Starting phenix.real_space_refine on Mon Sep 14 16:37:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.cif" model { file = "/net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7chw_30376/09_2026/7chw_30376.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 131 5.16 5 C 19551 2.51 5 N 5623 2.21 5 O 6333 1.98 5 H 529 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.25s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32282 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1312 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "K" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1046 Classifications: {'peptide': 67} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10561 Classifications: {'peptide': 1339} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain breaks: 1 Chain: "D" Number of atoms: 10363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10363 Classifications: {'peptide': 1343} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 55, 'TRANS': 1287} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain breaks: 2 Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3845 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 14, 'TRANS': 457} Chain breaks: 2 Chain: "G" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 992 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16933 SG CYS D 70 116.388 84.361 69.816 1.00 9.43 S ATOM 16947 SG CYS D 72 117.380 83.406 66.626 1.00 11.87 S ATOM 17055 SG CYS D 85 119.879 84.047 69.740 1.00 18.96 S ATOM 22726 SG CYS D 814 84.595 102.674 127.210 1.00 10.30 S ATOM 23289 SG CYS D 888 84.406 103.233 123.754 1.00 11.55 S ATOM 23340 SG CYS D 895 82.237 99.674 125.106 1.00 4.80 S ATOM 23361 SG CYS D 898 81.427 103.044 125.450 1.00 4.80 S Time building chain proxies: 6.66, per 1000 atoms: 0.21 Number of scatterers: 32282 At special positions: 0 Unit cell: (175.138, 196.05, 159.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 131 16.00 P 112 15.00 Mg 1 11.99 O 6333 8.00 N 5623 7.00 C 19551 6.00 H 529 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " Number of angles added : 6 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 53 sheets defined 36.2% alpha, 10.4% beta 19 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'K' and resid 257 through 261 removed outlier: 4.314A pdb=" N LEU K 260 " --> pdb=" O VAL K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 271 removed outlier: 4.103A pdb=" N CYS K 269 " --> pdb=" O ARG K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 274 No H-bonds generated for 'chain 'K' and resid 272 through 274' Processing helix chain 'K' and resid 277 through 284 Processing helix chain 'K' and resid 299 through 309 removed outlier: 3.892A pdb=" N ILE K 303 " --> pdb=" O SER K 299 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP K 305 " --> pdb=" O THR K 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.773A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.796A pdb=" N LEU A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.745A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.536A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.575A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 233' Processing helix chain 'B' and resid 36 through 50 removed outlier: 4.054A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.652A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 4.353A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.922A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 28 through 35 removed outlier: 3.764A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 84 through 89 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.718A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.888A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.749A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.580A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.993A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.950A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 removed outlier: 4.332A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 3.586A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.820A pdb=" N HIS C 554 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 551 through 555' Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.518A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 613' Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.799A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 683 removed outlier: 3.590A pdb=" N ALA C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.515A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 905 Processing helix chain 'C' and resid 944 through 952 removed outlier: 3.517A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 966 removed outlier: 3.519A pdb=" N ALA C 956 " --> pdb=" O GLN C 952 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 979 removed outlier: 4.142A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1033 removed outlier: 3.963A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1038 removed outlier: 3.534A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.997A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1114 removed outlier: 3.700A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1122 removed outlier: 3.516A pdb=" N ALA C1121 " --> pdb=" O LEU C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1132 removed outlier: 4.012A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1148 removed outlier: 3.520A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1176 removed outlier: 3.940A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.818A pdb=" N LYS C1196 " --> pdb=" O GLU C1192 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C1197 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 1275 through 1280 Processing helix chain 'C' and resid 1283 through 1291 removed outlier: 3.624A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C1289 " --> pdb=" O TYR C1285 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) Processing helix chain 'C' and resid 1302 through 1310 removed outlier: 3.739A pdb=" N ILE C1308 " --> pdb=" O MET C1304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.947A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C1329 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.589A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.556A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.546A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 163 through 172 removed outlier: 3.877A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.554A pdb=" N ALA D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 200 through 208 removed outlier: 3.721A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 228 removed outlier: 4.035A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.878A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.611A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 308 removed outlier: 3.651A pdb=" N LYS D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.798A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.589A pdb=" N LEU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.671A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 404 removed outlier: 3.674A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.714A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.681A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 538 removed outlier: 3.678A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.627A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.646A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 622 through 634 removed outlier: 3.632A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 660 removed outlier: 3.768A pdb=" N ALA D 657 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 670 removed outlier: 3.913A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 668 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 696 removed outlier: 4.039A pdb=" N ILE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'D' and resid 720 through 728 removed outlier: 4.021A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 741 removed outlier: 3.827A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.834A pdb=" N ILE D 774 " --> pdb=" O LEU D 770 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 removed outlier: 4.017A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 804 removed outlier: 3.685A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.736A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.542A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.709A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1223 removed outlier: 3.684A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1242 removed outlier: 3.777A pdb=" N TYR D1232 " --> pdb=" O ALA D1228 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1284 Processing helix chain 'D' and resid 1285 through 1290 Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 3.590A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1349 through 1354 removed outlier: 4.252A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1371 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.613A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.597A pdb=" N ALA E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.599A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.701A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.726A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.509A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 123 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU F 136 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 153 removed outlier: 3.822A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 232 removed outlier: 3.811A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 254 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 262 through 296 removed outlier: 4.370A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET F 277 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP F 278 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 279 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR F 282 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.639A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 324 through 330 removed outlier: 3.501A pdb=" N GLU F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 341 Processing helix chain 'F' and resid 341 through 352 removed outlier: 3.681A pdb=" N GLN F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 4.416A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS F 371 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.566A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 removed outlier: 3.505A pdb=" N GLU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.719A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 446 removed outlier: 4.916A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP F 445 " --> pdb=" O ARG F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.639A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 487 Processing helix chain 'F' and resid 493 through 498 removed outlier: 3.506A pdb=" N LEU F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 removed outlier: 4.028A pdb=" N GLU F 515 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.604A pdb=" N PHE F 522 " --> pdb=" O LEU F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 548 removed outlier: 3.737A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 563 Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.557A pdb=" N GLY F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 598 removed outlier: 4.556A pdb=" N ALA F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 611 removed outlier: 3.595A pdb=" N LEU F 611 " --> pdb=" O ARG F 608 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 5.625A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.517A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 103 removed outlier: 5.974A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.651A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'B' and resid 189 through 190 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.574A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 68 through 75 removed outlier: 5.316A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 68 through 75 removed outlier: 5.316A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.230A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC1, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC2, first strand: chain 'C' and resid 227 through 230 Processing sheet with id=AC3, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AC4, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.757A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.508A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.242A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC9, first strand: chain 'C' and resid 722 through 724 Processing sheet with id=AD1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.647A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD3, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.517A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 830 through 837 removed outlier: 6.931A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 830 through 837 removed outlier: 3.646A pdb=" N TYR C1053 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.844A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.580A pdb=" N ARG D 352 " --> pdb=" O HIS C1244 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 422 " --> pdb=" O HIS D 469 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.580A pdb=" N ARG D 352 " --> pdb=" O HIS C1244 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.522A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1336 through 1338 removed outlier: 3.565A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.845A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.772A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AE6, first strand: chain 'D' and resid 547 through 550 Processing sheet with id=AE7, first strand: chain 'D' and resid 553 through 554 removed outlier: 3.569A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AF1, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF2, first strand: chain 'D' and resid 957 through 958 removed outlier: 4.276A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AF4, first strand: chain 'D' and resid 1060 through 1061 removed outlier: 4.553A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1079 through 1080 removed outlier: 3.996A pdb=" N ALA D1097 " --> pdb=" O ILE D1080 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 4.103A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1174 through 1176 Processing sheet with id=AF8, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.357A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 801 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 528 1.03 - 1.23: 307 1.23 - 1.42: 12940 1.42 - 1.62: 18973 1.62 - 1.81: 230 Bond restraints: 32978 Sorted by residual: bond pdb=" C3' DG G 46 " pdb=" C2' DG G 46 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG G 58 " pdb=" C2' DG G 58 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG H 62 " pdb=" C2' DG H 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.62e+00 bond pdb=" C1' DT G 55 " pdb=" N1 DT G 55 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.32e+00 bond pdb=" C3' DC G 31 " pdb=" C2' DC G 31 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.25e+00 ... (remaining 32973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 44021 2.01 - 4.03: 1354 4.03 - 6.04: 106 6.04 - 8.05: 13 8.05 - 10.06: 3 Bond angle restraints: 45497 Sorted by residual: angle pdb=" N ASP C1160 " pdb=" CA ASP C1160 " pdb=" C ASP C1160 " ideal model delta sigma weight residual 110.41 120.30 -9.89 1.23e+00 6.61e-01 6.47e+01 angle pdb=" N GLY D 333 " pdb=" CA GLY D 333 " pdb=" C GLY D 333 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.17e+00 7.31e-01 2.98e+01 angle pdb=" N GLN C1157 " pdb=" CA GLN C1157 " pdb=" C GLN C1157 " ideal model delta sigma weight residual 111.36 117.13 -5.77 1.09e+00 8.42e-01 2.81e+01 angle pdb=" N VAL C1159 " pdb=" CA VAL C1159 " pdb=" C VAL C1159 " ideal model delta sigma weight residual 109.34 119.40 -10.06 2.08e+00 2.31e-01 2.34e+01 angle pdb=" O4' DG H 43 " pdb=" C4' DG H 43 " pdb=" C3' DG H 43 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 ... (remaining 45492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 18705 32.97 - 65.95: 1100 65.95 - 98.92: 62 98.92 - 131.90: 0 131.90 - 164.87: 2 Dihedral angle restraints: 19869 sinusoidal: 9050 harmonic: 10819 Sorted by residual: dihedral pdb=" CA PRO D 502 " pdb=" C PRO D 502 " pdb=" N SER D 503 " pdb=" CA SER D 503 " ideal model delta harmonic sigma weight residual 180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA SER D 119 " pdb=" C SER D 119 " pdb=" N LEU D 120 " pdb=" CA LEU D 120 " ideal model delta harmonic sigma weight residual 180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL C1159 " pdb=" C VAL C1159 " pdb=" N ASP C1160 " pdb=" CA ASP C1160 " ideal model delta harmonic sigma weight residual -180.00 -153.86 -26.14 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 19866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4393 0.069 - 0.137: 644 0.137 - 0.206: 13 0.206 - 0.275: 3 0.275 - 0.343: 2 Chirality restraints: 5055 Sorted by residual: chirality pdb=" CA ASP C1160 " pdb=" N ASP C1160 " pdb=" C ASP C1160 " pdb=" CB ASP C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA VAL E 32 " pdb=" N VAL E 32 " pdb=" C VAL E 32 " pdb=" CB VAL E 32 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA GLN C1157 " pdb=" N GLN C1157 " pdb=" C GLN C1157 " pdb=" CB GLN C1157 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 5052 not shown) Planarity restraints: 5452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO C 520 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C1156 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.74e+00 pdb=" C ARG C1156 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG C1156 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C1157 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C1103 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO C1104 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C1104 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C1104 " -0.034 5.00e-02 4.00e+02 ... (remaining 5449 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 438 2.35 - 2.92: 15548 2.92 - 3.48: 36713 3.48 - 4.04: 56450 4.04 - 4.60: 85458 Nonbonded interactions: 194607 Sorted by model distance: nonbonded pdb=" H GLU K 302 " pdb=" OP2 DT G 56 " model vdw 1.792 2.450 nonbonded pdb=" O LEU K 300 " pdb=" H ILE K 303 " model vdw 1.869 2.450 nonbonded pdb=" O ASP K 259 " pdb="HH12 ARG K 310 " model vdw 1.888 2.450 nonbonded pdb=" OD1 ASP C1160 " pdb=" N LEU C1161 " model vdw 1.911 2.950 nonbonded pdb=" O CYS K 269 " pdb=" H GLU K 273 " model vdw 1.969 2.450 ... (remaining 194602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 233) selection = (chain 'B' and resid 7 through 233) } 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.480 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.007 0.129 32456 Z= 0.370 Angle : 0.839 22.507 44292 Z= 0.540 Chirality : 0.046 0.343 5055 Planarity : 0.005 0.068 5391 Dihedral : 18.313 164.870 12739 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 28.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.89 % Favored : 89.01 % Rotamer: Outliers : 11.62 % Allowed : 12.56 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.67 (0.11), residues: 3720 helix: -4.61 (0.07), residues: 1250 sheet: -3.62 (0.21), residues: 394 loop : -3.30 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 346 TYR 0.016 0.002 TYR C 92 PHE 0.030 0.002 PHE D 62 TRP 0.007 0.002 TRP D1193 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.37 (32449) covalent geometry : angle 0.81334 / 0.54 (44286) hydrogen bonds : bond 0.33231 / 37.53 ( 830) hydrogen bonds : angle 11.82778 / 15.87 ( 2301) metal coordination : bond 0.07917 / 6.57 ( 7) metal coordination : angle 17.59829 / 32.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 885 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 371 poor density : 514 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1762 (OUTLIER) cc_final: 0.1344 (m-80) REVERT: K 316 MET cc_start: 0.2921 (mmp) cc_final: 0.2172 (tmm) REVERT: A 33 ARG cc_start: 0.7836 (tpm170) cc_final: 0.7617 (tpt-90) REVERT: A 80 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 150 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8707 (ptm-80) REVERT: A 177 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8760 (m-80) REVERT: B 17 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: B 29 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: B 98 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7816 (t) REVERT: B 172 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7582 (mp) REVERT: C 11 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8917 (mt) REVERT: C 46 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: C 60 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: C 80 PHE cc_start: 0.8200 (m-80) cc_final: 0.7989 (m-80) REVERT: C 158 ASP cc_start: 0.7162 (t0) cc_final: 0.6829 (t0) REVERT: C 197 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8070 (ptm160) REVERT: C 203 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8154 (pttt) REVERT: C 234 ASP cc_start: 0.5018 (OUTLIER) cc_final: 0.4725 (t0) REVERT: C 327 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: C 360 LEU cc_start: 0.8617 (tp) cc_final: 0.8353 (tp) REVERT: C 369 MET cc_start: 0.8247 (tmm) cc_final: 0.8020 (ttp) REVERT: C 413 GLU cc_start: 0.8087 (pm20) cc_final: 0.7847 (pt0) REVERT: C 444 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7420 (p0) REVERT: C 465 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7667 (ttt-90) REVERT: C 481 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6724 (mp) REVERT: C 549 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: C 598 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8581 (t) REVERT: C 704 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7077 (tmm) REVERT: C 1089 GLU cc_start: 0.7580 (tp30) cc_final: 0.7322 (tm-30) REVERT: C 1158 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4595 (ptpp) REVERT: C 1246 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8097 (ttt-90) REVERT: D 136 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: D 208 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.6953 (p) REVERT: D 264 ASP cc_start: 0.8599 (p0) cc_final: 0.8064 (p0) REVERT: D 297 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8842 (ptp-170) REVERT: D 314 ARG cc_start: 0.7175 (mtm110) cc_final: 0.6724 (mtm110) REVERT: D 460 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: D 564 VAL cc_start: 0.8483 (t) cc_final: 0.7999 (p) REVERT: D 619 ILE cc_start: 0.8948 (tt) cc_final: 0.8670 (mt) REVERT: D 653 ILE cc_start: 0.9004 (mt) cc_final: 0.8783 (mt) REVERT: D 664 ILE cc_start: 0.8499 (mt) cc_final: 0.8181 (mt) REVERT: D 738 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7882 (ptp-170) REVERT: D 872 LEU cc_start: 0.8457 (mt) cc_final: 0.8218 (mt) REVERT: D 895 CYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7110 (p) REVERT: D 929 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7201 (pp30) REVERT: D 1095 MET cc_start: 0.1501 (tpt) cc_final: 0.0552 (tpt) REVERT: D 1281 GLU cc_start: 0.7421 (mp0) cc_final: 0.7081 (mp0) REVERT: D 1282 TYR cc_start: 0.7230 (m-10) cc_final: 0.6954 (m-10) REVERT: D 1342 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: E 30 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8308 (mmm) REVERT: E 63 ILE cc_start: 0.9370 (mm) cc_final: 0.8973 (mt) REVERT: F 146 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5484 (tt0) REVERT: F 277 MET cc_start: 0.7827 (tpt) cc_final: 0.7209 (tpt) REVERT: F 293 GLU cc_start: 0.4405 (OUTLIER) cc_final: 0.3361 (mp0) REVERT: F 360 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5564 (t0) REVERT: F 400 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7371 (mt0) REVERT: F 445 ASP cc_start: 0.7487 (t70) cc_final: 0.7115 (t70) REVERT: F 489 MET cc_start: 0.6238 (mtp) cc_final: 0.6006 (mtt) REVERT: F 500 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7715 (mp) REVERT: F 529 GLU cc_start: 0.7950 (pm20) cc_final: 0.7687 (pm20) REVERT: F 591 GLU cc_start: 0.6880 (pt0) cc_final: 0.6678 (pt0) outliers start: 371 outliers final: 206 residues processed: 825 average time/residue: 0.2333 time to fit residues: 299.6758 Evaluate side-chains 592 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 350 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1341 ARG Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 383 ASN Chi-restraints excluded: chain F residue 400 GLN Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 546 ASP Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 566 ASP Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 590 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0040 chunk 244 optimal weight: 0.0050 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 93 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 60 GLN C 69 GLN C 120 GLN C 526 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 628 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN C 808 ASN C1108 ASN C1116 HIS C1268 GLN D 300 GLN D 365 GLN D 488 ASN D 702 GLN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN D 792 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 865 HIS D 907 HIS D 910 ASN D1197 ASN D1235 ASN D1252 HIS E 29 GLN F 227 GLN F 294 GLN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN F 455 HIS F 464 ASN F 472 GLN F 545 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138947 restraints weight = 42357.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.137195 restraints weight = 99046.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139033 restraints weight = 68120.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.139462 restraints weight = 35163.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140404 restraints weight = 31826.551| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32456 Z= 0.126 Angle : 0.574 8.004 44292 Z= 0.319 Chirality : 0.042 0.180 5055 Planarity : 0.004 0.047 5391 Dihedral : 19.169 161.888 5832 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 7.17 % Allowed : 17.92 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.11), residues: 3720 helix: -3.62 (0.10), residues: 1284 sheet: -3.04 (0.23), residues: 397 loop : -3.04 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 281 TYR 0.020 0.001 TYR B 68 PHE 0.014 0.001 PHE C 405 TRP 0.007 0.001 TRP D 33 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (32449) covalent geometry : angle 0.57376 / 0.32 (44286) hydrogen bonds : bond 0.05984 / 6.73 ( 830) hydrogen bonds : angle 6.34764 / 8.29 ( 2301) metal coordination : bond 0.00633 / 0.50 ( 7) metal coordination : angle 2.24407 / 4.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 615 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 386 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1450 (OUTLIER) cc_final: 0.1088 (m-80) REVERT: K 316 MET cc_start: 0.2366 (mmp) cc_final: 0.1671 (tmm) REVERT: A 150 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8615 (ptt90) REVERT: B 17 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6310 (tt0) REVERT: C 39 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8521 (pp) REVERT: C 60 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: C 197 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7863 (ptm160) REVERT: C 327 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: C 334 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: C 481 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6695 (mp) REVERT: C 538 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8983 (mt) REVERT: C 678 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8788 (mmm160) REVERT: C 798 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7647 (mm110) REVERT: C 834 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: C 1034 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.7146 (mmt-90) REVERT: C 1089 GLU cc_start: 0.7495 (tp30) cc_final: 0.7270 (tm-30) REVERT: C 1127 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8603 (mmmm) REVERT: C 1158 LYS cc_start: 0.4853 (OUTLIER) cc_final: 0.4235 (mptt) REVERT: D 264 ASP cc_start: 0.8250 (p0) cc_final: 0.8022 (p0) REVERT: D 299 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8134 (tp) REVERT: D 314 ARG cc_start: 0.7295 (mtm110) cc_final: 0.6827 (mtm110) REVERT: D 375 GLU cc_start: 0.7980 (tp30) cc_final: 0.7446 (tp30) REVERT: D 738 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7165 (ptm160) REVERT: D 929 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7107 (pp30) REVERT: D 1095 MET cc_start: 0.1375 (tpt) cc_final: 0.0312 (tpt) REVERT: E 63 ILE cc_start: 0.9122 (mm) cc_final: 0.8879 (mt) REVERT: E 71 GLU cc_start: 0.7760 (tp30) cc_final: 0.7488 (tp30) REVERT: F 146 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5577 (tt0) REVERT: F 445 ASP cc_start: 0.7518 (t70) cc_final: 0.7169 (t0) REVERT: F 500 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7677 (mp) outliers start: 229 outliers final: 161 residues processed: 575 average time/residue: 0.2052 time to fit residues: 188.8179 Evaluate side-chains 519 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 338 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 798 GLN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 590 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 261 optimal weight: 10.0000 chunk 13 optimal weight: 0.0060 chunk 100 optimal weight: 8.9990 chunk 314 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 0.0570 chunk 209 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 247 optimal weight: 0.0040 overall best weight: 0.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 127 GLN B 66 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN D 94 GLN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147114 restraints weight = 42046.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145634 restraints weight = 131926.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145276 restraints weight = 60974.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144011 restraints weight = 52711.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144866 restraints weight = 37023.590| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 32456 Z= 0.094 Angle : 0.479 8.480 44292 Z= 0.266 Chirality : 0.039 0.216 5055 Planarity : 0.003 0.046 5391 Dihedral : 18.549 161.995 5643 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 30.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.45 % Allowed : 19.96 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.12), residues: 3720 helix: -2.72 (0.12), residues: 1297 sheet: -2.60 (0.23), residues: 411 loop : -2.69 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1206 TYR 0.019 0.001 TYR B 68 PHE 0.010 0.001 PHE C 405 TRP 0.027 0.001 TRP F 433 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (32449) covalent geometry : angle 0.47879 / 0.27 (44286) hydrogen bonds : bond 0.04766 / 5.31 ( 830) hydrogen bonds : angle 5.28956 / 6.91 ( 2301) metal coordination : bond 0.00245 / 0.29 ( 7) metal coordination : angle 2.16691 / 4.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 539 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 365 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1395 (OUTLIER) cc_final: 0.0962 (m-80) REVERT: K 316 MET cc_start: 0.2803 (mmp) cc_final: 0.2027 (tmm) REVERT: A 71 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8525 (ttpt) REVERT: A 150 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8605 (ptt90) REVERT: B 17 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: B 29 GLU cc_start: 0.7542 (pp20) cc_final: 0.7311 (pt0) REVERT: C 60 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: C 197 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7709 (ptm160) REVERT: C 327 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: C 538 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8932 (mt) REVERT: C 678 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8822 (mmt180) REVERT: C 966 ILE cc_start: 0.6093 (OUTLIER) cc_final: 0.5851 (mt) REVERT: C 1089 GLU cc_start: 0.7568 (tp30) cc_final: 0.7319 (tm-30) REVERT: C 1127 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8517 (mmmm) REVERT: C 1150 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: C 1151 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8243 (tp) REVERT: C 1304 MET cc_start: 0.8875 (tpp) cc_final: 0.8641 (tpp) REVERT: D 299 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8262 (tp) REVERT: D 314 ARG cc_start: 0.7221 (mtm110) cc_final: 0.6712 (mtm110) REVERT: D 375 GLU cc_start: 0.7754 (tp30) cc_final: 0.7281 (tp30) REVERT: D 678 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7623 (tmm160) REVERT: D 738 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7197 (ptp-170) REVERT: D 789 LYS cc_start: 0.6734 (mmtt) cc_final: 0.6259 (mmtt) REVERT: D 1095 MET cc_start: 0.1184 (tpt) cc_final: 0.0240 (tpt) REVERT: E 63 ILE cc_start: 0.8997 (mm) cc_final: 0.8727 (mt) REVERT: F 146 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5846 (tt0) REVERT: F 155 GLU cc_start: 0.5412 (tt0) cc_final: 0.5184 (tt0) REVERT: F 445 ASP cc_start: 0.7579 (t70) cc_final: 0.7250 (t0) REVERT: F 500 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7850 (mp) REVERT: F 529 GLU cc_start: 0.6846 (pm20) cc_final: 0.6391 (tt0) outliers start: 174 outliers final: 111 residues processed: 506 average time/residue: 0.2072 time to fit residues: 169.8620 Evaluate side-chains 466 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 337 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 587 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 255 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 13 optimal weight: 0.0470 chunk 251 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 chunk 360 optimal weight: 0.6980 chunk 367 optimal weight: 8.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN B 66 HIS B 84 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 720 ASN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.179640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145622 restraints weight = 41939.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144207 restraints weight = 130397.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143689 restraints weight = 59641.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.142308 restraints weight = 52471.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143106 restraints weight = 37644.049| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32456 Z= 0.107 Angle : 0.466 7.821 44292 Z= 0.256 Chirality : 0.039 0.211 5055 Planarity : 0.003 0.044 5391 Dihedral : 18.195 162.510 5549 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.73 % Allowed : 20.33 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.13), residues: 3720 helix: -2.26 (0.13), residues: 1306 sheet: -2.38 (0.25), residues: 392 loop : -2.57 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 275 TYR 0.012 0.001 TYR C1281 PHE 0.011 0.001 PHE C 405 TRP 0.017 0.001 TRP F 433 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (32449) covalent geometry : angle 0.46606 / 0.26 (44286) hydrogen bonds : bond 0.03967 / 4.49 ( 830) hydrogen bonds : angle 4.89383 / 6.44 ( 2301) metal coordination : bond 0.00366 / 0.35 ( 7) metal coordination : angle 1.80848 / 3.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 519 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 336 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1395 (OUTLIER) cc_final: 0.0980 (m-80) REVERT: A 71 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8563 (ttpt) REVERT: A 150 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8653 (ptm-80) REVERT: B 17 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: C 60 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: C 197 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7459 (ptm160) REVERT: C 327 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: C 678 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7814 (mpt180) REVERT: C 966 ILE cc_start: 0.6175 (OUTLIER) cc_final: 0.5947 (mt) REVERT: C 1089 GLU cc_start: 0.7508 (tp30) cc_final: 0.7303 (tm-30) REVERT: C 1127 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8511 (mmmm) REVERT: C 1151 LEU cc_start: 0.8565 (tp) cc_final: 0.8343 (tp) REVERT: C 1157 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7322 (mm-40) REVERT: C 1170 MET cc_start: 0.7461 (mmm) cc_final: 0.7249 (mmm) REVERT: C 1304 MET cc_start: 0.8896 (tpp) cc_final: 0.8681 (tpp) REVERT: D 299 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8251 (tp) REVERT: D 314 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6727 (mtm110) REVERT: D 375 GLU cc_start: 0.7802 (tp30) cc_final: 0.7338 (tp30) REVERT: D 678 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7487 (tmt170) REVERT: D 738 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7070 (ptm160) REVERT: D 1095 MET cc_start: 0.1590 (tpt) cc_final: 0.0362 (tpt) REVERT: E 63 ILE cc_start: 0.8928 (mm) cc_final: 0.8681 (mt) REVERT: F 124 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: F 146 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5843 (tt0) REVERT: F 155 GLU cc_start: 0.5369 (tt0) cc_final: 0.5122 (tt0) REVERT: F 293 GLU cc_start: 0.4169 (OUTLIER) cc_final: 0.2760 (mp0) REVERT: F 329 LYS cc_start: 0.4195 (OUTLIER) cc_final: 0.3884 (pttp) REVERT: F 445 ASP cc_start: 0.7605 (t70) cc_final: 0.7112 (t70) REVERT: F 500 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7764 (mp) REVERT: F 529 GLU cc_start: 0.6895 (pm20) cc_final: 0.6578 (tt0) outliers start: 183 outliers final: 134 residues processed: 476 average time/residue: 0.2056 time to fit residues: 160.1448 Evaluate side-chains 484 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 331 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 587 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 205 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 287 optimal weight: 30.0000 chunk 226 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 127 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 760 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 365 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1279 GLN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132742 restraints weight = 42193.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131320 restraints weight = 106638.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132597 restraints weight = 56291.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132636 restraints weight = 33775.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133032 restraints weight = 32217.188| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 32456 Z= 0.305 Angle : 0.643 8.722 44292 Z= 0.341 Chirality : 0.045 0.205 5055 Planarity : 0.005 0.047 5391 Dihedral : 18.358 162.807 5516 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 33.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.13 % Favored : 88.84 % Rotamer: Outliers : 7.93 % Allowed : 19.49 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.12), residues: 3720 helix: -2.34 (0.13), residues: 1305 sheet: -2.43 (0.25), residues: 389 loop : -2.75 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 275 TYR 0.018 0.002 TYR D 349 PHE 0.020 0.002 PHE D 62 TRP 0.022 0.002 TRP F 433 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.31 (32449) covalent geometry : angle 0.64213 / 0.34 (44286) hydrogen bonds : bond 0.04856 / 5.50 ( 830) hydrogen bonds : angle 5.19807 / 6.84 ( 2301) metal coordination : bond 0.01358 / 1.39 ( 7) metal coordination : angle 3.18387 / 6.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 575 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 322 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1356 (OUTLIER) cc_final: 0.1024 (m-80) REVERT: A 150 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8696 (ptm-80) REVERT: B 17 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6798 (tt0) REVERT: C 60 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: C 197 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7532 (ptp90) REVERT: C 327 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: C 678 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7639 (mpt180) REVERT: C 966 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5850 (mt) REVERT: C 1069 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8753 (mtt180) REVERT: C 1127 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: D 136 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 299 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 314 ARG cc_start: 0.7450 (mtm110) cc_final: 0.7061 (mtm110) REVERT: D 352 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7775 (ptm160) REVERT: D 678 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7847 (ttp80) REVERT: D 738 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7283 (mtm180) REVERT: D 857 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6970 (pt) REVERT: D 1095 MET cc_start: 0.1673 (tpt) cc_final: 0.0208 (tpt) REVERT: E 63 ILE cc_start: 0.9124 (mm) cc_final: 0.8888 (mt) REVERT: E 65 ASP cc_start: 0.8191 (m-30) cc_final: 0.7840 (m-30) REVERT: F 124 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: F 146 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5762 (tt0) REVERT: F 445 ASP cc_start: 0.7838 (t70) cc_final: 0.7302 (t70) REVERT: F 500 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8047 (mp) REVERT: F 529 GLU cc_start: 0.7416 (pm20) cc_final: 0.6974 (tt0) outliers start: 253 outliers final: 187 residues processed: 531 average time/residue: 0.2001 time to fit residues: 174.6748 Evaluate side-chains 521 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 315 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 590 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 96 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 286 optimal weight: 20.0000 chunk 216 optimal weight: 4.9990 chunk 203 optimal weight: 0.0870 chunk 257 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 222 optimal weight: 0.0980 chunk 290 optimal weight: 20.0000 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.137702 restraints weight = 42069.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.136005 restraints weight = 104436.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137522 restraints weight = 56771.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137634 restraints weight = 30792.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138040 restraints weight = 26558.136| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32456 Z= 0.141 Angle : 0.499 8.994 44292 Z= 0.270 Chirality : 0.040 0.195 5055 Planarity : 0.003 0.045 5391 Dihedral : 18.202 162.235 5514 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 32.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.06 % Favored : 91.91 % Rotamer: Outliers : 6.11 % Allowed : 21.40 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.13), residues: 3720 helix: -2.04 (0.13), residues: 1309 sheet: -2.17 (0.26), residues: 377 loop : -2.61 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 275 TYR 0.012 0.001 TYR C1281 PHE 0.014 0.001 PHE C 405 TRP 0.014 0.001 TRP F 433 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32449) covalent geometry : angle 0.49880 / 0.27 (44286) hydrogen bonds : bond 0.03950 / 4.48 ( 830) hydrogen bonds : angle 4.84308 / 6.38 ( 2301) metal coordination : bond 0.00453 / 0.43 ( 7) metal coordination : angle 2.00870 / 4.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 328 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1333 (OUTLIER) cc_final: 0.0988 (m-80) REVERT: A 71 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8687 (ttpt) REVERT: A 150 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8697 (ptm-80) REVERT: B 17 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: C 60 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: C 197 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8014 (ptp-170) REVERT: C 310 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5842 (mp) REVERT: C 327 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: C 678 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7738 (mpt180) REVERT: C 966 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5842 (mt) REVERT: C 1069 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8584 (mtt180) REVERT: C 1127 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8456 (mmmm) REVERT: C 1246 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8333 (ttt-90) REVERT: D 207 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: D 299 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 300 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: D 314 ARG cc_start: 0.7403 (mtm110) cc_final: 0.6982 (mtm110) REVERT: D 434 ILE cc_start: 0.9328 (mt) cc_final: 0.9070 (tt) REVERT: D 678 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7474 (tmt170) REVERT: D 684 ASP cc_start: 0.6402 (m-30) cc_final: 0.6167 (m-30) REVERT: D 738 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7217 (mtm180) REVERT: D 1095 MET cc_start: 0.1619 (tpt) cc_final: 0.0208 (tpt) REVERT: E 63 ILE cc_start: 0.9007 (mm) cc_final: 0.8769 (mt) REVERT: F 124 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: F 146 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5653 (tt0) REVERT: F 148 TYR cc_start: 0.3268 (t80) cc_final: 0.2060 (t80) REVERT: F 155 GLU cc_start: 0.4810 (tt0) cc_final: 0.4385 (tt0) REVERT: F 445 ASP cc_start: 0.7797 (t70) cc_final: 0.7257 (t70) REVERT: F 500 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7865 (mp) REVERT: F 529 GLU cc_start: 0.7142 (pm20) cc_final: 0.6939 (tt0) outliers start: 195 outliers final: 150 residues processed: 486 average time/residue: 0.2046 time to fit residues: 163.5256 Evaluate side-chains 485 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 314 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 587 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 271 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 378 optimal weight: 50.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D 861 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142873 restraints weight = 42378.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140998 restraints weight = 129535.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140105 restraints weight = 56999.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138473 restraints weight = 56203.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.139134 restraints weight = 37612.054| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32456 Z= 0.214 Angle : 0.556 9.315 44292 Z= 0.297 Chirality : 0.042 0.177 5055 Planarity : 0.004 0.044 5391 Dihedral : 18.203 162.704 5509 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 34.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.48 % Favored : 88.49 % Rotamer: Outliers : 7.39 % Allowed : 20.58 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.13), residues: 3720 helix: -1.97 (0.13), residues: 1327 sheet: -2.20 (0.25), residues: 388 loop : -2.64 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 268 TYR 0.013 0.001 TYR D 349 PHE 0.015 0.001 PHE D 62 TRP 0.019 0.001 TRP F 433 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (32449) covalent geometry : angle 0.55529 / 0.30 (44286) hydrogen bonds : bond 0.04167 / 4.71 ( 830) hydrogen bonds : angle 4.86762 / 6.42 ( 2301) metal coordination : bond 0.00891 / 0.91 ( 7) metal coordination : angle 2.32567 / 4.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 555 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 319 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1570 (OUTLIER) cc_final: 0.1124 (m-80) REVERT: A 150 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8709 (ptm-80) REVERT: B 17 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: C 60 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: C 197 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7926 (ptp-170) REVERT: C 310 ILE cc_start: 0.6053 (OUTLIER) cc_final: 0.5798 (mp) REVERT: C 327 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: C 678 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7698 (mpt180) REVERT: C 966 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5919 (mt) REVERT: C 1069 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8698 (mtt180) REVERT: C 1127 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8626 (mmmm) REVERT: C 1246 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8293 (ttt-90) REVERT: D 136 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: D 299 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8691 (tp) REVERT: D 300 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: D 314 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7116 (mtm110) REVERT: D 352 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7626 (ptm-80) REVERT: D 678 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7464 (tmt170) REVERT: D 684 ASP cc_start: 0.6260 (m-30) cc_final: 0.6017 (m-30) REVERT: D 738 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7285 (mtm180) REVERT: D 857 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7035 (pt) REVERT: D 902 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6816 (t0) REVERT: D 1095 MET cc_start: 0.1471 (tpt) cc_final: 0.0244 (tpt) REVERT: D 1178 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7589 (p) REVERT: E 63 ILE cc_start: 0.9084 (mm) cc_final: 0.8859 (mt) REVERT: F 124 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: F 146 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5504 (tt0) REVERT: F 148 TYR cc_start: 0.3308 (t80) cc_final: 0.2179 (t80) REVERT: F 155 GLU cc_start: 0.5204 (tt0) cc_final: 0.4721 (tt0) REVERT: F 293 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.2612 (mp0) REVERT: F 445 ASP cc_start: 0.7757 (t70) cc_final: 0.7209 (t70) REVERT: F 500 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8072 (mp) outliers start: 236 outliers final: 185 residues processed: 518 average time/residue: 0.2021 time to fit residues: 171.3330 Evaluate side-chains 526 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 316 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 590 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 80 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 361 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 272 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D 861 ASN D 907 HIS ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136350 restraints weight = 42103.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134786 restraints weight = 106001.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.136225 restraints weight = 57093.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136071 restraints weight = 31818.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.136830 restraints weight = 27233.792| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32456 Z= 0.145 Angle : 0.493 9.253 44292 Z= 0.267 Chirality : 0.040 0.165 5055 Planarity : 0.003 0.044 5391 Dihedral : 18.100 162.717 5506 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 33.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 6.52 % Allowed : 21.62 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.13), residues: 3720 helix: -1.75 (0.14), residues: 1331 sheet: -2.07 (0.26), residues: 371 loop : -2.55 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 214 TYR 0.013 0.001 TYR D 349 PHE 0.013 0.001 PHE C 405 TRP 0.017 0.001 TRP F 433 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (32449) covalent geometry : angle 0.49286 / 0.27 (44286) hydrogen bonds : bond 0.03739 / 4.22 ( 830) hydrogen bonds : angle 4.67056 / 6.18 ( 2301) metal coordination : bond 0.00498 / 0.48 ( 7) metal coordination : angle 1.94609 / 3.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 529 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 321 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1517 (OUTLIER) cc_final: 0.1124 (m-80) REVERT: A 71 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8699 (ttpt) REVERT: A 150 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8717 (ptm-80) REVERT: B 17 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: C 60 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7221 (mt0) REVERT: C 310 ILE cc_start: 0.6095 (OUTLIER) cc_final: 0.5874 (mp) REVERT: C 678 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7746 (mpt180) REVERT: C 1127 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8617 (mmmm) REVERT: C 1246 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8337 (ttt-90) REVERT: D 136 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: D 299 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8607 (tp) REVERT: D 300 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: D 314 ARG cc_start: 0.7385 (mtm110) cc_final: 0.6977 (mtm110) REVERT: D 678 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7548 (tmt170) REVERT: D 684 ASP cc_start: 0.6363 (m-30) cc_final: 0.6101 (m-30) REVERT: D 738 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7140 (mtm180) REVERT: D 1095 MET cc_start: 0.1458 (tpt) cc_final: 0.0075 (tpt) REVERT: D 1178 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7680 (p) REVERT: E 63 ILE cc_start: 0.8942 (mm) cc_final: 0.8735 (mt) REVERT: F 124 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: F 146 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5320 (tt0) REVERT: F 148 TYR cc_start: 0.3130 (t80) cc_final: 0.1901 (t80) REVERT: F 155 GLU cc_start: 0.4871 (tt0) cc_final: 0.4393 (tt0) REVERT: F 293 GLU cc_start: 0.3370 (OUTLIER) cc_final: 0.2471 (mp0) REVERT: F 445 ASP cc_start: 0.7817 (t70) cc_final: 0.7267 (t70) REVERT: F 500 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7909 (mp) outliers start: 208 outliers final: 174 residues processed: 491 average time/residue: 0.1987 time to fit residues: 160.4398 Evaluate side-chains 509 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 316 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1007 LYS Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 96 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 chunk 348 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 907 HIS ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141370 restraints weight = 41674.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140114 restraints weight = 125817.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139373 restraints weight = 56613.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137430 restraints weight = 58772.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138170 restraints weight = 41009.156| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32456 Z= 0.178 Angle : 0.517 9.678 44292 Z= 0.278 Chirality : 0.041 0.152 5055 Planarity : 0.003 0.044 5391 Dihedral : 18.051 162.994 5490 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.54 % Favored : 89.44 % Rotamer: Outliers : 6.80 % Allowed : 21.46 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.13), residues: 3720 helix: -1.68 (0.14), residues: 1331 sheet: -2.08 (0.26), residues: 375 loop : -2.54 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 214 TYR 0.012 0.001 TYR D 349 PHE 0.013 0.001 PHE C 405 TRP 0.018 0.001 TRP F 433 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (32449) covalent geometry : angle 0.51688 / 0.28 (44286) hydrogen bonds : bond 0.03811 / 4.30 ( 830) hydrogen bonds : angle 4.66473 / 6.18 ( 2301) metal coordination : bond 0.00684 / 0.68 ( 7) metal coordination : angle 2.04059 / 4.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 537 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 320 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1567 (OUTLIER) cc_final: 0.1146 (m-80) REVERT: K 316 MET cc_start: 0.2960 (mmp) cc_final: 0.2091 (tmm) REVERT: A 71 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8695 (ttpt) REVERT: A 150 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8710 (ptm-80) REVERT: B 17 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: C 60 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7240 (mt0) REVERT: C 678 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7716 (mpt180) REVERT: C 1127 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8571 (mmmm) REVERT: C 1246 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8370 (ttt-90) REVERT: D 136 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: D 299 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8659 (tp) REVERT: D 300 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: D 678 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7792 (ttp80) REVERT: D 684 ASP cc_start: 0.6209 (m-30) cc_final: 0.5957 (m-30) REVERT: D 738 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7282 (mtm180) REVERT: D 805 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: D 857 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6855 (pt) REVERT: D 1095 MET cc_start: 0.1467 (tpt) cc_final: 0.0574 (tpt) REVERT: D 1178 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7762 (p) REVERT: E 63 ILE cc_start: 0.9040 (mm) cc_final: 0.8830 (mt) REVERT: F 124 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: F 146 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5228 (tt0) REVERT: F 148 TYR cc_start: 0.3173 (t80) cc_final: 0.2013 (t80) REVERT: F 155 GLU cc_start: 0.5167 (tt0) cc_final: 0.4681 (tt0) REVERT: F 293 GLU cc_start: 0.3900 (OUTLIER) cc_final: 0.2885 (mp0) REVERT: F 445 ASP cc_start: 0.7793 (t70) cc_final: 0.7259 (t70) REVERT: F 500 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7985 (mp) REVERT: F 585 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6469 (mm-30) REVERT: F 588 ARG cc_start: 0.7939 (ptp90) cc_final: 0.6788 (tmt-80) outliers start: 217 outliers final: 184 residues processed: 498 average time/residue: 0.2018 time to fit residues: 165.4556 Evaluate side-chains 523 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 319 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1127 LYS Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 154 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 296 optimal weight: 30.0000 chunk 226 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 318 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 907 HIS ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142859 restraints weight = 42451.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141515 restraints weight = 134953.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141853 restraints weight = 62200.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141059 restraints weight = 46615.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.142284 restraints weight = 32780.909| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32456 Z= 0.117 Angle : 0.465 9.388 44292 Z= 0.254 Chirality : 0.039 0.134 5055 Planarity : 0.003 0.044 5391 Dihedral : 17.930 162.981 5486 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 32.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.90 % Favored : 92.07 % Rotamer: Outliers : 5.64 % Allowed : 22.56 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.13), residues: 3720 helix: -1.41 (0.14), residues: 1338 sheet: -1.91 (0.27), residues: 371 loop : -2.40 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 214 TYR 0.012 0.001 TYR C1281 PHE 0.012 0.001 PHE D 62 TRP 0.018 0.001 TRP F 433 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (32449) covalent geometry : angle 0.46506 / 0.25 (44286) hydrogen bonds : bond 0.03415 / 3.86 ( 830) hydrogen bonds : angle 4.45238 / 5.90 ( 2301) metal coordination : bond 0.00363 / 0.34 ( 7) metal coordination : angle 1.80190 / 3.60 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 266 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 325 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 277 TYR cc_start: 0.1535 (OUTLIER) cc_final: 0.1115 (m-80) REVERT: K 316 MET cc_start: 0.3038 (mmp) cc_final: 0.1918 (tmm) REVERT: A 71 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8676 (ttpt) REVERT: A 150 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8712 (ptm-80) REVERT: B 17 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: C 60 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: C 678 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7788 (mpt180) REVERT: C 1246 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8358 (ttt-90) REVERT: D 299 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8608 (tp) REVERT: D 684 ASP cc_start: 0.6249 (m-30) cc_final: 0.5999 (m-30) REVERT: D 738 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7049 (mtm180) REVERT: D 857 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6725 (pt) REVERT: D 1095 MET cc_start: 0.1483 (tpt) cc_final: 0.0573 (tpt) REVERT: F 124 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5972 (mp0) REVERT: F 146 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5213 (tt0) REVERT: F 148 TYR cc_start: 0.3104 (t80) cc_final: 0.1963 (t80) REVERT: F 155 GLU cc_start: 0.5062 (tt0) cc_final: 0.4596 (tt0) REVERT: F 293 GLU cc_start: 0.3843 (OUTLIER) cc_final: 0.2864 (mp0) REVERT: F 445 ASP cc_start: 0.7776 (t70) cc_final: 0.7242 (t70) REVERT: F 500 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (mp) REVERT: F 585 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6481 (mm-30) REVERT: F 588 ARG cc_start: 0.7923 (ptp90) cc_final: 0.6712 (tmt-80) outliers start: 180 outliers final: 156 residues processed: 471 average time/residue: 0.2096 time to fit residues: 160.9954 Evaluate side-chains 490 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 320 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1193 TRP Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 359 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 373 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 381 optimal weight: 50.0000 chunk 379 optimal weight: 30.0000 chunk 314 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 777 HIS D 861 ASN D 907 HIS ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133194 restraints weight = 42454.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132031 restraints weight = 130778.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133646 restraints weight = 54379.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132988 restraints weight = 36671.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132988 restraints weight = 26119.831| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 32456 Z= 0.359 Angle : 0.689 9.855 44292 Z= 0.361 Chirality : 0.046 0.182 5055 Planarity : 0.005 0.060 5391 Dihedral : 18.171 163.900 5477 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 35.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.98 % Favored : 86.94 % Rotamer: Outliers : 6.92 % Allowed : 21.40 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.13), residues: 3720 helix: -1.79 (0.14), residues: 1334 sheet: -2.14 (0.25), residues: 402 loop : -2.67 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 281 TYR 0.017 0.002 TYR C 591 PHE 0.019 0.002 PHE D 62 TRP 0.017 0.002 TRP F 433 HIS 0.008 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00856 / 0.36 (32449) covalent geometry : angle 0.68831 / 0.36 (44286) hydrogen bonds : bond 0.04602 / 5.20 ( 830) hydrogen bonds : angle 4.97748 / 6.59 ( 2301) metal coordination : bond 0.01527 / 1.57 ( 7) metal coordination : angle 3.22742 / 6.38 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5391.05 seconds wall clock time: 94 minutes 15.20 seconds (5655.20 seconds total)