlier: 3.795A pdb=" N LEU B 865 " --> pdb=" O PRO B 862 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 868 " --> pdb=" O LEU B 865 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 869 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 871 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 872 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 890 removed outlier: 3.541A pdb=" N LEU B 888 " --> pdb=" O ALA B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 934 through 940 Processing helix chain 'B' and resid 943 through 959 Proline residue: B 948 - end of helix removed outlier: 3.782A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 966 Processing helix chain 'B' and resid 968 through 982 removed outlier: 3.633A pdb=" N VAL B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1003 removed outlier: 3.528A pdb=" N VAL B 987 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Proline residue: B 991 - end of helix removed outlier: 4.583A pdb=" N MET B 994 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Proline residue: B 995 - end of helix removed outlier: 3.589A pdb=" N LEU B 998 " --> pdb=" O PRO B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1041 removed outlier: 3.538A pdb=" N LEU B1016 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS B1024 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER B1025 " --> pdb=" O PHE B1022 " (cutoff:3.500A) Proline residue: B1029 - end of helix removed outlier: 4.400A pdb=" N ASP B1032 " --> pdb=" O PRO B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1083 removed outlier: 6.993A pdb=" N GLY B1065 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU B1066 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU B1069 " --> pdb=" O GLY B1065 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) Proline residue: B1072 - end of helix Proline residue: B1076 - end of helix removed outlier: 3.515A pdb=" N PHE B1082 " --> pdb=" O MET B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1123 removed outlier: 3.736A pdb=" N ILE B1091 " --> pdb=" O PRO B1088 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL B1092 " --> pdb=" O GLY B1089 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B1095 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B1101 " --> pdb=" O ALA B1098 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B1104 " --> pdb=" O GLN B1101 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA B1105 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP B1108 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP B1109 " --> pdb=" O ASN B1106 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B1111 " --> pdb=" O ASP B1108 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HIS B1112 " --> pdb=" O ASP B1109 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B1115 " --> pdb=" O HIS B1112 " (cutoff:3.500A) Proline residue: B1116 - end of helix removed outlier: 3.669A pdb=" N ASP B1123 " --> pdb=" O LYS B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1145 removed outlier: 3.539A pdb=" N GLU B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1165 Proline residue: B1158 - end of helix Processing helix chain 'B' and resid 1170 through 1202 removed outlier: 6.884A pdb=" N LYS B1186 " --> pdb=" O PHE B1182 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B1187 " --> pdb=" O GLN B1183 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR B1188 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN B1189 " --> pdb=" O GLY B1185 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B1190 " --> pdb=" O LYS B1186 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE B1191 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Proline residue: B1193 - end of helix removed outlier: 3.614A pdb=" N HIS B1202 " --> pdb=" O VAL B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1218 Processing helix chain 'B' and resid 1264 through 1269 Processing helix chain 'B' and resid 1277 through 1294 Processing helix chain 'B' and resid 1298 through 1309 removed outlier: 4.023A pdb=" N CYS B1303 " --> pdb=" O SER B1299 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP B1304 " --> pdb=" O LEU B1300 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA B1305 " --> pdb=" O ARG B1301 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B1306 " --> pdb=" O SER B1302 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1316 Processing helix chain 'B' and resid 1318 through 1328 removed outlier: 3.515A pdb=" N GLU B1328 " --> pdb=" O SER B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1346 Processing helix chain 'B' and resid 1351 through 1366 Processing helix chain 'B' and resid 1377 through 1379 No H-bonds generated for 'chain 'B' and resid 1377 through 1379' Processing helix chain 'B' and resid 1382 through 1389 Processing helix chain 'B' and resid 1393 through 1406 Processing helix chain 'B' and resid 1410 through 1422 Processing helix chain 'B' and resid 1426 through 1440 Processing helix chain 'B' and resid 1447 through 1452 Processing helix chain 'B' and resid 1456 through 1469 Processing helix chain 'B' and resid 1474 through 1487 Processing helix chain 'B' and resid 1490 through 1499 Processing helix chain 'B' and resid 1506 through 1523 removed outlier: 3.517A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B1518 " --> pdb=" O ARG B1514 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1535 removed outlier: 3.605A pdb=" N MET B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 Processing helix chain 'B' and resid 1557 through 1607 removed outlier: 4.543A pdb=" N ALA B1573 " --> pdb=" O ASP B1569 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER B1582 " --> pdb=" O MET B1578 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR B1583 " --> pdb=" O ALA B1579 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER B1584 " --> pdb=" O GLY B1580 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG B1585 " --> pdb=" O GLU B1581 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B1586 " --> pdb=" O SER B1582 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B1588 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA B1589 " --> pdb=" O ARG B1585 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B1603 " --> pdb=" O LEU B1599 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B1604 " --> pdb=" O GLU B1600 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B1605 " --> pdb=" O GLU B1601 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1625 removed outlier: 3.600A pdb=" N ARG B1612 " --> pdb=" O PRO B1609 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU B1613 " --> pdb=" O GLU B1610 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B1616 " --> pdb=" O GLU B1613 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B1624 " --> pdb=" O GLU B1621 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1642 removed outlier: 3.709A pdb=" N LEU B1642 " --> pdb=" O MET B1638 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1648 No H-bonds generated for 'chain 'B' and resid 1646 through 1648' Processing helix chain 'B' and resid 1650 through 1662 Processing helix chain 'B' and resid 1666 through 1677 Processing helix chain 'B' and resid 1694 through 1706 removed outlier: 3.510A pdb=" N LYS B1706 " --> pdb=" O LYS B1702 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1731 Processing helix chain 'B' and resid 1738 through 1761 Processing helix chain 'B' and resid 1766 through 1782 Proline residue: B1770 - end of helix Processing helix chain 'B' and resid 1787 through 1811 Processing helix chain 'B' and resid 1868 through 1895 removed outlier: 3.570A pdb=" N VAL B1882 " --> pdb=" O LEU B1878 " (cutoff:3.500A) Proline residue: B1883 - end of helix Processing helix chain 'B' and resid 1900 through 1913 Processing helix chain 'B' and resid 1917 through 1929 Processing helix chain 'B' and resid 1934 through 1945 removed outlier: 3.588A pdb=" N ILE B1939 " --> pdb=" O LEU B1936 " (cutoff:3.500A) Proline residue: B1940 - end of helix removed outlier: 3.529A pdb=" N ALA B1944 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1951 through 1966 removed outlier: 3.743A pdb=" N LEU B1956 " --> pdb=" O LEU B1952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1969 through 1971 No H-bonds generated for 'chain 'B' and resid 1969 through 1971' Processing helix chain 'B' and resid 1973 through 1980 Processing helix chain 'B' and resid 1985 through 2001 removed outlier: 4.029A pdb=" N GLU B2000 " --> pdb=" O LYS B1996 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS B2001 " --> pdb=" O ASN B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2004 through 2020 Processing helix chain 'B' and resid 2023 through 2038 Processing helix chain 'B' and resid 2044 through 2060 Proline residue: B2053 - end of helix removed outlier: 3.777A pdb=" N ARG B2060 " --> pdb=" O ALA B2056 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2073 Processing helix chain 'B' and resid 2075 through 2090 removed outlier: 3.714A pdb=" N LYS B2090 " --> pdb=" O ARG B2086 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2117 removed outlier: 3.752A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Proline residue: B2116 - end of helix Processing helix chain 'B' and resid 2123 through 2126 No H-bonds generated for 'chain 'B' and resid 2123 through 2126' Processing helix chain 'B' and resid 2128 through 2132 Processing helix chain 'B' and resid 2193 through 2211 Processing helix chain 'B' and resid 2213 through 2218 Processing helix chain 'B' and resid 2246 through 2256 Processing helix chain 'B' and resid 2263 through 2271 Processing helix chain 'B' and resid 2275 through 2277 No H-bonds generated for 'chain 'B' and resid 2275 through 2277' Processing helix chain 'B' and resid 2280 through 2292 Processing helix chain 'B' and resid 2298 through 2306 Processing helix chain 'B' and resid 2310 through 2334 removed outlier: 3.514A pdb=" N ASP B2315 " --> pdb=" O GLU B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2364 through 2367 No H-bonds generated for 'chain 'B' and resid 2364 through 2367' Processing helix chain 'B' and resid 2381 through 2386 Processing helix chain 'B' and resid 2395 through 2409 Processing helix chain 'B' and resid 2411 through 2423 removed outlier: 3.598A pdb=" N PHE B2421 " --> pdb=" O VAL B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2426 through 2434 removed outlier: 4.145A pdb=" N TRP B2429 " --> pdb=" O LEU B2426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B2430 " --> pdb=" O LEU B2427 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2509 Processing helix chain 'B' and resid 2521 through 2533 Processing helix chain 'B' and resid 2535 through 2540 removed outlier: 3.729A pdb=" N GLN B2540 " --> pdb=" O GLU B2536 " (cutoff:3.500A) Processing helix chain 'B' and resid 2543 through 2545 No H-bonds generated for 'chain 'B' and resid 2543 through 2545' Processing helix chain 'F' and resid 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 33 through 36 No H-bonds generated for 'chain 'F' and resid 33 through 36' Processing helix chain 'F' and resid 95 through 113 removed outlier: 4.066A pdb=" N TRP F 113 " --> pdb=" O GLN F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 140 Processing helix chain 'F' and resid 179 through 185 Processing helix chain 'F' and resid 199 through 218 removed outlier: 3.692A pdb=" N GLU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 268 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 282 through 284 No H-bonds generated for 'chain 'F' and resid 282 through 284' Processing helix chain 'F' and resid 292 through 296 Processing helix chain 'F' and resid 308 through 327 Processing helix chain 'F' and resid 330 through 337 Processing helix chain 'F' and resid 341 through 360 removed outlier: 3.849A pdb=" N LEU F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 359 " --> pdb=" O ARG F 355 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR F 360 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 391 removed outlier: 3.758A pdb=" N ALA F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 408 through 422 removed outlier: 3.968A pdb=" N MET F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 441 Proline residue: F 434 - end of helix Processing helix chain 'F' and resid 446 through 459 removed outlier: 3.543A pdb=" N LEU F 459 " --> pdb=" O ARG F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'F' and resid 473 through 481 removed outlier: 3.813A pdb=" N LEU F 480 " --> pdb=" O VAL F 476 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN F 481 " --> pdb=" O LEU F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 501 Proline residue: F 489 - end of helix removed outlier: 3.502A pdb=" N VAL F 501 " --> pdb=" O LYS F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 511 removed outlier: 3.570A pdb=" N LEU F 509 " --> pdb=" O GLN F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 522 removed outlier: 3.511A pdb=" N VAL F 521 " --> pdb=" O TYR F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 542 Processing helix chain 'F' and resid 547 through 555 Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'F' and resid 571 through 584 Processing helix chain 'F' and resid 589 through 598 Processing helix chain 'F' and resid 600 through 604 Processing helix chain 'F' and resid 607 through 609 No H-bonds generated for 'chain 'F' and resid 607 through 609' Processing helix chain 'F' and resid 613 through 629 removed outlier: 3.904A pdb=" N ASN F 629 " --> pdb=" O THR F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 648 Processing helix chain 'F' and resid 657 through 673 removed outlier: 3.531A pdb=" N LEU F 670 " --> pdb=" O ALA F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 684 removed outlier: 3.668A pdb=" N THR F 680 " --> pdb=" O SER F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 819 Processing helix chain 'F' and resid 824 through 838 removed outlier: 3.529A pdb=" N ILE F 837 " --> pdb=" O VAL F 833 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 838 " --> pdb=" O LEU F 834 " (cutoff:3.500A) Processing helix chain 'F' and resid 959 through 968 removed outlier: 4.023A pdb=" N TYR F 966 " --> pdb=" O TRP F 962 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE F 967 " --> pdb=" O SER F 963 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 968 " --> pdb=" O ALA F 964 " (cutoff:3.500A) Processing helix chain 'F' and resid 983 through 1007 Processing helix chain 'J' and resid 360 through 363 No H-bonds generated for 'chain 'J' and resid 360 through 363' Processing helix chain 'J' and resid 385 through 394 Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.829A pdb=" N UNK A 52 " --> pdb=" O UNK A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 83 through 97 removed outlier: 3.538A pdb=" N SER A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.234A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.586A pdb=" N ALA A 142 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 146 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.520A pdb=" N GLN A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.746A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.742A pdb=" N VAL A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.575A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.765A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.603A pdb=" N UNK A 369 " --> pdb=" O UNK A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 387 through 402 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 410 through 425 removed outlier: 3.689A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.628A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 removed outlier: 3.583A pdb=" N VAL A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Proline residue: A 453 - end of helix removed outlier: 3.903A pdb=" N LEU A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 463 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.574A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.735A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 681 through 687 removed outlier: 4.584A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 687 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 701 removed outlier: 3.564A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 Processing helix chain 'A' and resid 723 through 742 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'A' and resid 765 through 783 Proline residue: A 770 - end of helix removed outlier: 5.319A pdb=" N GLU A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Proline residue: A 774 - end of helix Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.858A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 removed outlier: 4.726A pdb=" N ASP A 818 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 821 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 828 " --> pdb=" O MET A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.795A pdb=" N LEU A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 868 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 869 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 871 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 removed outlier: 3.541A pdb=" N LEU A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 934 through 940 Processing helix chain 'A' and resid 943 through 959 Proline residue: A 948 - end of helix removed outlier: 3.782A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 966 Processing helix chain 'A' and resid 968 through 982 removed outlier: 3.632A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1003 removed outlier: 3.529A pdb=" N VAL A 987 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Proline residue: A 991 - end of helix removed outlier: 4.583A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 3.589A pdb=" N LEU A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1041 removed outlier: 3.537A pdb=" N LEU A1016 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A1024 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER A1025 " --> pdb=" O PHE A1022 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 4.400A pdb=" N ASP A1032 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1083 removed outlier: 6.993A pdb=" N GLY A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR A1070 " --> pdb=" O GLU A1066 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix removed outlier: 3.517A pdb=" N PHE A1082 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1123 removed outlier: 3.736A pdb=" N ILE A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A1092 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A1095 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A1101 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A1104 " --> pdb=" O GLN A1101 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA A1105 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP A1109 " --> pdb=" O ASN A1106 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1111 " --> pdb=" O ASP A1108 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HIS A1112 " --> pdb=" O ASP A1109 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A1115 " --> pdb=" O HIS A1112 " (cutoff:3.500A) Proline residue: A1116 - end of helix removed outlier: 3.669A pdb=" N ASP A1123 " --> pdb=" O LYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.538A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1170 through 1202 removed outlier: 6.884A pdb=" N LYS A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN A1189 " --> pdb=" O GLY A1185 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE A1190 " --> pdb=" O LYS A1186 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.614A pdb=" N HIS A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1264 through 1269 Processing helix chain 'A' and resid 1277 through 1294 Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 4.024A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1318 through 1328 removed outlier: 3.516A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1346 Processing helix chain 'A' and resid 1351 through 1366 Processing helix chain 'A' and resid 1377 through 1379 No H-bonds generated for 'chain 'A' and resid 1377 through 1379' Processing helix chain 'A' and resid 1382 through 1389 Processing helix chain 'A' and resid 1393 through 1406 Processing helix chain 'A' and resid 1410 through 1422 Processing helix chain 'A' and resid 1426 through 1440 Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'A' and resid 1456 through 1469 Processing helix chain 'A' and resid 1474 through 1487 Processing helix chain 'A' and resid 1490 through 1499 Processing helix chain 'A' and resid 1506 through 1523 removed outlier: 3.517A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.604A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 Processing helix chain 'A' and resid 1557 through 1607 removed outlier: 4.543A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A1582 " --> pdb=" O MET A1578 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR A1583 " --> pdb=" O ALA A1579 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER A1584 " --> pdb=" O GLY A1580 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A1586 " --> pdb=" O SER A1582 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A1604 " --> pdb=" O GLU A1600 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1625 removed outlier: 3.600A pdb=" N ARG A1612 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A1613 " --> pdb=" O GLU A1610 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A1616 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A1624 " --> pdb=" O GLU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1642 removed outlier: 3.709A pdb=" N LEU A1642 " --> pdb=" O MET A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1648 No H-bonds generated for 'chain 'A' and resid 1646 through 1648' Processing helix chain 'A' and resid 1650 through 1662 Processing helix chain 'A' and resid 1666 through 1677 Processing helix chain 'A' and resid 1694 through 1706 removed outlier: 3.511A pdb=" N LYS A1706 " --> pdb=" O LYS A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1731 Processing helix chain 'A' and resid 1738 through 1761 Processing helix chain 'A' and resid 1766 through 1782 Proline residue: A1770 - end of helix Processing helix chain 'A' and resid 1787 through 1811 Processing helix chain 'A' and resid 1868 through 1895 removed outlier: 3.569A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix Processing helix chain 'A' and resid 1900 through 1913 Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1934 through 1945 removed outlier: 3.588A pdb=" N ILE A1939 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Proline residue: A1940 - end of helix removed outlier: 3.530A pdb=" N ALA A1944 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1966 removed outlier: 3.743A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1971 No H-bonds generated for 'chain 'A' and resid 1969 through 1971' Processing helix chain 'A' and resid 1973 through 1980 Processing helix chain 'A' and resid 1985 through 2001 removed outlier: 4.029A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2020 Processing helix chain 'A' and resid 2023 through 2038 Processing helix chain 'A' and resid 2044 through 2060 Proline residue: A2053 - end of helix removed outlier: 3.778A pdb=" N ARG A2060 " --> pdb=" O ALA A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2073 Processing helix chain 'A' and resid 2075 through 2090 removed outlier: 3.713A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2117 removed outlier: 3.752A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Proline residue: A2116 - end of helix Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2128 through 2132 Processing helix chain 'A' and resid 2193 through 2211 Processing helix chain 'A' and resid 2213 through 2218 Processing helix chain 'A' and resid 2246 through 2256 Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2275 through 2277 No H-bonds generated for 'chain 'A' and resid 2275 through 2277' Processing helix chain 'A' and resid 2280 through 2292 Processing helix chain 'A' and resid 2298 through 2306 Processing helix chain 'A' and resid 2310 through 2334 removed outlier: 3.514A pdb=" N ASP A2315 " --> pdb=" O GLU A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2364 through 2367 No H-bonds generated for 'chain 'A' and resid 2364 through 2367' Processing helix chain 'A' and resid 2381 through 2386 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2423 removed outlier: 3.599A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2434 removed outlier: 4.145A pdb=" N TRP A2429 " --> pdb=" O LEU A2426 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A2430 " --> pdb=" O LEU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2509 Processing helix chain 'A' and resid 2521 through 2533 Processing helix chain 'A' and resid 2535 through 2540 removed outlier: 3.730A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 33 through 36 No H-bonds generated for 'chain 'E' and resid 33 through 36' Processing helix chain 'E' and resid 95 through 113 removed outlier: 4.066A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'E' and resid 199 through 218 removed outlier: 3.692A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 268 Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'E' and resid 292 through 296 Processing helix chain 'E' and resid 308 through 327 Processing helix chain 'E' and resid 330 through 337 Processing helix chain 'E' and resid 341 through 360 removed outlier: 3.848A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR E 360 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.758A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 397 Processing helix chain 'E' and resid 408 through 422 removed outlier: 3.967A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 441 Proline residue: E 434 - end of helix Processing helix chain 'E' and resid 446 through 459 removed outlier: 3.543A pdb=" N LEU E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'E' and resid 473 through 481 removed outlier: 3.812A pdb=" N LEU E 480 " --> pdb=" O VAL E 476 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 501 Proline residue: E 489 - end of helix removed outlier: 3.502A pdb=" N VAL E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 511 removed outlier: 3.569A pdb=" N LEU E 509 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.509A pdb=" N VAL E 521 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 542 Processing helix chain 'E' and resid 547 through 555 Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'E' and resid 571 through 584 Processing helix chain 'E' and resid 589 through 598 Processing helix chain 'E' and resid 600 through 604 Processing helix chain 'E' and resid 607 through 609 No H-bonds generated for 'chain 'E' and resid 607 through 609' Processing helix chain 'E' and resid 613 through 629 removed outlier: 3.903A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 648 Processing helix chain 'E' and resid 657 through 673 removed outlier: 3.532A pdb=" N LEU E 670 " --> pdb=" O ALA E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 684 removed outlier: 3.669A pdb=" N THR E 680 " --> pdb=" O SER E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 819 Processing helix chain 'E' and resid 824 through 838 removed outlier: 3.529A pdb=" N ILE E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 968 removed outlier: 4.024A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 1007 Processing helix chain 'I' and resid 360 through 363 No H-bonds generated for 'chain 'I' and resid 360 through 363' Processing helix chain 'I' and resid 385 through 394 Processing sheet with id= A, first strand: chain 'B' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'B' and resid 2181 through 2183 removed outlier: 3.547A pdb=" N SER B2155 " --> pdb=" O MET B2175 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 2184 through 2187 Processing sheet with id= D, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id= E, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.098A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 18 " --> pdb=" O CYS D 317 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 47 through 50 Processing sheet with id= G, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.586A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 123 through 126 removed outlier: 3.978A pdb=" N ARG D 123 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY D 104 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 110 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 102 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 134 through 136 Processing sheet with id= J, first strand: chain 'D' and resid 215 through 217 removed outlier: 4.219A pdb=" N ASN D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN D 189 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 175 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 197 through 199 Processing sheet with id= L, first strand: chain 'D' and resid 223 through 228 removed outlier: 6.690A pdb=" N CYS D 238 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS D 226 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA D 236 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 228 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU D 234 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER D 239 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 256 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 284 through 288 removed outlier: 6.722A pdb=" N CYS D 298 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 304 " --> pdb=" O CYS D 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 118 through 123 removed outlier: 3.632A pdb=" N LEU F 62 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 163 through 167 Processing sheet with id= P, first strand: chain 'F' and resid 1019 through 1021 removed outlier: 3.642A pdb=" N ASN F1020 " --> pdb=" O ILE F1325 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER F1326 " --> pdb=" O VAL F1318 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL F1318 " --> pdb=" O SER F1326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS F1306 " --> pdb=" O GLY F1319 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 1028 through 1031 removed outlier: 4.230A pdb=" N VAL F1028 " --> pdb=" O ALA F1041 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F1039 " --> pdb=" O LYS F1030 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F1046 " --> pdb=" O PHE F1060 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP F1058 " --> pdb=" O PHE F1048 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 1070 through 1073 removed outlier: 3.708A pdb=" N THR F1071 " --> pdb=" O ALA F1087 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA F1087 " --> pdb=" O THR F1071 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N MET F1073 " --> pdb=" O LEU F1085 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU F1085 " --> pdb=" O MET F1073 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA F1092 " --> pdb=" O THR F1088 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR F1110 " --> pdb=" O VAL F1095 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS F1097 " --> pdb=" O MET F1108 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET F1108 " --> pdb=" O LYS F1097 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 1181 through 1184 removed outlier: 4.186A pdb=" N TYR F1207 " --> pdb=" O ILE F1190 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET F1205 " --> pdb=" O VAL F1192 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 1227 through 1230 removed outlier: 3.883A pdb=" N SER F1229 " --> pdb=" O ARG F1237 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN F1248 " --> pdb=" O ILE F1238 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 1267 through 1269 removed outlier: 3.652A pdb=" N TYR F1280 " --> pdb=" O ILE F1268 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN F1288 " --> pdb=" O ILE F1279 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN F1281 " --> pdb=" O LEU F1286 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU F1286 " --> pdb=" O ASN F1281 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 1146 through 1151 removed outlier: 3.927A pdb=" N GLN F1159 " --> pdb=" O ILE F1149 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F1151 " --> pdb=" O LYS F1157 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS F1157 " --> pdb=" O ASP F1151 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 329 through 333 Processing sheet with id= X, first strand: chain 'J' and resid 342 through 344 Processing sheet with id= Y, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= Z, first strand: chain 'A' and resid 2181 through 2183 removed outlier: 3.547A pdb=" N SER A2155 " --> pdb=" O MET A2175 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 2184 through 2187 Processing sheet with id= AB, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id= AC, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.097A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= AE, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.586A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 123 through 126 removed outlier: 3.977A pdb=" N ARG C 123 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 110 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 102 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 134 through 136 Processing sheet with id= AH, first strand: chain 'C' and resid 215 through 217 removed outlier: 4.220A pdb=" N ASN C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 189 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 197 through 199 Processing sheet with id= AJ, first strand: chain 'C' and resid 223 through 228 removed outlier: 6.691A pdb=" N CYS C 238 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS C 226 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA C 236 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 228 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU C 234 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 284 through 288 removed outlier: 6.721A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 118 through 123 removed outlier: 3.632A pdb=" N LEU E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 163 through 167 Processing sheet with id= AN, first strand: chain 'E' and resid 1019 through 1021 removed outlier: 3.640A pdb=" N ASN E1020 " --> pdb=" O ILE E1325 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E1326 " --> pdb=" O VAL E1318 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E1318 " --> pdb=" O SER E1326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS E1306 " --> pdb=" O GLY E1319 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 4.229A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E1039 " --> pdb=" O LYS E1030 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE E1046 " --> pdb=" O PHE E1060 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 1070 through 1073 removed outlier: 3.707A pdb=" N THR E1071 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA E1087 " --> pdb=" O THR E1071 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N MET E1073 " --> pdb=" O LEU E1085 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU E1085 " --> pdb=" O MET E1073 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR E1110 " --> pdb=" O VAL E1095 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E1097 " --> pdb=" O MET E1108 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET E1108 " --> pdb=" O LYS E1097 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 1181 through 1184 removed outlier: 4.186A pdb=" N TYR E1207 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET E1205 " --> pdb=" O VAL E1192 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 1227 through 1230 removed outlier: 3.882A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 1267 through 1269 removed outlier: 3.653A pdb=" N TYR E1280 " --> pdb=" O ILE E1268 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN E1281 " --> pdb=" O LEU E1286 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU E1286 " --> pdb=" O ASN E1281 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'E' and resid 1146 through 1151 removed outlier: 3.927A pdb=" N GLN E1159 " --> pdb=" O ILE E1149 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP E1151 " --> pdb=" O LYS E1157 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS E1157 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 329 through 333 Processing sheet with id= AV, first strand: chain 'I' and resid 342 through 344 2817 hydrogen bonds defined for protein. 7662 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: 23.98 Time building geometry restraints manager: 18.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 19162 1.34 - 1.46: 12172 1.46 - 1.58: 27530 1.58 - 1.69: 12 1.69 - 1.81: 616 Bond restraints: 59492 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.597 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O12 IHP B2601 " pdb=" P2 IHP B2601 " ideal model delta sigma weight residual 1.675 1.597 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.602 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O14 IHP B2601 " pdb=" P4 IHP B2601 " ideal model delta sigma weight residual 1.671 1.602 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C5 IHP B2601 " pdb=" O15 IHP B2601 " ideal model delta sigma weight residual 1.389 1.445 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 59487 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.08: 1905 107.08 - 113.82: 33791 113.82 - 120.56: 22623 120.56 - 127.30: 21621 127.30 - 134.04: 802 Bond angle restraints: 80742 Sorted by residual: angle pdb=" N VAL F1330 " pdb=" CA VAL F1330 " pdb=" C VAL F1330 " ideal model delta sigma weight residual 106.21 109.19 -2.98 1.07e+00 8.73e-01 7.76e+00 angle pdb=" C GLY I 323 " pdb=" N ALA I 324 " pdb=" CA ALA I 324 " ideal model delta sigma weight residual 121.80 128.53 -6.73 2.44e+00 1.68e-01 7.61e+00 angle pdb=" C GLY J 323 " pdb=" N ALA J 324 " pdb=" CA ALA J 324 " ideal model delta sigma weight residual 121.80 128.52 -6.72 2.44e+00 1.68e-01 7.59e+00 angle pdb=" N VAL E1330 " pdb=" CA VAL E1330 " pdb=" C VAL E1330 " ideal model delta sigma weight residual 106.21 109.14 -2.93 1.07e+00 8.73e-01 7.48e+00 angle pdb=" CA LYS B1024 " pdb=" CB LYS B1024 " pdb=" CG LYS B1024 " ideal model delta sigma weight residual 114.10 119.45 -5.35 2.00e+00 2.50e-01 7.15e+00 ... (remaining 80737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 32432 17.29 - 34.58: 2669 34.58 - 51.88: 658 51.88 - 69.17: 173 69.17 - 86.46: 34 Dihedral angle restraints: 35966 sinusoidal: 14508 harmonic: 21458 Sorted by residual: dihedral pdb=" CA PHE F1060 " pdb=" C PHE F1060 " pdb=" N HIS F1061 " pdb=" CA HIS F1061 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA I 324 " pdb=" C ALA I 324 " pdb=" N PRO I 325 " pdb=" CA PRO I 325 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 35963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 8076 0.058 - 0.116: 1014 0.116 - 0.175: 90 0.175 - 0.233: 2 0.233 - 0.291: 4 Chirality restraints: 9186 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.61 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 IHP B2601 " pdb=" C2 IHP B2601 " pdb=" C6 IHP B2601 " pdb=" O11 IHP B2601 " both_signs ideal model delta sigma weight residual False 2.32 2.61 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 9183 not shown) Planarity restraints: 10282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E1105 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO E1106 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E1106 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E1106 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F1105 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO F1106 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F1106 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F1106 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 324 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO J 325 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO J 325 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 325 " 0.032 5.00e-02 4.00e+02 ... (remaining 10279 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 9790 2.77 - 3.30: 57906 3.30 - 3.84: 95918 3.84 - 4.37: 113570 4.37 - 4.90: 192316 Nonbonded interactions: 469500 Sorted by model distance: nonbonded pdb=" O ASN B 701 " pdb=" OG SER A1153 " model vdw 2.239 2.440 nonbonded pdb=" OE1 GLU F 981 " pdb=" OG SER A 645 " model vdw 2.250 2.440 nonbonded pdb=" O ALA A1268 " pdb=" NE1 TRP A1283 " model vdw 2.255 2.520 nonbonded pdb=" O ALA B1268 " pdb=" NE1 TRP B1283 " model vdw 2.255 2.520 nonbonded pdb=" O LEU B1877 " pdb=" OG1 THR B1881 " model vdw 2.262 2.440 ... (remaining 469495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 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: 23.630 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 118.470 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.002 0.078 59492 Z= 0.141 Angle : 0.473 8.612 80742 Z= 0.245 Chirality : 0.038 0.291 9186 Planarity : 0.005 0.057 10282 Dihedral : 14.259 86.459 21982 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 4.24 % Allowed : 6.35 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.09), residues: 7118 helix: -1.32 (0.07), residues: 4168 sheet: -3.23 (0.16), residues: 720 loop : -1.37 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2023 HIS 0.006 0.001 HIS E1315 PHE 0.021 0.001 PHE B 610 TYR 0.011 0.001 TYR E 546 ARG 0.005 0.000 ARG B1161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1397 time to evaluate : 5.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 268 outliers final: 31 residues processed: 1587 average time/residue: 0.5805 time to fit residues: 1536.5327 Evaluate side-chains 709 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 678 time to evaluate : 5.071 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.4313 time to fit residues: 32.3745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 616 optimal weight: 7.9990 chunk 553 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 295 optimal weight: 0.3980 chunk 572 optimal weight: 0.0020 chunk 221 optimal weight: 0.4980 chunk 347 optimal weight: 0.0670 chunk 425 optimal weight: 5.9990 chunk 662 optimal weight: 0.2980 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN B1112 HIS B1157 HIS B1366 HIS B1425 GLN B1541 HIS B1730 HIS ** B1758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1968 HIS B2055 HIS ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN F 153 HIS F 326 ASN F1210 HIS ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 499 GLN ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 937 ASN A1165 GLN ** A1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1992 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2055 HIS A2289 HIS ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2293 ASN E 151 ASN E 326 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 810 GLN ** E1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 59492 Z= 0.200 Angle : 0.620 12.345 80742 Z= 0.314 Chirality : 0.042 0.211 9186 Planarity : 0.005 0.079 10282 Dihedral : 4.473 50.190 7996 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7118 helix: 0.62 (0.08), residues: 4182 sheet: -2.73 (0.17), residues: 690 loop : -1.01 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 585 HIS 0.012 0.001 HIS B 609 PHE 0.029 0.002 PHE B 610 TYR 0.026 0.001 TYR B 853 ARG 0.017 0.001 ARG F 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 873 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 877 average time/residue: 0.5802 time to fit residues: 863.8206 Evaluate side-chains 566 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 5.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 368 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 551 optimal weight: 6.9990 chunk 451 optimal weight: 0.0970 chunk 182 optimal weight: 1.9990 chunk 664 optimal weight: 0.1980 chunk 717 optimal weight: 8.9990 chunk 591 optimal weight: 0.0020 chunk 658 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 532 optimal weight: 0.5980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1366 HIS B1424 GLN B1494 HIS B1541 HIS B1758 GLN B1968 HIS ** B2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 39 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN F 515 HIS F 586 GLN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 GLN ** A1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2117 GLN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 59492 Z= 0.175 Angle : 0.567 13.719 80742 Z= 0.285 Chirality : 0.040 0.184 9186 Planarity : 0.004 0.082 10282 Dihedral : 4.308 50.067 7996 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7118 helix: 1.08 (0.08), residues: 4150 sheet: -2.35 (0.18), residues: 686 loop : -0.89 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 297 HIS 0.013 0.001 HIS B2401 PHE 0.025 0.001 PHE A1122 TYR 0.025 0.001 TYR B1030 ARG 0.006 0.000 ARG F 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 746 time to evaluate : 5.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 748 average time/residue: 0.5558 time to fit residues: 719.7468 Evaluate side-chains 530 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 5.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 656 optimal weight: 2.9990 chunk 499 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 445 optimal weight: 0.9990 chunk 666 optimal weight: 0.8980 chunk 705 optimal weight: 40.0000 chunk 348 optimal weight: 4.9990 chunk 631 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 HIS B 701 ASN B1084 HIS B1366 HIS ** B1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1541 HIS B1774 GLN ** B2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2265 HIS ** B2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 225 GLN F 35 HIS F 149 HIS F 153 HIS F 198 ASN F 586 GLN F1098 ASN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS A 878 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1719 HIS ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 ASN E1003 GLN ** E1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 59492 Z= 0.249 Angle : 0.626 11.459 80742 Z= 0.316 Chirality : 0.042 0.216 9186 Planarity : 0.005 0.077 10282 Dihedral : 4.421 53.492 7996 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.10), residues: 7118 helix: 1.14 (0.08), residues: 4178 sheet: -1.94 (0.18), residues: 696 loop : -0.76 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 277 HIS 0.011 0.001 HIS B2355 PHE 0.044 0.002 PHE I 331 TYR 0.019 0.002 TYR B1151 ARG 0.014 0.001 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 688 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.5759 time to fit residues: 683.8003 Evaluate side-chains 485 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 5.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 587 optimal weight: 8.9990 chunk 400 optimal weight: 1.9990 chunk 10 optimal weight: 40.0000 chunk 525 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 602 optimal weight: 7.9990 chunk 487 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 360 optimal weight: 1.9990 chunk 633 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN B 609 HIS B1206 HIS B1541 HIS B1791 HIS B1968 HIS ** B2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2154 GLN ** B2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS F 326 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 586 GLN F1098 ASN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A1026 HIS A1165 GLN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1077 ASN E1210 HIS ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 59492 Z= 0.202 Angle : 0.570 15.383 80742 Z= 0.287 Chirality : 0.040 0.167 9186 Planarity : 0.004 0.067 10282 Dihedral : 4.312 54.857 7996 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 0.02 % Allowed : 1.98 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.10), residues: 7118 helix: 1.31 (0.08), residues: 4168 sheet: -1.70 (0.18), residues: 690 loop : -0.73 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP F 585 HIS 0.008 0.001 HIS B2401 PHE 0.026 0.001 PHE B1122 TYR 0.017 0.001 TYR B1450 ARG 0.005 0.000 ARG A2060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 673 time to evaluate : 5.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 674 average time/residue: 0.5786 time to fit residues: 673.7194 Evaluate side-chains 492 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 5.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 237 optimal weight: 10.0000 chunk 635 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 414 optimal weight: 0.0870 chunk 174 optimal weight: 5.9990 chunk 706 optimal weight: 7.9990 chunk 586 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 370 optimal weight: 7.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 HIS B1026 HIS B1541 HIS B1968 HIS B2043 ASN ** B2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS F 326 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN F1098 ASN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A1157 HIS ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1541 HIS A1758 GLN A1809 GLN ** A1992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59492 Z= 0.201 Angle : 0.572 8.708 80742 Z= 0.287 Chirality : 0.041 0.234 9186 Planarity : 0.004 0.078 10282 Dihedral : 4.288 56.147 7996 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 7118 helix: 1.40 (0.08), residues: 4140 sheet: -1.49 (0.18), residues: 708 loop : -0.69 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 585 HIS 0.014 0.001 HIS B2355 PHE 0.026 0.001 PHE B1122 TYR 0.029 0.001 TYR A2275 ARG 0.007 0.000 ARG B1514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 5.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.5695 time to fit residues: 646.5119 Evaluate side-chains 472 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 5.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 680 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 402 optimal weight: 0.9980 chunk 515 optimal weight: 0.7980 chunk 399 optimal weight: 4.9990 chunk 594 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 703 optimal weight: 9.9990 chunk 440 optimal weight: 6.9990 chunk 428 optimal weight: 0.7980 chunk 324 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 HIS B1541 HIS B1809 GLN B1968 HIS B1989 ASN ** B2293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS F 326 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN F 978 HIS F1098 ASN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 609 HIS A 701 ASN A 967 HIS A1026 HIS ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2003 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN E1098 ASN ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 59492 Z= 0.168 Angle : 0.565 12.738 80742 Z= 0.282 Chirality : 0.040 0.210 9186 Planarity : 0.004 0.066 10282 Dihedral : 4.223 56.469 7996 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 0.02 % Allowed : 1.06 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 7118 helix: 1.45 (0.08), residues: 4132 sheet: -1.33 (0.18), residues: 708 loop : -0.67 (0.14), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 585 HIS 0.013 0.001 HIS A 609 PHE 0.032 0.001 PHE B1363 TYR 0.019 0.001 TYR B1151 ARG 0.006 0.000 ARG B1285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 650 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 651 average time/residue: 0.5678 time to fit residues: 639.3466 Evaluate side-chains 476 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 5.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 435 optimal weight: 0.9980 chunk 280 optimal weight: 0.9980 chunk 420 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 447 optimal weight: 2.9990 chunk 479 optimal weight: 4.9990 chunk 347 optimal weight: 7.9990 chunk 65 optimal weight: 0.0040 chunk 553 optimal weight: 0.0170 overall best weight: 0.5430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN ** B1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1809 GLN ** B2293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS F 326 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN ** F1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1098 ASN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 59492 Z= 0.158 Angle : 0.562 11.530 80742 Z= 0.280 Chirality : 0.040 0.203 9186 Planarity : 0.004 0.066 10282 Dihedral : 4.170 56.368 7996 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7118 helix: 1.48 (0.08), residues: 4106 sheet: -1.23 (0.18), residues: 714 loop : -0.67 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2545 HIS 0.009 0.001 HIS B1744 PHE 0.027 0.001 PHE B1122 TYR 0.022 0.001 TYR A 673 ARG 0.006 0.000 ARG B1285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 5.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.5662 time to fit residues: 629.7037 Evaluate side-chains 483 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 5.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 640 optimal weight: 3.9990 chunk 674 optimal weight: 20.0000 chunk 614 optimal weight: 10.0000 chunk 655 optimal weight: 0.7980 chunk 673 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 514 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 592 optimal weight: 0.9990 chunk 620 optimal weight: 0.0040 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN B1541 HIS ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1968 HIS ** B2293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2343 ASN ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS F 326 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN F1098 ASN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 HIS ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59492 Z= 0.163 Angle : 0.563 11.603 80742 Z= 0.280 Chirality : 0.040 0.247 9186 Planarity : 0.004 0.066 10282 Dihedral : 4.132 56.612 7996 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 7118 helix: 1.52 (0.08), residues: 4108 sheet: -1.06 (0.19), residues: 700 loop : -0.68 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP E 585 HIS 0.015 0.001 HIS A1988 PHE 0.027 0.001 PHE A 610 TYR 0.021 0.001 TYR A 673 ARG 0.013 0.000 ARG B1651 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 632 time to evaluate : 5.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.5960 time to fit residues: 656.2180 Evaluate side-chains 479 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 5.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 653 optimal weight: 0.0060 chunk 430 optimal weight: 2.9990 chunk 693 optimal weight: 8.9990 chunk 423 optimal weight: 0.8980 chunk 328 optimal weight: 3.9990 chunk 481 optimal weight: 3.9990 chunk 727 optimal weight: 2.9990 chunk 669 optimal weight: 2.9990 chunk 579 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 447 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 269 ASN B 646 GLN B1541 HIS B1803 HIS B1809 GLN B1968 HIS ** B2293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 59492 Z= 0.185 Angle : 0.576 13.646 80742 Z= 0.287 Chirality : 0.040 0.251 9186 Planarity : 0.004 0.072 10282 Dihedral : 4.143 57.343 7996 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 7118 helix: 1.52 (0.08), residues: 4106 sheet: -1.00 (0.19), residues: 698 loop : -0.64 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 585 HIS 0.011 0.001 HIS B2355 PHE 0.027 0.001 PHE A 610 TYR 0.015 0.001 TYR A2038 ARG 0.008 0.000 ARG B1651 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14236 Ramachandran restraints generated. 7118 Oldfield, 0 Emsley, 7118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 5.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.5963 time to fit residues: 642.6699 Evaluate side-chains 463 residues out of total 6328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 5.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 730 random chunks: chunk 355 optimal weight: 0.0570 chunk 460 optimal weight: 0.6980 chunk 616 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 533 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 580 optimal weight: 5.9990 chunk 242 optimal weight: 0.0370 chunk 595 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 269 ASN B1541 HIS ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1968 HIS ** B2293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 153 HIS F 326 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.091761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070758 restraints weight = 341124.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.072360 restraints weight = 198536.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072986 restraints weight = 131742.174| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 59492 Z= 0.153 Angle : 0.558 10.261 80742 Z= 0.278 Chirality : 0.040 0.250 9186 Planarity : 0.004 0.066 10282 Dihedral : 4.097 57.491 7996 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.10), residues: 7118 helix: 1.52 (0.08), residues: 4112 sheet: -0.89 (0.19), residues: 696 loop : -0.63 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP E 585 HIS 0.007 0.001 HIS B2355 PHE 0.037 0.001 PHE B1889 TYR 0.014 0.001 TYR E1323 ARG 0.015 0.000 ARG A 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12693.82 seconds wall clock time: 224 minutes 39.04 seconds (13479.04 seconds total)