Starting phenix.real_space_refine on Sat Mar 7 06:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sx4_25493/03_2026/7sx4_25493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sx4_25493/03_2026/7sx4_25493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sx4_25493/03_2026/7sx4_25493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sx4_25493/03_2026/7sx4_25493.map" model { file = "/net/cci-nas-00/data/ceres_data/7sx4_25493/03_2026/7sx4_25493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sx4_25493/03_2026/7sx4_25493.cif" } resolution = 3.5 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= -0.044 sd= 2.276 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 298 5.16 5 C 24457 2.51 5 N 6208 2.21 5 O 6540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1383, 11319 Classifications: {'peptide': 1383} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1331} Chain breaks: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYS:plan-2': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1241 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 3 Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 5 Chain: "D" Number of atoms: 11012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1406, 11012 Classifications: {'peptide': 1406} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1344} Chain breaks: 30 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 12799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1587, 12799 Classifications: {'peptide': 1587} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1501} Chain breaks: 27 Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 208 Unusual residues: {'NAG': 2, 'PEV': 1, 'PGV': 1, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.45, per 1000 atoms: 0.20 Number of scatterers: 37505 At special positions: 0 Unit cell: (200.617, 175.98, 285.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 298 16.00 P 2 15.00 O 6540 8.00 N 6208 7.00 C 24457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.03 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=2.03 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 Links applied NAG-ASN " NAG A2102 " - " ASN A1064 " Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8964 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 7 sheets defined 79.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 56 removed outlier: 3.728A pdb=" N HIS A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 64 through 89 removed outlier: 3.934A pdb=" N GLN A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.769A pdb=" N GLY A 140 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.968A pdb=" N ALA A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 154' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 163 through 201 removed outlier: 4.117A pdb=" N ILE A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 311 through 333 removed outlier: 3.782A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.008A pdb=" N ARG A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.587A pdb=" N HIS A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 447 removed outlier: 6.697A pdb=" N PHE A 442 " --> pdb=" O TRP A 438 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 443 " --> pdb=" O CYS A 439 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.599A pdb=" N GLN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 502 through 529 removed outlier: 4.268A pdb=" N LEU A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 589 through 603 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 632 through 637 removed outlier: 4.097A pdb=" N LYS A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 637' Processing helix chain 'A' and resid 659 through 669 removed outlier: 3.790A pdb=" N ARG A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 Processing helix chain 'A' and resid 818 through 830 Processing helix chain 'A' and resid 835 through 839 removed outlier: 3.556A pdb=" N ILE A 839 " --> pdb=" O PRO A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 856 Processing helix chain 'A' and resid 877 through 883 Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.824A pdb=" N PHE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 914 Processing helix chain 'A' and resid 915 through 938 removed outlier: 3.695A pdb=" N GLN A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 938 " --> pdb=" O ASN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 972 Processing helix chain 'A' and resid 980 through 990 Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.913A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1013 removed outlier: 4.446A pdb=" N GLY A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1040 removed outlier: 3.582A pdb=" N ALA A1040 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1113 removed outlier: 3.746A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1129 removed outlier: 3.527A pdb=" N VAL A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1144 removed outlier: 3.918A pdb=" N ILE A1136 " --> pdb=" O HIS A1132 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A1139 " --> pdb=" O TYR A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1164 removed outlier: 3.644A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1199 through 1208 removed outlier: 3.520A pdb=" N MET A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.721A pdb=" N LYS A1213 " --> pdb=" O HIS A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1237 through 1263 removed outlier: 3.561A pdb=" N LEU A1241 " --> pdb=" O VAL A1237 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A1248 " --> pdb=" O MET A1244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A1263 " --> pdb=" O LYS A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1271 removed outlier: 4.063A pdb=" N SER A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1292 removed outlier: 3.539A pdb=" N PHE A1292 " --> pdb=" O VAL A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1313 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.349A pdb=" N LYS A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A1318 " --> pdb=" O ILE A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1313 through 1318' Processing helix chain 'A' and resid 1319 through 1335 Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1374 through 1388 Processing helix chain 'A' and resid 1390 through 1399 Processing helix chain 'A' and resid 1419 through 1437 Processing helix chain 'A' and resid 1437 through 1454 removed outlier: 3.810A pdb=" N LEU A1441 " --> pdb=" O ILE A1437 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1478 Processing helix chain 'A' and resid 1486 through 1495 removed outlier: 3.600A pdb=" N VAL A1490 " --> pdb=" O PRO A1486 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A1491 " --> pdb=" O THR A1487 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A1493 " --> pdb=" O ARG A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1502 removed outlier: 3.666A pdb=" N LEU A1501 " --> pdb=" O ARG A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1523 removed outlier: 4.138A pdb=" N HIS A1523 " --> pdb=" O MET A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1541 Processing helix chain 'A' and resid 1543 through 1548 Processing helix chain 'A' and resid 1549 through 1584 Processing helix chain 'A' and resid 1585 through 1596 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.766A pdb=" N VAL B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 191' Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.518A pdb=" N ASP B 220 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.695A pdb=" N LEU B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 288 removed outlier: 3.585A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 Processing helix chain 'B' and resid 331 through 341 removed outlier: 4.157A pdb=" N LEU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.607A pdb=" N GLU C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 17 " --> pdb=" O PHE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.556A pdb=" N MET C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.750A pdb=" N ASP C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.819A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.919A pdb=" N ASP C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.614A pdb=" N PHE C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 86 through 105 Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 148 through 165 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 181 through 184 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 200 through 206 Processing helix chain 'D' and resid 220 through 234 removed outlier: 4.339A pdb=" N SER D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 251 removed outlier: 3.715A pdb=" N HIS D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.880A pdb=" N ASP D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 439 through 456 Processing helix chain 'D' and resid 498 through 511 Processing helix chain 'D' and resid 519 through 538 Processing helix chain 'D' and resid 553 through 568 removed outlier: 4.582A pdb=" N LYS D 559 " --> pdb=" O GLN D 555 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP D 560 " --> pdb=" O PHE D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.704A pdb=" N MET D 572 " --> pdb=" O ARG D 568 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 611 Processing helix chain 'D' and resid 618 through 635 removed outlier: 4.429A pdb=" N GLU D 622 " --> pdb=" O GLN D 618 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Proline residue: D 626 - end of helix Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.638A pdb=" N LYS D 650 " --> pdb=" O GLU D 646 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET D 651 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 667 removed outlier: 3.705A pdb=" N PHE D 667 " --> pdb=" O MET D 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 667' Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 678 through 695 removed outlier: 3.894A pdb=" N GLN D 682 " --> pdb=" O PRO D 678 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN D 684 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 796 through 815 removed outlier: 4.254A pdb=" N CYS D 800 " --> pdb=" O MET D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 841 Processing helix chain 'D' and resid 860 through 879 Processing helix chain 'D' and resid 950 through 964 removed outlier: 3.501A pdb=" N ARG D 954 " --> pdb=" O PRO D 950 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 964 " --> pdb=" O PHE D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 984 Processing helix chain 'D' and resid 987 through 996 removed outlier: 3.761A pdb=" N ARG D 993 " --> pdb=" O LEU D 989 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS D 994 " --> pdb=" O TYR D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1007 Processing helix chain 'D' and resid 1007 through 1016 Processing helix chain 'D' and resid 1020 through 1036 removed outlier: 3.845A pdb=" N SER D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D1026 " --> pdb=" O GLN D1022 " (cutoff:3.500A) Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1039 through 1053 removed outlier: 3.923A pdb=" N ILE D1043 " --> pdb=" O HIS D1039 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D1053 " --> pdb=" O ASN D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1073 removed outlier: 3.505A pdb=" N ARG D1060 " --> pdb=" O ASP D1056 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D1065 " --> pdb=" O PHE D1061 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1100 removed outlier: 3.565A pdb=" N LYS D1086 " --> pdb=" O ASN D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1116 removed outlier: 3.938A pdb=" N ASP D1116 " --> pdb=" O GLY D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1119 through 1137 removed outlier: 3.574A pdb=" N THR D1136 " --> pdb=" O PHE D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1155 Processing helix chain 'D' and resid 1162 through 1181 Processing helix chain 'D' and resid 1209 through 1220 Processing helix chain 'D' and resid 1227 through 1232 removed outlier: 4.031A pdb=" N LYS D1232 " --> pdb=" O ARG D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1273 through 1290 Processing helix chain 'D' and resid 1298 through 1316 Processing helix chain 'D' and resid 1328 through 1335 Processing helix chain 'D' and resid 1335 through 1352 removed outlier: 3.619A pdb=" N GLY D1344 " --> pdb=" O ALA D1340 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D1346 " --> pdb=" O ILE D1342 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN D1347 " --> pdb=" O ALA D1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 1352 through 1372 removed outlier: 3.815A pdb=" N HIS D1358 " --> pdb=" O ASN D1354 " (cutoff:3.500A) Proline residue: D1361 - end of helix removed outlier: 3.675A pdb=" N SER D1371 " --> pdb=" O LEU D1367 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS D1372 " --> pdb=" O LYS D1368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1374 through 1379 removed outlier: 3.501A pdb=" N PHE D1379 " --> pdb=" O ARG D1376 " (cutoff:3.500A) Processing helix chain 'D' and resid 1386 through 1390 removed outlier: 3.833A pdb=" N SER D1389 " --> pdb=" O SER D1386 " (cutoff:3.500A) Processing helix chain 'D' and resid 1391 through 1409 removed outlier: 3.957A pdb=" N GLN D1396 " --> pdb=" O PRO D1392 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET D1397 " --> pdb=" O HIS D1393 " (cutoff:3.500A) Processing helix chain 'D' and resid 1413 through 1433 removed outlier: 4.233A pdb=" N LYS D1418 " --> pdb=" O CYS D1414 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE D1419 " --> pdb=" O ASP D1415 " (cutoff:3.500A) Processing helix chain 'D' and resid 2019 through 2037 Processing helix chain 'D' and resid 2037 through 2042 Processing helix chain 'D' and resid 2044 through 2058 removed outlier: 3.530A pdb=" N LEU D2055 " --> pdb=" O SER D2051 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER D2058 " --> pdb=" O ARG D2054 " (cutoff:3.500A) Processing helix chain 'D' and resid 2073 through 2090 removed outlier: 3.568A pdb=" N VAL D2077 " --> pdb=" O ASN D2073 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2100 removed outlier: 3.500A pdb=" N GLN D2097 " --> pdb=" O GLY D2093 " (cutoff:3.500A) Processing helix chain 'D' and resid 2107 through 2116 removed outlier: 3.529A pdb=" N THR D2111 " --> pdb=" O THR D2107 " (cutoff:3.500A) Processing helix chain 'D' and resid 2123 through 2138 Processing helix chain 'D' and resid 2144 through 2159 removed outlier: 3.768A pdb=" N ILE D2148 " --> pdb=" O GLY D2144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS D2150 " --> pdb=" O ALA D2146 " (cutoff:3.500A) Processing helix chain 'D' and resid 2169 through 2182 removed outlier: 3.852A pdb=" N ALA D2182 " --> pdb=" O GLN D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2183 through 2187 Processing helix chain 'D' and resid 2194 through 2206 removed outlier: 4.271A pdb=" N LEU D2198 " --> pdb=" O LEU D2194 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS D2206 " --> pdb=" O ILE D2202 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2215 removed outlier: 3.872A pdb=" N SER D2215 " --> pdb=" O ASN D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2216 through 2231 Processing helix chain 'D' and resid 2234 through 2249 removed outlier: 3.857A pdb=" N LEU D2238 " --> pdb=" O THR D2234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D2247 " --> pdb=" O GLY D2243 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D2249 " --> pdb=" O CYS D2245 " (cutoff:3.500A) Processing helix chain 'D' and resid 2251 through 2256 Processing helix chain 'D' and resid 2256 through 2271 Processing helix chain 'D' and resid 2277 through 2293 Processing helix chain 'D' and resid 2317 through 2323 removed outlier: 3.855A pdb=" N CYS D2320 " --> pdb=" O ALA D2317 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D2323 " --> pdb=" O CYS D2320 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2334 removed outlier: 3.981A pdb=" N ASP D2334 " --> pdb=" O ASP D2330 " (cutoff:3.500A) Processing helix chain 'D' and resid 2336 through 2343 Processing helix chain 'D' and resid 2356 through 2378 Processing helix chain 'D' and resid 2383 through 2388 Processing helix chain 'D' and resid 2389 through 2393 removed outlier: 3.509A pdb=" N TYR D2392 " --> pdb=" O PRO D2389 " (cutoff:3.500A) Processing helix chain 'D' and resid 2407 through 2429 Processing helix chain 'D' and resid 2440 through 2442 No H-bonds generated for 'chain 'D' and resid 2440 through 2442' Processing helix chain 'D' and resid 2443 through 2458 removed outlier: 3.679A pdb=" N ILE D2454 " --> pdb=" O HIS D2450 " (cutoff:3.500A) Processing helix chain 'D' and resid 2471 through 2490 removed outlier: 3.532A pdb=" N ALA D2479 " --> pdb=" O ALA D2475 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D2480 " --> pdb=" O PHE D2476 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA D2490 " --> pdb=" O CYS D2486 " (cutoff:3.500A) Processing helix chain 'D' and resid 2504 through 2527 Proline residue: D2518 - end of helix removed outlier: 3.759A pdb=" N ASN D2527 " --> pdb=" O LEU D2523 " (cutoff:3.500A) Processing helix chain 'D' and resid 2531 through 2548 Processing helix chain 'D' and resid 2550 through 2566 removed outlier: 4.290A pdb=" N VAL D2554 " --> pdb=" O SER D2550 " (cutoff:3.500A) Proline residue: D2558 - end of helix Proline residue: D2562 - end of helix Processing helix chain 'D' and resid 2575 through 2585 Processing helix chain 'D' and resid 2605 through 2625 Processing helix chain 'E' and resid 22 through 34 removed outlier: 3.768A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 55 removed outlier: 4.043A pdb=" N VAL E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Proline residue: E 83 - end of helix Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 195 through 200 removed outlier: 4.257A pdb=" N LYS E 200 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.873A pdb=" N GLU E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 4.207A pdb=" N ALA E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 339 removed outlier: 3.814A pdb=" N LEU E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 365 Processing helix chain 'E' and resid 654 through 665 removed outlier: 3.511A pdb=" N ASN E 665 " --> pdb=" O TYR E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 687 Processing helix chain 'E' and resid 786 through 798 Processing helix chain 'E' and resid 819 through 836 removed outlier: 4.212A pdb=" N PHE E 823 " --> pdb=" O ARG E 819 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS E 836 " --> pdb=" O THR E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 853 removed outlier: 3.578A pdb=" N ASN E 851 " --> pdb=" O ARG E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 867 Processing helix chain 'E' and resid 896 through 914 removed outlier: 5.331A pdb=" N LYS E 906 " --> pdb=" O SER E 902 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER E 907 " --> pdb=" O ALA E 903 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER E 914 " --> pdb=" O THR E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 915 through 921 removed outlier: 3.765A pdb=" N SER E 921 " --> pdb=" O HIS E 917 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 941 removed outlier: 3.574A pdb=" N TYR E 928 " --> pdb=" O ASN E 924 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP E 930 " --> pdb=" O GLY E 926 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 941 " --> pdb=" O PHE E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 944 through 951 removed outlier: 3.695A pdb=" N ARG E 948 " --> pdb=" O ASN E 944 " (cutoff:3.500A) Processing helix chain 'E' and resid 951 through 956 Processing helix chain 'E' and resid 1176 through 1192 Processing helix chain 'E' and resid 1201 through 1208 Processing helix chain 'E' and resid 1214 through 1235 Processing helix chain 'E' and resid 1268 through 1293 removed outlier: 3.565A pdb=" N ALA E1274 " --> pdb=" O GLN E1270 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E1275 " --> pdb=" O TRP E1271 " (cutoff:3.500A) Processing helix chain 'E' and resid 1338 through 1360 Processing helix chain 'E' and resid 1459 through 1469 Processing helix chain 'E' and resid 1484 through 1504 Processing helix chain 'E' and resid 1556 through 1564 Processing helix chain 'E' and resid 1570 through 1579 Processing helix chain 'E' and resid 1580 through 1583 Processing helix chain 'E' and resid 1584 through 1598 removed outlier: 3.529A pdb=" N GLY E1589 " --> pdb=" O GLU E1585 " (cutoff:3.500A) Proline residue: E1593 - end of helix Processing helix chain 'E' and resid 1599 through 1601 No H-bonds generated for 'chain 'E' and resid 1599 through 1601' Processing helix chain 'E' and resid 1603 through 1621 Processing helix chain 'E' and resid 1621 through 1634 removed outlier: 3.573A pdb=" N VAL E1625 " --> pdb=" O VAL E1621 " (cutoff:3.500A) Processing helix chain 'E' and resid 1637 through 1654 removed outlier: 3.605A pdb=" N ARG E1641 " --> pdb=" O GLU E1637 " (cutoff:3.500A) Processing helix chain 'E' and resid 1658 through 1662 Processing helix chain 'E' and resid 1665 through 1670 removed outlier: 4.467A pdb=" N ILE E1669 " --> pdb=" O GLY E1665 " (cutoff:3.500A) Processing helix chain 'E' and resid 1737 through 1750 removed outlier: 3.511A pdb=" N ALA E1750 " --> pdb=" O LEU E1746 " (cutoff:3.500A) Processing helix chain 'E' and resid 1752 through 1756 removed outlier: 3.526A pdb=" N ALA E1755 " --> pdb=" O LEU E1752 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE E1756 " --> pdb=" O ILE E1753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1752 through 1756' Processing helix chain 'E' and resid 1757 through 1762 Processing helix chain 'E' and resid 1844 through 1849 removed outlier: 3.749A pdb=" N CYS E1848 " --> pdb=" O PRO E1844 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E1849 " --> pdb=" O ALA E1845 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1844 through 1849' Processing helix chain 'E' and resid 1850 through 1858 Processing helix chain 'E' and resid 1869 through 1885 Processing helix chain 'E' and resid 1885 through 1890 removed outlier: 3.753A pdb=" N VAL E1889 " --> pdb=" O ASP E1885 " (cutoff:3.500A) Processing helix chain 'E' and resid 1893 through 1900 removed outlier: 4.046A pdb=" N THR E1898 " --> pdb=" O LEU E1894 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE E1899 " --> pdb=" O GLU E1895 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER E1900 " --> pdb=" O LYS E1896 " (cutoff:3.500A) Processing helix chain 'E' and resid 1902 through 1918 Processing helix chain 'E' and resid 1921 through 1942 Processing helix chain 'E' and resid 1946 through 1962 removed outlier: 3.649A pdb=" N PHE E1957 " --> pdb=" O ALA E1953 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP E1959 " --> pdb=" O LEU E1955 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU E1960 " --> pdb=" O THR E1956 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E1961 " --> pdb=" O PHE E1957 " (cutoff:3.500A) Processing helix chain 'E' and resid 1969 through 1981 Processing helix chain 'E' and resid 1982 through 1986 removed outlier: 4.069A pdb=" N LYS E1985 " --> pdb=" O CYS E1982 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E1986 " --> pdb=" O GLU E1983 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1982 through 1986' Processing helix chain 'E' and resid 2019 through 2031 removed outlier: 3.738A pdb=" N LEU E2023 " --> pdb=" O GLN E2019 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2039 removed outlier: 4.702A pdb=" N THR E2039 " --> pdb=" O SER E2036 " (cutoff:3.500A) Processing helix chain 'E' and resid 2057 through 2062 Processing helix chain 'E' and resid 2078 through 2109 Processing helix chain 'E' and resid 2112 through 2130 removed outlier: 4.231A pdb=" N GLN E2117 " --> pdb=" O THR E2113 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER E2118 " --> pdb=" O ALA E2114 " (cutoff:3.500A) Processing helix chain 'E' and resid 2132 through 2139 Processing helix chain 'E' and resid 2141 through 2146 removed outlier: 3.957A pdb=" N PHE E2145 " --> pdb=" O GLU E2141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER E2146 " --> pdb=" O PHE E2142 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2141 through 2146' Processing helix chain 'E' and resid 2150 through 2176 removed outlier: 3.756A pdb=" N LEU E2160 " --> pdb=" O GLY E2156 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E2176 " --> pdb=" O MET E2172 " (cutoff:3.500A) Processing helix chain 'E' and resid 2185 through 2200 removed outlier: 3.877A pdb=" N PHE E2189 " --> pdb=" O GLU E2185 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL E2192 " --> pdb=" O LEU E2188 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE E2193 " --> pdb=" O PHE E2189 " (cutoff:3.500A) Processing helix chain 'E' and resid 2203 through 2221 removed outlier: 3.540A pdb=" N GLN E2209 " --> pdb=" O ALA E2205 " (cutoff:3.500A) Processing helix chain 'E' and resid 2221 through 2226 Processing helix chain 'E' and resid 2233 through 2244 Processing helix chain 'E' and resid 2247 through 2266 Processing helix chain 'E' and resid 2266 through 2278 removed outlier: 3.591A pdb=" N VAL E2270 " --> pdb=" O ARG E2266 " (cutoff:3.500A) Processing helix chain 'E' and resid 2279 through 2281 No H-bonds generated for 'chain 'E' and resid 2279 through 2281' Processing helix chain 'E' and resid 2296 through 2308 Processing helix chain 'E' and resid 2316 through 2320 removed outlier: 3.593A pdb=" N LEU E2320 " --> pdb=" O ILE E2317 " (cutoff:3.500A) Processing helix chain 'E' and resid 2342 through 2357 removed outlier: 3.678A pdb=" N THR E2352 " --> pdb=" O LYS E2348 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL E2353 " --> pdb=" O LEU E2349 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E2354 " --> pdb=" O CYS E2350 " (cutoff:3.500A) Processing helix chain 'E' and resid 2360 through 2388 Proline residue: E2375 - end of helix Processing helix chain 'E' and resid 2390 through 2415 removed outlier: 3.721A pdb=" N ALA E2394 " --> pdb=" O THR E2390 " (cutoff:3.500A) Processing helix chain 'E' and resid 2416 through 2420 Processing helix chain 'E' and resid 2480 through 2518 Proline residue: E2492 - end of helix Proline residue: E2509 - end of helix removed outlier: 3.877A pdb=" N LYS E2512 " --> pdb=" O GLY E2508 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E2513 " --> pdb=" O PRO E2509 " (cutoff:3.500A) Processing helix chain 'E' and resid 2530 through 2548 removed outlier: 3.614A pdb=" N LEU E2547 " --> pdb=" O SER E2543 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2556 Processing helix chain 'E' and resid 2557 through 2567 Processing helix chain 'E' and resid 2578 through 2599 removed outlier: 3.969A pdb=" N LEU E2582 " --> pdb=" O VAL E2578 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET E2599 " --> pdb=" O LYS E2595 " (cutoff:3.500A) Processing helix chain 'E' and resid 2599 through 2606 removed outlier: 3.774A pdb=" N ARG E2603 " --> pdb=" O MET E2599 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN E2605 " --> pdb=" O THR E2601 " (cutoff:3.500A) Processing helix chain 'E' and resid 2608 through 2625 Processing helix chain 'E' and resid 2626 through 2630 removed outlier: 3.770A pdb=" N PHE E2630 " --> pdb=" O ILE E2627 " (cutoff:3.500A) Processing helix chain 'E' and resid 2631 through 2646 removed outlier: 4.430A pdb=" N ARG E2635 " --> pdb=" O LEU E2631 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER E2636 " --> pdb=" O PRO E2632 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E2637 " --> pdb=" O HIS E2633 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET E2646 " --> pdb=" O VAL E2642 " (cutoff:3.500A) Processing helix chain 'E' and resid 2670 through 2688 Processing helix chain 'E' and resid 2694 through 2699 removed outlier: 3.547A pdb=" N ILE E2698 " --> pdb=" O LEU E2694 " (cutoff:3.500A) Processing helix chain 'E' and resid 2700 through 2702 No H-bonds generated for 'chain 'E' and resid 2700 through 2702' Processing helix chain 'E' and resid 2706 through 2714 Processing helix chain 'E' and resid 2715 through 2722 Processing helix chain 'E' and resid 2733 through 2749 removed outlier: 4.003A pdb=" N VAL E2747 " --> pdb=" O THR E2743 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU E2748 " --> pdb=" O VAL E2744 " (cutoff:3.500A) Processing helix chain 'E' and resid 2787 through 2805 Processing helix chain 'E' and resid 2805 through 2810 removed outlier: 3.764A pdb=" N GLY E2810 " --> pdb=" O GLU E2806 " (cutoff:3.500A) Processing helix chain 'E' and resid 2812 through 2820 Processing helix chain 'E' and resid 2820 through 2827 removed outlier: 4.292A pdb=" N ALA E2824 " --> pdb=" O VAL E2820 " (cutoff:3.500A) Processing helix chain 'E' and resid 2831 through 2844 Processing helix chain 'E' and resid 2845 through 2852 removed outlier: 3.844A pdb=" N VAL E2849 " --> pdb=" O ILE E2845 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU E2850 " --> pdb=" O PRO E2846 " (cutoff:3.500A) Processing helix chain 'E' and resid 2856 through 2861 removed outlier: 3.740A pdb=" N ALA E2861 " --> pdb=" O CYS E2857 " (cutoff:3.500A) Processing helix chain 'E' and resid 2867 through 2871 Processing helix chain 'E' and resid 2872 through 2880 Processing helix chain 'E' and resid 2890 through 2909 removed outlier: 3.603A pdb=" N LEU E2894 " --> pdb=" O CYS E2890 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E2896 " --> pdb=" O SER E2892 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E2897 " --> pdb=" O SER E2893 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 209 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 350 removed outlier: 3.634A pdb=" N MET A 350 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 362 " --> pdb=" O MET A 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1045 through 1046 removed outlier: 3.901A pdb=" N LYS A1045 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A1091 " --> pdb=" O LYS A1045 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1060 through 1064 Processing sheet with id=AA5, first strand: chain 'A' and resid 1484 through 1485 removed outlier: 3.507A pdb=" N VAL A1528 " --> pdb=" O ILE A1485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'E' and resid 2010 through 2013 2343 hydrogen bonds defined for protein. 6906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5907 1.31 - 1.45: 10156 1.45 - 1.58: 21806 1.58 - 1.71: 6 1.71 - 1.84: 463 Bond restraints: 38338 Sorted by residual: bond pdb=" O1 TYS A 287 " pdb=" S TYS A 287 " ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" OH TYS A 287 " pdb=" S TYS A 287 " ideal model delta sigma weight residual 1.679 1.534 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" C31 PEV A2103 " pdb=" O2 PEV A2103 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CAI Y01 A2105 " pdb=" CAK Y01 A2105 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CAI Y01 A2107 " pdb=" CAK Y01 A2107 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 38333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 51619 3.28 - 6.56: 268 6.56 - 9.83: 20 9.83 - 13.11: 6 13.11 - 16.39: 2 Bond angle restraints: 51915 Sorted by residual: angle pdb=" O11 PGV A2104 " pdb=" P PGV A2104 " pdb=" O12 PGV A2104 " ideal model delta sigma weight residual 92.97 109.36 -16.39 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O3P PEV A2103 " pdb=" P PEV A2103 " pdb=" O4P PEV A2103 " ideal model delta sigma weight residual 93.57 109.35 -15.78 3.00e+00 1.11e-01 2.77e+01 angle pdb=" N GLU E2396 " pdb=" CA GLU E2396 " pdb=" CB GLU E2396 " ideal model delta sigma weight residual 110.12 116.73 -6.61 1.47e+00 4.63e-01 2.02e+01 angle pdb=" OAG Y01 A2107 " pdb=" CAY Y01 A2107 " pdb=" OAW Y01 A2107 " ideal model delta sigma weight residual 123.38 111.40 11.98 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CAM Y01 A2106 " pdb=" CAY Y01 A2106 " pdb=" OAW Y01 A2106 " ideal model delta sigma weight residual 111.19 122.90 -11.71 3.00e+00 1.11e-01 1.52e+01 ... (remaining 51910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 22566 32.09 - 64.18: 578 64.18 - 96.27: 77 96.27 - 128.36: 0 128.36 - 160.45: 1 Dihedral angle restraints: 23222 sinusoidal: 9565 harmonic: 13657 Sorted by residual: dihedral pdb=" CB CYS B 330 " pdb=" SG CYS B 330 " pdb=" SG CYS B 376 " pdb=" CB CYS B 376 " ideal model delta sinusoidal sigma weight residual 93.00 174.38 -81.38 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 334 " pdb=" SG CYS B 334 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 161.91 -68.91 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CA CYS A 229 " pdb=" C CYS A 229 " pdb=" N SER A 230 " pdb=" CA SER A 230 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 23219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4757 0.042 - 0.083: 971 0.083 - 0.125: 238 0.125 - 0.167: 29 0.167 - 0.208: 11 Chirality restraints: 6006 Sorted by residual: chirality pdb=" CA LEU D2184 " pdb=" N LEU D2184 " pdb=" C LEU D2184 " pdb=" CB LEU D2184 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA GLN E 821 " pdb=" N GLN E 821 " pdb=" C GLN E 821 " pdb=" CB GLN E 821 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CBG Y01 A2106 " pdb=" CAQ Y01 A2106 " pdb=" CBD Y01 A2106 " pdb=" CBI Y01 A2106 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 6003 not shown) Planarity restraints: 6424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 924 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C VAL A 924 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL A 924 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 925 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 926 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL A 926 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 926 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 927 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 239 " -0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 240 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.045 5.00e-02 4.00e+02 ... (remaining 6421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3335 2.74 - 3.28: 40666 3.28 - 3.82: 60733 3.82 - 4.36: 67902 4.36 - 4.90: 117756 Nonbonded interactions: 290392 Sorted by model distance: nonbonded pdb=" OD1 ASP B 349 " pdb=" N GLU B 350 " model vdw 2.199 3.120 nonbonded pdb=" O LYS E2903 " pdb=" OE1 GLU E2907 " model vdw 2.200 3.040 nonbonded pdb=" NH1 ARG E2707 " pdb=" OG1 THR E2790 " model vdw 2.211 3.120 nonbonded pdb=" O GLU E 345 " pdb=" OG1 THR E 348 " model vdw 2.226 3.040 nonbonded pdb=" O PRO E 224 " pdb=" OG1 THR E 230 " model vdw 2.226 3.040 ... (remaining 290387 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.690 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 38349 Z= 0.157 Angle : 0.629 16.388 51938 Z= 0.305 Chirality : 0.038 0.208 6006 Planarity : 0.005 0.082 6423 Dihedral : 14.488 160.447 14228 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 2.04 (0.13), residues: 4418 helix: 1.99 (0.10), residues: 3061 sheet: -0.51 (0.85), residues: 37 loop : -0.04 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E2490 TYR 0.052 0.001 TYR A 299 PHE 0.026 0.001 PHE E2261 TRP 0.016 0.001 TRP D 506 HIS 0.008 0.001 HIS E1926 Details of bonding type rmsd covalent geometry : bond 0.00331 (38338) covalent geometry : angle 0.62755 (51915) SS BOND : bond 0.00420 ( 10) SS BOND : angle 2.38630 ( 20) hydrogen bonds : bond 0.13607 ( 2343) hydrogen bonds : angle 5.56644 ( 6906) link_NAG-ASN : bond 0.00312 ( 1) link_NAG-ASN : angle 0.65916 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 890 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.7382 (tp) cc_final: 0.6761 (mt) REVERT: A 176 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 243 PHE cc_start: 0.8508 (m-10) cc_final: 0.7724 (m-10) REVERT: A 405 TYR cc_start: 0.7552 (p90) cc_final: 0.7326 (p90) REVERT: A 1003 MET cc_start: 0.8391 (mmt) cc_final: 0.8114 (mmm) REVERT: A 1270 GLN cc_start: 0.6991 (mm110) cc_final: 0.6571 (tm-30) REVERT: A 1290 LEU cc_start: 0.8313 (mt) cc_final: 0.8087 (mt) REVERT: A 1410 PHE cc_start: 0.7866 (m-10) cc_final: 0.7610 (m-80) REVERT: A 1530 PHE cc_start: 0.7877 (t80) cc_final: 0.7661 (t80) REVERT: B 269 GLN cc_start: 0.8121 (mt0) cc_final: 0.7897 (mp10) REVERT: B 295 TYR cc_start: 0.8591 (p90) cc_final: 0.7894 (p90) REVERT: B 340 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7660 (mtt-85) REVERT: C 140 GLU cc_start: 0.7403 (tp30) cc_final: 0.6623 (pt0) REVERT: C 146 MET cc_start: 0.5451 (ppp) cc_final: 0.4943 (ppp) REVERT: D 204 MET cc_start: 0.5680 (mpp) cc_final: 0.5400 (mpp) REVERT: D 228 MET cc_start: 0.8536 (pmm) cc_final: 0.8313 (pmm) REVERT: D 276 MET cc_start: 0.7912 (mmt) cc_final: 0.7022 (mtt) REVERT: D 529 MET cc_start: 0.8463 (ptp) cc_final: 0.8203 (ptp) REVERT: D 812 MET cc_start: 0.8957 (tpp) cc_final: 0.8316 (mtt) REVERT: D 2240 GLU cc_start: 0.7502 (tp30) cc_final: 0.7144 (tp30) REVERT: E 788 LEU cc_start: 0.8211 (mp) cc_final: 0.7958 (mp) REVERT: E 792 MET cc_start: 0.8412 (mtp) cc_final: 0.8154 (mtp) REVERT: E 1272 ASN cc_start: 0.7912 (m110) cc_final: 0.7611 (m110) REVERT: E 1557 MET cc_start: 0.7518 (mmm) cc_final: 0.7318 (mmm) REVERT: E 2186 ILE cc_start: 0.8166 (tp) cc_final: 0.7932 (tt) REVERT: E 2385 THR cc_start: 0.8245 (m) cc_final: 0.7687 (p) REVERT: E 2530 ASP cc_start: 0.7461 (m-30) cc_final: 0.7191 (m-30) REVERT: E 2535 MET cc_start: 0.7772 (tpp) cc_final: 0.7244 (tpt) outliers start: 0 outliers final: 0 residues processed: 890 average time/residue: 0.2011 time to fit residues: 308.5381 Evaluate side-chains 689 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 689 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN A 665 GLN A 876 HIS A 877 GLN A1189 HIS B 287 HIS D 996 HIS ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1374 GLN E 820 HIS E 857 ASN E2076 HIS E2087 GLN E2119 HIS E2597 HIS E2633 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.189249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.143221 restraints weight = 74411.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.148128 restraints weight = 31329.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.150413 restraints weight = 17574.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.150977 restraints weight = 12975.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.151433 restraints weight = 11753.931| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38349 Z= 0.154 Angle : 0.652 10.787 51938 Z= 0.324 Chirality : 0.041 0.193 6006 Planarity : 0.005 0.070 6423 Dihedral : 6.052 150.361 5235 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.75 % Allowed : 9.75 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 2.07 (0.13), residues: 4418 helix: 1.98 (0.09), residues: 3092 sheet: -0.36 (0.98), residues: 27 loop : 0.02 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1053 TYR 0.018 0.001 TYR A1517 PHE 0.023 0.002 PHE E1893 TRP 0.023 0.001 TRP D2390 HIS 0.012 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00357 (38338) covalent geometry : angle 0.65117 (51915) SS BOND : bond 0.00537 ( 10) SS BOND : angle 1.86885 ( 20) hydrogen bonds : bond 0.04366 ( 2343) hydrogen bonds : angle 4.27140 ( 6906) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 1.30093 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 783 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7137 (tpp) cc_final: 0.6866 (tpp) REVERT: A 157 TYR cc_start: 0.7654 (m-10) cc_final: 0.7180 (m-80) REVERT: A 176 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 197 VAL cc_start: 0.8705 (t) cc_final: 0.8387 (p) REVERT: A 257 GLU cc_start: 0.7796 (pt0) cc_final: 0.7082 (mp0) REVERT: A 405 TYR cc_start: 0.7658 (p90) cc_final: 0.7308 (p90) REVERT: A 554 GLU cc_start: 0.8654 (tp30) cc_final: 0.8446 (tp30) REVERT: A 636 LYS cc_start: 0.7025 (mttt) cc_final: 0.5903 (tptp) REVERT: A 738 MET cc_start: 0.7041 (tpp) cc_final: 0.6321 (mpp) REVERT: A 894 ILE cc_start: 0.8578 (mm) cc_final: 0.8282 (tp) REVERT: A 1009 GLU cc_start: 0.8556 (tt0) cc_final: 0.7996 (tp30) REVERT: A 1072 ASN cc_start: 0.8115 (t0) cc_final: 0.7575 (t0) REVERT: A 1162 ASN cc_start: 0.8738 (t0) cc_final: 0.8096 (t0) REVERT: A 1234 GLU cc_start: 0.8336 (mp0) cc_final: 0.7951 (tp30) REVERT: A 1244 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6650 (tpp) REVERT: A 1298 TYR cc_start: 0.5947 (m-80) cc_final: 0.5614 (m-80) REVERT: A 1409 GLU cc_start: 0.8268 (pt0) cc_final: 0.7408 (pt0) REVERT: A 1419 ASN cc_start: 0.8325 (t0) cc_final: 0.7995 (t0) REVERT: A 1501 LEU cc_start: 0.8212 (mt) cc_final: 0.7919 (pp) REVERT: B 269 GLN cc_start: 0.8151 (mt0) cc_final: 0.7914 (mp10) REVERT: B 357 SER cc_start: 0.8143 (t) cc_final: 0.7930 (t) REVERT: C 110 MET cc_start: 0.7539 (tpp) cc_final: 0.7329 (tpp) REVERT: C 127 ARG cc_start: 0.4298 (ptp90) cc_final: 0.3996 (ptt180) REVERT: C 140 GLU cc_start: 0.7412 (tp30) cc_final: 0.6564 (pt0) REVERT: C 146 MET cc_start: 0.5573 (ppp) cc_final: 0.5207 (ppp) REVERT: D 228 MET cc_start: 0.8365 (pmm) cc_final: 0.7329 (ppp) REVERT: D 276 MET cc_start: 0.8012 (mmt) cc_final: 0.7108 (mtt) REVERT: D 812 MET cc_start: 0.9105 (tpp) cc_final: 0.8575 (mtt) REVERT: D 829 LYS cc_start: 0.7911 (mttp) cc_final: 0.7696 (mmmm) REVERT: D 830 ASP cc_start: 0.8806 (t0) cc_final: 0.8397 (t0) REVERT: D 975 MET cc_start: 0.8599 (mtt) cc_final: 0.8369 (mtt) REVERT: D 1171 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6524 (tm-30) REVERT: D 1275 GLN cc_start: 0.7850 (mp10) cc_final: 0.7598 (mt0) REVERT: D 1397 MET cc_start: 0.8494 (mpp) cc_final: 0.8040 (mpt) REVERT: D 2246 TYR cc_start: 0.7453 (t80) cc_final: 0.7246 (t80) REVERT: D 2331 PHE cc_start: 0.7636 (t80) cc_final: 0.7317 (t80) REVERT: D 2563 MET cc_start: 0.7670 (mmm) cc_final: 0.7419 (ppp) REVERT: D 2609 LYS cc_start: 0.8298 (pttt) cc_final: 0.7775 (tttt) REVERT: E 792 MET cc_start: 0.8371 (mtp) cc_final: 0.8148 (mtp) REVERT: E 857 ASN cc_start: 0.7549 (m110) cc_final: 0.7342 (m-40) REVERT: E 1272 ASN cc_start: 0.8077 (m110) cc_final: 0.7812 (m110) REVERT: E 1339 PHE cc_start: 0.8234 (t80) cc_final: 0.8032 (t80) REVERT: E 1906 LEU cc_start: 0.8856 (tt) cc_final: 0.8086 (mt) REVERT: E 1981 GLN cc_start: 0.8269 (tt0) cc_final: 0.7768 (pp30) REVERT: E 2126 ASP cc_start: 0.8233 (m-30) cc_final: 0.8029 (m-30) REVERT: E 2422 MET cc_start: 0.6807 (tmm) cc_final: 0.6489 (tmm) REVERT: E 2530 ASP cc_start: 0.7594 (m-30) cc_final: 0.7214 (m-30) REVERT: E 2535 MET cc_start: 0.8076 (tpp) cc_final: 0.7522 (tpt) REVERT: E 2823 MET cc_start: 0.7270 (mpp) cc_final: 0.7001 (mpp) outliers start: 72 outliers final: 38 residues processed: 816 average time/residue: 0.1960 time to fit residues: 277.7687 Evaluate side-chains 720 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 681 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1244 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1172 THR Chi-restraints excluded: chain D residue 2216 LEU Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 925 LEU Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2061 ILE Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 357 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 421 optimal weight: 10.0000 chunk 338 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 197 optimal weight: 0.0970 chunk 406 optimal weight: 2.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 665 GLN A1318 HIS B 287 HIS B 315 GLN D 232 GLN ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 820 HIS E 920 HIS ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2633 HIS E2696 HIS ** E2856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.185343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.138811 restraints weight = 74875.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.143563 restraints weight = 32533.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145179 restraints weight = 18183.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.145729 restraints weight = 14496.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146048 restraints weight = 13224.983| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 38349 Z= 0.178 Angle : 0.633 10.422 51938 Z= 0.318 Chirality : 0.041 0.201 6006 Planarity : 0.005 0.063 6423 Dihedral : 6.086 144.213 5235 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.58 % Allowed : 12.69 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.88 (0.13), residues: 4418 helix: 1.84 (0.09), residues: 3124 sheet: -0.48 (0.97), residues: 27 loop : -0.13 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D2110 TYR 0.018 0.002 TYR E2210 PHE 0.046 0.002 PHE A 127 TRP 0.027 0.001 TRP D2390 HIS 0.013 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00423 (38338) covalent geometry : angle 0.63259 (51915) SS BOND : bond 0.00319 ( 10) SS BOND : angle 1.37483 ( 20) hydrogen bonds : bond 0.04455 ( 2343) hydrogen bonds : angle 4.21154 ( 6906) link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.29783 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 746 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8433 (tp40) cc_final: 0.8205 (tp40) REVERT: A 150 MET cc_start: 0.7090 (tpp) cc_final: 0.6757 (tpp) REVERT: A 157 TYR cc_start: 0.7760 (m-10) cc_final: 0.7368 (m-80) REVERT: A 176 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7216 (mm-30) REVERT: A 280 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7478 (tp30) REVERT: A 405 TYR cc_start: 0.7786 (p90) cc_final: 0.7436 (p90) REVERT: A 606 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6793 (pm20) REVERT: A 636 LYS cc_start: 0.7180 (mttt) cc_final: 0.6092 (tptp) REVERT: A 663 MET cc_start: 0.9264 (tpt) cc_final: 0.8805 (tpp) REVERT: A 894 ILE cc_start: 0.8597 (mm) cc_final: 0.8347 (pt) REVERT: A 1009 GLU cc_start: 0.8454 (tt0) cc_final: 0.8188 (tm-30) REVERT: A 1072 ASN cc_start: 0.8204 (t0) cc_final: 0.7962 (t0) REVERT: A 1177 ASP cc_start: 0.8308 (m-30) cc_final: 0.8099 (t0) REVERT: A 1234 GLU cc_start: 0.8440 (mp0) cc_final: 0.7793 (tp30) REVERT: A 1244 MET cc_start: 0.7911 (mpp) cc_final: 0.6785 (ttm) REVERT: A 1270 GLN cc_start: 0.7305 (mm110) cc_final: 0.6985 (mm110) REVERT: A 1298 TYR cc_start: 0.5998 (m-80) cc_final: 0.5784 (m-80) REVERT: A 1419 ASN cc_start: 0.8559 (t0) cc_final: 0.8205 (t0) REVERT: A 1501 LEU cc_start: 0.8286 (mt) cc_final: 0.7976 (pp) REVERT: B 231 LEU cc_start: 0.6548 (tt) cc_final: 0.6346 (mp) REVERT: B 232 TRP cc_start: 0.5258 (t60) cc_final: 0.4874 (t60) REVERT: B 269 GLN cc_start: 0.8183 (mt0) cc_final: 0.7963 (mp10) REVERT: B 368 PHE cc_start: 0.4649 (t80) cc_final: 0.4441 (t80) REVERT: C 105 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 146 MET cc_start: 0.5441 (ppp) cc_final: 0.4998 (ppp) REVERT: D 228 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: D 276 MET cc_start: 0.8233 (mmt) cc_final: 0.7467 (mtt) REVERT: D 572 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6859 (tpt) REVERT: D 665 GLU cc_start: 0.6467 (tp30) cc_final: 0.6250 (tp30) REVERT: D 812 MET cc_start: 0.9141 (tpp) cc_final: 0.8600 (mtt) REVERT: D 829 LYS cc_start: 0.8438 (mttp) cc_final: 0.8221 (mmmm) REVERT: D 830 ASP cc_start: 0.8741 (t0) cc_final: 0.8294 (t0) REVERT: D 1171 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6561 (tm-30) REVERT: D 1355 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8213 (tt) REVERT: D 2117 MET cc_start: 0.8316 (tpp) cc_final: 0.8031 (tpp) REVERT: D 2147 MET cc_start: 0.7971 (tpp) cc_final: 0.7443 (tpt) REVERT: D 2609 LYS cc_start: 0.8254 (pttt) cc_final: 0.7742 (mttt) REVERT: E 346 GLU cc_start: 0.6599 (tp30) cc_final: 0.6231 (tp30) REVERT: E 361 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7064 (t-90) REVERT: E 786 HIS cc_start: 0.7078 (t-170) cc_final: 0.6791 (t-170) REVERT: E 792 MET cc_start: 0.8401 (mtp) cc_final: 0.8028 (mtp) REVERT: E 936 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8490 (mm-40) REVERT: E 1192 ASN cc_start: 0.8979 (t0) cc_final: 0.8748 (t0) REVERT: E 1272 ASN cc_start: 0.8127 (m110) cc_final: 0.7910 (m110) REVERT: E 1492 CYS cc_start: 0.8483 (m) cc_final: 0.8242 (m) REVERT: E 1630 MET cc_start: 0.8363 (mmm) cc_final: 0.8114 (mmm) REVERT: E 1741 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7169 (tm-30) REVERT: E 1981 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7777 (pp30) REVERT: E 2198 ILE cc_start: 0.9176 (mm) cc_final: 0.8936 (mt) REVERT: E 2530 ASP cc_start: 0.7714 (m-30) cc_final: 0.7435 (m-30) REVERT: E 2535 MET cc_start: 0.8171 (tpp) cc_final: 0.7757 (tpt) REVERT: E 2546 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8518 (mmtp) REVERT: E 2710 MET cc_start: 0.8200 (tmm) cc_final: 0.7806 (ppp) REVERT: E 2852 ARG cc_start: 0.6751 (mtp180) cc_final: 0.6390 (ptp-170) outliers start: 106 outliers final: 62 residues processed: 808 average time/residue: 0.1951 time to fit residues: 273.7132 Evaluate side-chains 721 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 654 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1567 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 819 ILE Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1048 ILE Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1172 THR Chi-restraints excluded: chain D residue 1174 SER Chi-restraints excluded: chain D residue 1355 LEU Chi-restraints excluded: chain D residue 1367 LEU Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2045 LEU Chi-restraints excluded: chain D residue 2101 SER Chi-restraints excluded: chain D residue 2107 THR Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 910 THR Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 1203 SER Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1895 GLU Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 1981 GLN Chi-restraints excluded: chain E residue 2061 ILE Chi-restraints excluded: chain E residue 2164 LEU Chi-restraints excluded: chain E residue 2321 VAL Chi-restraints excluded: chain E residue 2339 LEU Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 441 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 410 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 301 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1189 HIS B 287 HIS B 315 GLN ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2178 GLN E 820 HIS E 857 ASN E1188 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2633 HIS E2742 GLN E2856 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.185945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139886 restraints weight = 74993.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.144503 restraints weight = 32316.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.146125 restraints weight = 18583.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147444 restraints weight = 14056.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147505 restraints weight = 12264.831| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38349 Z= 0.143 Angle : 0.604 13.535 51938 Z= 0.299 Chirality : 0.040 0.370 6006 Planarity : 0.004 0.065 6423 Dihedral : 5.942 140.466 5235 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.60 % Allowed : 15.29 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.86 (0.13), residues: 4418 helix: 1.83 (0.09), residues: 3143 sheet: -0.34 (0.97), residues: 27 loop : -0.18 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D2110 TYR 0.016 0.001 TYR D 613 PHE 0.045 0.002 PHE A 127 TRP 0.026 0.001 TRP D2390 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00334 (38338) covalent geometry : angle 0.60307 (51915) SS BOND : bond 0.00545 ( 10) SS BOND : angle 1.27662 ( 20) hydrogen bonds : bond 0.04030 ( 2343) hydrogen bonds : angle 4.06022 ( 6906) link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.15390 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 728 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7047 (tpp) cc_final: 0.6682 (tpp) REVERT: A 157 TYR cc_start: 0.7788 (m-10) cc_final: 0.7466 (m-80) REVERT: A 176 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7216 (mm-30) REVERT: A 199 MET cc_start: 0.8151 (tpp) cc_final: 0.7938 (tpp) REVERT: A 280 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7545 (tp30) REVERT: A 405 TYR cc_start: 0.7721 (p90) cc_final: 0.7338 (p90) REVERT: A 422 GLU cc_start: 0.8388 (tp30) cc_final: 0.7982 (tp30) REVERT: A 442 PHE cc_start: 0.6277 (t80) cc_final: 0.5482 (p90) REVERT: A 499 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8018 (tt) REVERT: A 547 MET cc_start: 0.8317 (mmt) cc_final: 0.8082 (mmp) REVERT: A 602 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 636 LYS cc_start: 0.7254 (mttt) cc_final: 0.6122 (tptp) REVERT: A 894 ILE cc_start: 0.8654 (mm) cc_final: 0.8379 (pt) REVERT: A 1072 ASN cc_start: 0.8317 (t0) cc_final: 0.8066 (t0) REVERT: A 1162 ASN cc_start: 0.9036 (t0) cc_final: 0.8513 (t0) REVERT: A 1234 GLU cc_start: 0.8495 (mp0) cc_final: 0.7859 (tp30) REVERT: A 1244 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.6736 (tpp) REVERT: A 1270 GLN cc_start: 0.7321 (mm110) cc_final: 0.6997 (mm-40) REVERT: A 1395 MET cc_start: 0.8807 (ttp) cc_final: 0.8522 (ttp) REVERT: A 1419 ASN cc_start: 0.8533 (t0) cc_final: 0.8158 (t0) REVERT: A 1471 GLN cc_start: 0.7029 (mt0) cc_final: 0.6773 (mt0) REVERT: A 1501 LEU cc_start: 0.8199 (mt) cc_final: 0.7971 (pp) REVERT: A 1520 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6554 (mt-10) REVERT: B 232 TRP cc_start: 0.5115 (t60) cc_final: 0.4865 (t60) REVERT: B 269 GLN cc_start: 0.8249 (mt0) cc_final: 0.8037 (mp10) REVERT: B 274 HIS cc_start: 0.7825 (m-70) cc_final: 0.7555 (m-70) REVERT: B 302 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: C 105 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8066 (pp20) REVERT: C 110 MET cc_start: 0.7616 (tpp) cc_final: 0.7348 (tpp) REVERT: D 228 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7366 (tmm) REVERT: D 276 MET cc_start: 0.8191 (mmt) cc_final: 0.7541 (mtt) REVERT: D 665 GLU cc_start: 0.6453 (tp30) cc_final: 0.6213 (tp30) REVERT: D 812 MET cc_start: 0.9116 (tpp) cc_final: 0.8574 (mtt) REVERT: D 829 LYS cc_start: 0.8245 (mttp) cc_final: 0.8010 (mmmm) REVERT: D 830 ASP cc_start: 0.8706 (t0) cc_final: 0.8332 (t0) REVERT: D 1062 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7535 (tt0) REVERT: D 1075 ASP cc_start: 0.7815 (p0) cc_final: 0.7589 (p0) REVERT: D 1171 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6548 (tm-30) REVERT: D 1355 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8285 (tt) REVERT: D 1397 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: D 2117 MET cc_start: 0.8240 (tpp) cc_final: 0.7941 (tpp) REVERT: D 2147 MET cc_start: 0.7799 (tpp) cc_final: 0.7408 (tpt) REVERT: D 2178 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7195 (mm110) REVERT: D 2609 LYS cc_start: 0.8245 (pttt) cc_final: 0.7736 (mttt) REVERT: E 361 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7147 (t-90) REVERT: E 792 MET cc_start: 0.8392 (mtp) cc_final: 0.8027 (mtp) REVERT: E 936 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8443 (mm-40) REVERT: E 1184 MET cc_start: 0.9079 (mmm) cc_final: 0.8405 (mpp) REVERT: E 1192 ASN cc_start: 0.8922 (t0) cc_final: 0.8625 (t0) REVERT: E 1272 ASN cc_start: 0.8081 (m110) cc_final: 0.7842 (m110) REVERT: E 1693 MET cc_start: 0.7818 (mmm) cc_final: 0.7567 (mmm) REVERT: E 1741 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7093 (tm-30) REVERT: E 1920 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: E 1981 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7736 (pp30) REVERT: E 2069 SER cc_start: 0.8850 (p) cc_final: 0.8629 (t) REVERT: E 2198 ILE cc_start: 0.9158 (mm) cc_final: 0.8914 (mt) REVERT: E 2494 GLU cc_start: 0.8731 (tt0) cc_final: 0.8189 (tp30) REVERT: E 2530 ASP cc_start: 0.7797 (m-30) cc_final: 0.7573 (m-30) REVERT: E 2535 MET cc_start: 0.8258 (tpp) cc_final: 0.7625 (tpt) REVERT: E 2565 MET cc_start: 0.7920 (ttt) cc_final: 0.7681 (ttt) REVERT: E 2646 MET cc_start: 0.5703 (pmm) cc_final: 0.5004 (pmm) REVERT: E 2823 MET cc_start: 0.7729 (mpp) cc_final: 0.7344 (mpp) outliers start: 107 outliers final: 53 residues processed: 785 average time/residue: 0.1946 time to fit residues: 265.9470 Evaluate side-chains 725 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 662 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1244 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1355 LEU Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 1397 MET Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 910 THR Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1203 SER Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1759 THR Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1895 GLU Chi-restraints excluded: chain E residue 1920 PHE Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 1981 GLN Chi-restraints excluded: chain E residue 2061 ILE Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 111 optimal weight: 0.7980 chunk 320 optimal weight: 6.9990 chunk 270 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 397 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 205 optimal weight: 0.0170 overall best weight: 1.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS B 287 HIS B 338 GLN B 348 ASN ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 841 GLN E1188 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2633 HIS E2742 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.186040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.140111 restraints weight = 74679.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.144872 restraints weight = 31954.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146743 restraints weight = 17922.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.147715 restraints weight = 13709.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.147802 restraints weight = 11913.054| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38349 Z= 0.124 Angle : 0.594 12.495 51938 Z= 0.291 Chirality : 0.039 0.334 6006 Planarity : 0.004 0.066 6423 Dihedral : 5.798 134.996 5235 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.87 % Allowed : 16.61 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.89 (0.13), residues: 4418 helix: 1.86 (0.09), residues: 3152 sheet: -0.20 (0.96), residues: 27 loop : -0.25 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 127 TYR 0.026 0.001 TYR D 613 PHE 0.026 0.001 PHE D2478 TRP 0.029 0.001 TRP D2390 HIS 0.012 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00284 (38338) covalent geometry : angle 0.59328 (51915) SS BOND : bond 0.00232 ( 10) SS BOND : angle 1.24976 ( 20) hydrogen bonds : bond 0.03802 ( 2343) hydrogen bonds : angle 3.97799 ( 6906) link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.22808 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 719 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.5616 (tmm) cc_final: 0.5394 (tpp) REVERT: A 150 MET cc_start: 0.7024 (tpp) cc_final: 0.6614 (tpp) REVERT: A 157 TYR cc_start: 0.7809 (m-10) cc_final: 0.7501 (m-80) REVERT: A 176 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 199 MET cc_start: 0.8127 (tpp) cc_final: 0.7873 (tpp) REVERT: A 280 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7598 (tp30) REVERT: A 296 TRP cc_start: 0.7442 (p-90) cc_final: 0.7114 (p-90) REVERT: A 405 TYR cc_start: 0.7705 (p90) cc_final: 0.7318 (p90) REVERT: A 422 GLU cc_start: 0.8382 (tp30) cc_final: 0.7882 (tp30) REVERT: A 442 PHE cc_start: 0.6314 (t80) cc_final: 0.5466 (p90) REVERT: A 499 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 563 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9041 (t) REVERT: A 602 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 606 GLU cc_start: 0.9102 (pm20) cc_final: 0.7800 (mm-30) REVERT: A 636 LYS cc_start: 0.7295 (mttt) cc_final: 0.6127 (tmtt) REVERT: A 894 ILE cc_start: 0.8606 (mm) cc_final: 0.8341 (pt) REVERT: A 1072 ASN cc_start: 0.8341 (t0) cc_final: 0.7945 (t0) REVERT: A 1234 GLU cc_start: 0.8501 (mp0) cc_final: 0.7828 (tp30) REVERT: A 1244 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6682 (tpp) REVERT: A 1298 TYR cc_start: 0.5487 (m-80) cc_final: 0.5235 (m-80) REVERT: A 1419 ASN cc_start: 0.8451 (t0) cc_final: 0.8213 (t0) REVERT: A 1501 LEU cc_start: 0.8204 (mt) cc_final: 0.8003 (pp) REVERT: A 1520 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6469 (mt-10) REVERT: B 230 THR cc_start: 0.6026 (m) cc_final: 0.5516 (m) REVERT: B 269 GLN cc_start: 0.8193 (mt0) cc_final: 0.7973 (mp10) REVERT: B 274 HIS cc_start: 0.7783 (m-70) cc_final: 0.7519 (m-70) REVERT: B 302 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: C 90 PHE cc_start: 0.1188 (m-80) cc_final: 0.0956 (m-80) REVERT: C 105 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8318 (tm-30) REVERT: D 226 MET cc_start: 0.5191 (mtt) cc_final: 0.3857 (tpt) REVERT: D 228 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7460 (tmm) REVERT: D 276 MET cc_start: 0.8174 (mmt) cc_final: 0.7529 (mtt) REVERT: D 665 GLU cc_start: 0.6410 (tp30) cc_final: 0.6182 (tp30) REVERT: D 812 MET cc_start: 0.9127 (tpp) cc_final: 0.8591 (mtt) REVERT: D 1062 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7492 (tt0) REVERT: D 1171 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6438 (tm-30) REVERT: D 1275 GLN cc_start: 0.7879 (mp10) cc_final: 0.7532 (mt0) REVERT: D 1303 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7544 (tttt) REVERT: D 1355 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8296 (tt) REVERT: D 2117 MET cc_start: 0.8243 (tpp) cc_final: 0.7919 (tpp) REVERT: D 2158 MET cc_start: 0.8822 (mmm) cc_final: 0.8334 (mmt) REVERT: D 2559 MET cc_start: 0.7214 (tpp) cc_final: 0.6673 (tpt) REVERT: D 2609 LYS cc_start: 0.8240 (pttt) cc_final: 0.7738 (mttt) REVERT: E 346 GLU cc_start: 0.6717 (tp30) cc_final: 0.6482 (tp30) REVERT: E 361 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7154 (t-90) REVERT: E 792 MET cc_start: 0.8374 (mtp) cc_final: 0.8017 (mtp) REVERT: E 936 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8362 (mm-40) REVERT: E 1184 MET cc_start: 0.9031 (mmm) cc_final: 0.8535 (mpp) REVERT: E 1192 ASN cc_start: 0.8848 (t0) cc_final: 0.8512 (t0) REVERT: E 1272 ASN cc_start: 0.7888 (m110) cc_final: 0.7680 (m110) REVERT: E 1741 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7107 (tm-30) REVERT: E 1920 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: E 2069 SER cc_start: 0.8888 (p) cc_final: 0.8659 (t) REVERT: E 2157 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8691 (tp) REVERT: E 2198 ILE cc_start: 0.9162 (mm) cc_final: 0.8918 (mt) REVERT: E 2494 GLU cc_start: 0.8684 (tt0) cc_final: 0.8161 (tp30) REVERT: E 2530 ASP cc_start: 0.7731 (m-30) cc_final: 0.7511 (m-30) REVERT: E 2535 MET cc_start: 0.8230 (tpp) cc_final: 0.7589 (tpt) REVERT: E 2546 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8291 (mmtp) REVERT: E 2646 MET cc_start: 0.5824 (pmm) cc_final: 0.5301 (pmm) REVERT: E 2823 MET cc_start: 0.7761 (mpp) cc_final: 0.7396 (mpp) outliers start: 118 outliers final: 65 residues processed: 786 average time/residue: 0.1911 time to fit residues: 262.6369 Evaluate side-chains 745 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 670 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1244 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1048 ILE Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1355 LEU Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2107 THR Chi-restraints excluded: chain D residue 2125 ILE Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2341 LEU Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 825 GLU Chi-restraints excluded: chain E residue 831 LEU Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1203 SER Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1895 GLU Chi-restraints excluded: chain E residue 1920 PHE Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2157 LEU Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2302 ASP Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2597 HIS Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 65 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 165 optimal weight: 50.0000 chunk 459 optimal weight: 5.9990 chunk 434 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 322 optimal weight: 9.9990 chunk 248 optimal weight: 0.0980 chunk 454 optimal weight: 0.3980 chunk 303 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS B 323 ASN B 348 ASN ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN E 87 HIS E 841 GLN E1188 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.185892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.139888 restraints weight = 74408.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.144623 restraints weight = 31765.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.146537 restraints weight = 18208.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.147459 restraints weight = 13519.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.147633 restraints weight = 12035.342| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38349 Z= 0.116 Angle : 0.595 12.067 51938 Z= 0.289 Chirality : 0.039 0.308 6006 Planarity : 0.004 0.068 6423 Dihedral : 5.661 128.727 5235 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.70 % Allowed : 17.55 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.96 (0.13), residues: 4418 helix: 1.92 (0.09), residues: 3146 sheet: -0.09 (0.94), residues: 27 loop : -0.24 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D2110 TYR 0.016 0.001 TYR E 928 PHE 0.019 0.001 PHE D1153 TRP 0.034 0.001 TRP D2390 HIS 0.018 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00258 (38338) covalent geometry : angle 0.59428 (51915) SS BOND : bond 0.00227 ( 10) SS BOND : angle 1.13749 ( 20) hydrogen bonds : bond 0.03574 ( 2343) hydrogen bonds : angle 3.92194 ( 6906) link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.31012 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 715 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7206 (tpp) cc_final: 0.6759 (tpp) REVERT: A 157 TYR cc_start: 0.7793 (m-10) cc_final: 0.7527 (m-80) REVERT: A 176 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7199 (mm-30) REVERT: A 280 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7662 (tp30) REVERT: A 296 TRP cc_start: 0.7471 (p-90) cc_final: 0.7124 (p-90) REVERT: A 405 TYR cc_start: 0.7683 (p90) cc_final: 0.7298 (p90) REVERT: A 422 GLU cc_start: 0.8410 (tp30) cc_final: 0.7921 (tp30) REVERT: A 442 PHE cc_start: 0.6238 (t80) cc_final: 0.5405 (p90) REVERT: A 563 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9045 (t) REVERT: A 602 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8146 (mp) REVERT: A 606 GLU cc_start: 0.9118 (pm20) cc_final: 0.7832 (mm-30) REVERT: A 636 LYS cc_start: 0.7311 (mttt) cc_final: 0.6104 (tptp) REVERT: A 894 ILE cc_start: 0.8517 (mm) cc_final: 0.8221 (pt) REVERT: A 963 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8665 (mp) REVERT: A 1009 GLU cc_start: 0.8722 (tp30) cc_final: 0.8487 (tp30) REVERT: A 1072 ASN cc_start: 0.8337 (t0) cc_final: 0.7901 (t0) REVERT: A 1227 LEU cc_start: 0.8523 (mm) cc_final: 0.8137 (mm) REVERT: A 1244 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6772 (tpp) REVERT: A 1395 MET cc_start: 0.8718 (ttp) cc_final: 0.8431 (ttp) REVERT: A 1419 ASN cc_start: 0.8431 (t0) cc_final: 0.8219 (t0) REVERT: A 1471 GLN cc_start: 0.6984 (mt0) cc_final: 0.6717 (mt0) REVERT: A 1520 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6601 (mt-10) REVERT: A 1546 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7682 (mmtp) REVERT: B 230 THR cc_start: 0.5960 (m) cc_final: 0.5738 (m) REVERT: B 231 LEU cc_start: 0.6772 (tt) cc_final: 0.6570 (mp) REVERT: B 269 GLN cc_start: 0.8155 (mt0) cc_final: 0.7945 (mp10) REVERT: C 90 PHE cc_start: 0.1226 (m-80) cc_final: 0.0996 (m-80) REVERT: C 146 MET cc_start: 0.4927 (ppp) cc_final: 0.4335 (ppp) REVERT: D 226 MET cc_start: 0.5173 (mtt) cc_final: 0.3892 (tpt) REVERT: D 228 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7552 (ppp) REVERT: D 276 MET cc_start: 0.8113 (mmt) cc_final: 0.7456 (mtt) REVERT: D 812 MET cc_start: 0.9140 (tpp) cc_final: 0.8590 (mtt) REVERT: D 1062 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7460 (tt0) REVERT: D 1171 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6447 (tm-30) REVERT: D 1275 GLN cc_start: 0.7995 (mp10) cc_final: 0.7765 (mt0) REVERT: D 1303 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7559 (tttt) REVERT: D 1355 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8214 (tt) REVERT: D 2117 MET cc_start: 0.8235 (tpp) cc_final: 0.7905 (tpp) REVERT: D 2147 MET cc_start: 0.7493 (tpp) cc_final: 0.7115 (tpt) REVERT: D 2158 MET cc_start: 0.8682 (mmm) cc_final: 0.8439 (mmt) REVERT: D 2235 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7965 (mm) REVERT: D 2609 LYS cc_start: 0.8228 (pttt) cc_final: 0.7732 (mttt) REVERT: E 361 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.7202 (t-90) REVERT: E 792 MET cc_start: 0.8341 (mtp) cc_final: 0.8047 (mtp) REVERT: E 936 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8282 (mm-40) REVERT: E 1184 MET cc_start: 0.9059 (mmm) cc_final: 0.8645 (mpp) REVERT: E 1192 ASN cc_start: 0.8788 (t0) cc_final: 0.8455 (t0) REVERT: E 1741 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7106 (tm-30) REVERT: E 1916 ASN cc_start: 0.8861 (m-40) cc_final: 0.8341 (m-40) REVERT: E 1920 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8049 (m-10) REVERT: E 2003 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7452 (tm-30) REVERT: E 2157 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8643 (tp) REVERT: E 2198 ILE cc_start: 0.9184 (mm) cc_final: 0.8949 (mt) REVERT: E 2330 LEU cc_start: 0.8874 (tp) cc_final: 0.8622 (tp) REVERT: E 2530 ASP cc_start: 0.7711 (m-30) cc_final: 0.7498 (m-30) REVERT: E 2535 MET cc_start: 0.8199 (tpp) cc_final: 0.7568 (tpt) REVERT: E 2546 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8306 (mmtp) REVERT: E 2646 MET cc_start: 0.5799 (pmm) cc_final: 0.5241 (pmm) outliers start: 111 outliers final: 65 residues processed: 778 average time/residue: 0.2019 time to fit residues: 272.7070 Evaluate side-chains 745 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 670 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1244 MET Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1355 LEU Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2235 LEU Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2341 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 825 GLU Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1203 SER Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1920 PHE Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2157 LEU Chi-restraints excluded: chain E residue 2339 LEU Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2363 SER Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2619 CYS Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN B 287 HIS B 338 GLN B 348 ASN ** D 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2526 HIS D2537 HIS D2576 GLN E 87 HIS E 841 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2856 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.177903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131808 restraints weight = 73102.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.135766 restraints weight = 30418.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.138183 restraints weight = 18048.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139672 restraints weight = 13177.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.140521 restraints weight = 10925.361| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 38349 Z= 0.238 Angle : 0.739 13.367 51938 Z= 0.366 Chirality : 0.044 0.305 6006 Planarity : 0.005 0.068 6423 Dihedral : 6.041 109.981 5235 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.45 % Allowed : 18.53 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.42 (0.13), residues: 4418 helix: 1.54 (0.09), residues: 3134 sheet: -1.04 (0.77), residues: 37 loop : -0.44 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D2110 TYR 0.019 0.002 TYR E2210 PHE 0.062 0.002 PHE A 110 TRP 0.036 0.002 TRP D2390 HIS 0.006 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00568 (38338) covalent geometry : angle 0.73889 (51915) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.34802 ( 20) hydrogen bonds : bond 0.04970 ( 2343) hydrogen bonds : angle 4.35343 ( 6906) link_NAG-ASN : bond 0.00284 ( 1) link_NAG-ASN : angle 1.58134 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 713 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7362 (tpp) cc_final: 0.6949 (tpp) REVERT: A 176 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 280 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7722 (tp30) REVERT: A 296 TRP cc_start: 0.7599 (p-90) cc_final: 0.7343 (p-90) REVERT: A 405 TYR cc_start: 0.7948 (p90) cc_final: 0.7549 (p90) REVERT: A 422 GLU cc_start: 0.8383 (tp30) cc_final: 0.7889 (tp30) REVERT: A 474 PHE cc_start: 0.8212 (m-10) cc_final: 0.7789 (m-10) REVERT: A 602 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8317 (mp) REVERT: A 636 LYS cc_start: 0.7145 (mttt) cc_final: 0.6074 (tmtt) REVERT: A 894 ILE cc_start: 0.8687 (mm) cc_final: 0.8365 (tp) REVERT: A 938 MET cc_start: 0.8854 (mpp) cc_final: 0.8558 (mpp) REVERT: A 1173 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7548 (mtt90) REVERT: A 1227 LEU cc_start: 0.8766 (mm) cc_final: 0.8290 (mm) REVERT: A 1234 GLU cc_start: 0.8281 (mp0) cc_final: 0.7642 (tp30) REVERT: A 1244 MET cc_start: 0.7687 (mpp) cc_final: 0.6807 (tpp) REVERT: A 1335 SER cc_start: 0.9010 (m) cc_final: 0.8398 (p) REVERT: A 1471 GLN cc_start: 0.7044 (mt0) cc_final: 0.6662 (mt0) REVERT: A 1520 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6490 (mt-10) REVERT: A 1546 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7760 (mmmt) REVERT: A 1561 TYR cc_start: 0.6590 (t80) cc_final: 0.6372 (t80) REVERT: B 269 GLN cc_start: 0.8071 (mt0) cc_final: 0.7858 (mp10) REVERT: B 302 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: D 228 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7511 (ppp) REVERT: D 276 MET cc_start: 0.8226 (mmt) cc_final: 0.7500 (mtt) REVERT: D 812 MET cc_start: 0.9081 (tpp) cc_final: 0.8579 (mtt) REVERT: D 1062 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7667 (tt0) REVERT: D 1081 LYS cc_start: 0.7474 (pptt) cc_final: 0.7118 (pttp) REVERT: D 1171 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6823 (tm-30) REVERT: D 1303 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7525 (tttt) REVERT: D 2117 MET cc_start: 0.8307 (tpp) cc_final: 0.7875 (tpp) REVERT: D 2158 MET cc_start: 0.8723 (mmm) cc_final: 0.8446 (mmt) REVERT: D 2178 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7549 (mm-40) REVERT: D 2246 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: D 2609 LYS cc_start: 0.8291 (pttt) cc_final: 0.7778 (mttt) REVERT: E 361 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7252 (t-90) REVERT: E 792 MET cc_start: 0.8494 (mtp) cc_final: 0.8110 (mtp) REVERT: E 825 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: E 930 ASP cc_start: 0.8451 (m-30) cc_final: 0.8096 (m-30) REVERT: E 936 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8345 (mm-40) REVERT: E 1184 MET cc_start: 0.9180 (mmm) cc_final: 0.8667 (mpp) REVERT: E 1192 ASN cc_start: 0.8880 (t0) cc_final: 0.8533 (t0) REVERT: E 1269 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7346 (pp) REVERT: E 1471 SER cc_start: 0.8636 (m) cc_final: 0.8277 (p) REVERT: E 1606 MET cc_start: 0.8352 (tpp) cc_final: 0.7818 (tpp) REVERT: E 1741 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7113 (tm-30) REVERT: E 1907 MET cc_start: 0.8656 (mmm) cc_final: 0.8182 (mmm) REVERT: E 1909 MET cc_start: 0.8323 (tmm) cc_final: 0.7954 (tmm) REVERT: E 1937 MET cc_start: 0.7706 (mtp) cc_final: 0.7189 (mtp) REVERT: E 2003 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7954 (tm-30) REVERT: E 2157 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8896 (tp) REVERT: E 2198 ILE cc_start: 0.9172 (mm) cc_final: 0.8960 (mt) REVERT: E 2313 ASP cc_start: 0.8183 (t0) cc_final: 0.7978 (t70) REVERT: E 2530 ASP cc_start: 0.8088 (m-30) cc_final: 0.7884 (m-30) REVERT: E 2535 MET cc_start: 0.8153 (tpp) cc_final: 0.7880 (tpt) REVERT: E 2546 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8364 (mmtp) REVERT: E 2599 MET cc_start: 0.6383 (pmm) cc_final: 0.5859 (ppp) REVERT: E 2646 MET cc_start: 0.6347 (pmm) cc_final: 0.5481 (pmm) outliers start: 142 outliers final: 90 residues processed: 799 average time/residue: 0.2038 time to fit residues: 278.7601 Evaluate side-chains 762 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 664 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1026 LEU Chi-restraints excluded: chain D residue 1048 ILE Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1172 THR Chi-restraints excluded: chain D residue 1174 SER Chi-restraints excluded: chain D residue 1301 SER Chi-restraints excluded: chain D residue 1367 LEU Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2045 LEU Chi-restraints excluded: chain D residue 2107 THR Chi-restraints excluded: chain D residue 2235 LEU Chi-restraints excluded: chain D residue 2246 TYR Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2341 LEU Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2533 MET Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 825 GLU Chi-restraints excluded: chain E residue 909 ILE Chi-restraints excluded: chain E residue 910 THR Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1269 LEU Chi-restraints excluded: chain E residue 1499 ILE Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2157 LEU Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2164 LEU Chi-restraints excluded: chain E residue 2302 ASP Chi-restraints excluded: chain E residue 2316 ASP Chi-restraints excluded: chain E residue 2339 LEU Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2363 SER Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2597 HIS Chi-restraints excluded: chain E residue 2619 CYS Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 69 optimal weight: 0.9980 chunk 427 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 318 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 387 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS B 348 ASN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1320 GLN E 87 HIS E 933 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2633 HIS E2742 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.181519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135456 restraints weight = 74217.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.140153 restraints weight = 32179.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141880 restraints weight = 17949.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142867 restraints weight = 13892.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142960 restraints weight = 11989.745| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38349 Z= 0.168 Angle : 0.669 13.892 51938 Z= 0.326 Chirality : 0.042 0.312 6006 Planarity : 0.005 0.068 6423 Dihedral : 5.747 97.011 5235 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.87 % Allowed : 19.72 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.51 (0.13), residues: 4418 helix: 1.62 (0.09), residues: 3138 sheet: -1.07 (0.75), residues: 37 loop : -0.45 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D2110 TYR 0.019 0.001 TYR E 849 PHE 0.037 0.002 PHE A 110 TRP 0.041 0.002 TRP D2390 HIS 0.035 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00405 (38338) covalent geometry : angle 0.66817 (51915) SS BOND : bond 0.00261 ( 10) SS BOND : angle 1.20507 ( 20) hydrogen bonds : bond 0.04264 ( 2343) hydrogen bonds : angle 4.16339 ( 6906) link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 1.36777 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 709 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7300 (tt) REVERT: A 150 MET cc_start: 0.7305 (tpp) cc_final: 0.6875 (tpp) REVERT: A 176 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7095 (mm-30) REVERT: A 199 MET cc_start: 0.8340 (tpp) cc_final: 0.8126 (tpp) REVERT: A 280 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7703 (tp30) REVERT: A 296 TRP cc_start: 0.7735 (p-90) cc_final: 0.7366 (p-90) REVERT: A 405 TYR cc_start: 0.7879 (p90) cc_final: 0.7441 (p90) REVERT: A 422 GLU cc_start: 0.8427 (tp30) cc_final: 0.7911 (tp30) REVERT: A 430 ASP cc_start: 0.8078 (m-30) cc_final: 0.7432 (t0) REVERT: A 442 PHE cc_start: 0.6353 (t80) cc_final: 0.5626 (p90) REVERT: A 602 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 636 LYS cc_start: 0.7147 (mttt) cc_final: 0.6026 (tmtt) REVERT: A 894 ILE cc_start: 0.8676 (mm) cc_final: 0.8356 (tp) REVERT: A 1072 ASN cc_start: 0.8274 (t0) cc_final: 0.7721 (t0) REVERT: A 1173 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7570 (mtt90) REVERT: A 1227 LEU cc_start: 0.8696 (mm) cc_final: 0.8280 (mm) REVERT: A 1244 MET cc_start: 0.7636 (mpp) cc_final: 0.6821 (tpp) REVERT: A 1471 GLN cc_start: 0.7075 (mt0) cc_final: 0.6707 (mt0) REVERT: A 1520 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6660 (mt-10) REVERT: A 1546 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7713 (mmmt) REVERT: B 302 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: B 315 GLN cc_start: 0.7818 (tt0) cc_final: 0.7527 (mt0) REVERT: D 228 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7524 (ppp) REVERT: D 276 MET cc_start: 0.8289 (mmt) cc_final: 0.7568 (mtt) REVERT: D 1062 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7591 (tt0) REVERT: D 1171 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6765 (tm-30) REVERT: D 1303 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7549 (tttt) REVERT: D 2117 MET cc_start: 0.8292 (tpp) cc_final: 0.7899 (tpp) REVERT: D 2178 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7494 (mm-40) REVERT: D 2246 TYR cc_start: 0.8346 (t80) cc_final: 0.7337 (m-80) REVERT: D 2371 MET cc_start: 0.5640 (tpt) cc_final: 0.5261 (tpt) REVERT: D 2425 HIS cc_start: 0.7131 (t-90) cc_final: 0.6899 (t-90) REVERT: D 2486 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7703 (m) REVERT: D 2609 LYS cc_start: 0.8273 (pttt) cc_final: 0.7760 (mttt) REVERT: E 361 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: E 788 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8053 (mp) REVERT: E 792 MET cc_start: 0.8516 (mtp) cc_final: 0.8125 (mtp) REVERT: E 936 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8309 (mm-40) REVERT: E 1192 ASN cc_start: 0.8870 (t0) cc_final: 0.8563 (t0) REVERT: E 1471 SER cc_start: 0.8649 (m) cc_final: 0.8432 (p) REVERT: E 1741 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7175 (tm-30) REVERT: E 1909 MET cc_start: 0.8292 (tmm) cc_final: 0.7863 (tmm) REVERT: E 1920 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: E 2003 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7809 (tm-30) REVERT: E 2044 MET cc_start: 0.7143 (ttp) cc_final: 0.6867 (ttp) REVERT: E 2157 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8788 (tp) REVERT: E 2198 ILE cc_start: 0.9174 (mm) cc_final: 0.8948 (mt) REVERT: E 2313 ASP cc_start: 0.8098 (t0) cc_final: 0.7853 (t70) REVERT: E 2494 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8486 (tt0) REVERT: E 2530 ASP cc_start: 0.8101 (m-30) cc_final: 0.7887 (m-30) REVERT: E 2535 MET cc_start: 0.8251 (tpp) cc_final: 0.7974 (tpt) REVERT: E 2646 MET cc_start: 0.6123 (pmm) cc_final: 0.5346 (pmm) REVERT: E 2804 CYS cc_start: 0.8294 (t) cc_final: 0.7670 (p) outliers start: 118 outliers final: 86 residues processed: 776 average time/residue: 0.2074 time to fit residues: 275.4159 Evaluate side-chains 774 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 679 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1048 ILE Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1301 SER Chi-restraints excluded: chain D residue 1367 LEU Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2045 LEU Chi-restraints excluded: chain D residue 2068 MET Chi-restraints excluded: chain D residue 2107 THR Chi-restraints excluded: chain D residue 2235 LEU Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2281 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2486 CYS Chi-restraints excluded: chain D residue 2533 MET Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 825 GLU Chi-restraints excluded: chain E residue 831 LEU Chi-restraints excluded: chain E residue 910 THR Chi-restraints excluded: chain E residue 925 LEU Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1341 LEU Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1764 TYR Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1920 PHE Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2157 LEU Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2164 LEU Chi-restraints excluded: chain E residue 2302 ASP Chi-restraints excluded: chain E residue 2339 LEU Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2592 MET Chi-restraints excluded: chain E residue 2619 CYS Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 199 optimal weight: 6.9990 chunk 448 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 405 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 390 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 328 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 430 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS B 348 ASN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 933 GLN E1347 GLN E1880 ASN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2633 HIS E2742 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.179503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132793 restraints weight = 71264.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137187 restraints weight = 32171.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139010 restraints weight = 17644.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139691 restraints weight = 13228.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140010 restraints weight = 12167.895| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38349 Z= 0.137 Angle : 0.654 14.070 51938 Z= 0.318 Chirality : 0.041 0.340 6006 Planarity : 0.004 0.071 6423 Dihedral : 5.519 80.866 5235 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.58 % Allowed : 20.11 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.58 (0.13), residues: 4418 helix: 1.68 (0.09), residues: 3147 sheet: -0.94 (0.75), residues: 37 loop : -0.45 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D2110 TYR 0.018 0.001 TYR E 849 PHE 0.062 0.001 PHE D2478 TRP 0.049 0.001 TRP D2390 HIS 0.004 0.001 HIS D 240 Details of bonding type rmsd covalent geometry : bond 0.00321 (38338) covalent geometry : angle 0.65324 (51915) SS BOND : bond 0.00224 ( 10) SS BOND : angle 1.12922 ( 20) hydrogen bonds : bond 0.03957 ( 2343) hydrogen bonds : angle 4.08034 ( 6906) link_NAG-ASN : bond 0.00077 ( 1) link_NAG-ASN : angle 1.36432 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 706 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6810 (tpp) cc_final: 0.6408 (tpp) REVERT: A 150 MET cc_start: 0.7284 (tpp) cc_final: 0.6869 (tpp) REVERT: A 176 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 280 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7697 (tp30) REVERT: A 296 TRP cc_start: 0.7610 (p-90) cc_final: 0.7317 (p-90) REVERT: A 405 TYR cc_start: 0.7767 (p90) cc_final: 0.7340 (p90) REVERT: A 422 GLU cc_start: 0.8407 (tp30) cc_final: 0.7925 (tp30) REVERT: A 430 ASP cc_start: 0.8042 (m-30) cc_final: 0.7402 (t0) REVERT: A 442 PHE cc_start: 0.6382 (t80) cc_final: 0.5653 (p90) REVERT: A 602 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 894 ILE cc_start: 0.8667 (mm) cc_final: 0.8360 (pt) REVERT: A 1162 ASN cc_start: 0.8833 (t0) cc_final: 0.8408 (t0) REVERT: A 1173 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7822 (mtt90) REVERT: A 1227 LEU cc_start: 0.8620 (mm) cc_final: 0.8219 (mm) REVERT: A 1234 GLU cc_start: 0.8490 (mp0) cc_final: 0.7732 (tp30) REVERT: A 1244 MET cc_start: 0.7639 (mpp) cc_final: 0.6869 (tpp) REVERT: A 1471 GLN cc_start: 0.7168 (mt0) cc_final: 0.6780 (mt0) REVERT: A 1520 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6649 (mt-10) REVERT: A 1546 LYS cc_start: 0.8442 (mmmt) cc_final: 0.7846 (mmmt) REVERT: A 1561 TYR cc_start: 0.6545 (t80) cc_final: 0.6305 (t80) REVERT: B 269 GLN cc_start: 0.8163 (mp10) cc_final: 0.7723 (mp10) REVERT: B 302 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: B 315 GLN cc_start: 0.7816 (tt0) cc_final: 0.7569 (mt0) REVERT: D 228 MET cc_start: 0.8189 (pmm) cc_final: 0.7370 (ppp) REVERT: D 264 TYR cc_start: 0.5014 (m-80) cc_final: 0.4445 (m-10) REVERT: D 276 MET cc_start: 0.8334 (mmt) cc_final: 0.7639 (mtt) REVERT: D 1062 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7497 (tt0) REVERT: D 1171 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6607 (tm-30) REVERT: D 1303 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7671 (tttt) REVERT: D 2117 MET cc_start: 0.8283 (tpp) cc_final: 0.7976 (tpp) REVERT: D 2178 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7448 (mm-40) REVERT: D 2246 TYR cc_start: 0.8350 (t80) cc_final: 0.7278 (m-80) REVERT: D 2371 MET cc_start: 0.5664 (tpt) cc_final: 0.5309 (tpt) REVERT: D 2486 CYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7777 (m) REVERT: D 2609 LYS cc_start: 0.8273 (pttt) cc_final: 0.7764 (mttt) REVERT: E 361 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.7073 (t-90) REVERT: E 788 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8023 (mp) REVERT: E 792 MET cc_start: 0.8419 (mtp) cc_final: 0.8065 (mtp) REVERT: E 936 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8169 (mm-40) REVERT: E 1184 MET cc_start: 0.9007 (mmm) cc_final: 0.8284 (mpp) REVERT: E 1192 ASN cc_start: 0.8733 (t0) cc_final: 0.8489 (t0) REVERT: E 1741 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7151 (tm-30) REVERT: E 1906 LEU cc_start: 0.8967 (tt) cc_final: 0.8727 (tp) REVERT: E 1916 ASN cc_start: 0.8839 (m-40) cc_final: 0.8411 (m-40) REVERT: E 2003 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7771 (tm-30) REVERT: E 2044 MET cc_start: 0.7187 (ttp) cc_final: 0.6864 (ttp) REVERT: E 2087 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8386 (mm110) REVERT: E 2157 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8697 (tp) REVERT: E 2198 ILE cc_start: 0.9205 (mm) cc_final: 0.8978 (mt) REVERT: E 2494 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8358 (tt0) REVERT: E 2535 MET cc_start: 0.8131 (tpp) cc_final: 0.7853 (tpt) REVERT: E 2584 LEU cc_start: 0.8062 (tp) cc_final: 0.7838 (pp) REVERT: E 2599 MET cc_start: 0.6656 (pmm) cc_final: 0.6309 (ppp) REVERT: E 2646 MET cc_start: 0.6095 (pmm) cc_final: 0.5411 (pmm) REVERT: E 2804 CYS cc_start: 0.8478 (t) cc_final: 0.7829 (p) outliers start: 106 outliers final: 79 residues processed: 767 average time/residue: 0.2040 time to fit residues: 270.1235 Evaluate side-chains 762 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 677 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1301 SER Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2045 LEU Chi-restraints excluded: chain D residue 2068 MET Chi-restraints excluded: chain D residue 2107 THR Chi-restraints excluded: chain D residue 2175 ASN Chi-restraints excluded: chain D residue 2235 LEU Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2281 LEU Chi-restraints excluded: chain D residue 2341 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2486 CYS Chi-restraints excluded: chain D residue 2533 MET Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 825 GLU Chi-restraints excluded: chain E residue 831 LEU Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1341 LEU Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2157 LEU Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2302 ASP Chi-restraints excluded: chain E residue 2339 LEU Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2496 LEU Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2597 HIS Chi-restraints excluded: chain E residue 2619 CYS Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 426 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 137 optimal weight: 50.0000 chunk 392 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 435 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS ** D1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 933 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2633 HIS E2742 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.177215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130778 restraints weight = 70463.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134932 restraints weight = 32426.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136322 restraints weight = 17860.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137193 restraints weight = 14041.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137240 restraints weight = 12791.543| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 38349 Z= 0.187 Angle : 0.709 13.186 51938 Z= 0.346 Chirality : 0.043 0.347 6006 Planarity : 0.005 0.070 6423 Dihedral : 5.589 73.948 5235 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.67 % Allowed : 20.47 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.39 (0.13), residues: 4418 helix: 1.55 (0.09), residues: 3141 sheet: -1.16 (0.71), residues: 37 loop : -0.55 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D2110 TYR 0.021 0.002 TYR D1313 PHE 0.038 0.002 PHE A 110 TRP 0.052 0.002 TRP D2390 HIS 0.023 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00449 (38338) covalent geometry : angle 0.70835 (51915) SS BOND : bond 0.00222 ( 10) SS BOND : angle 1.19681 ( 20) hydrogen bonds : bond 0.04392 ( 2343) hydrogen bonds : angle 4.24593 ( 6906) link_NAG-ASN : bond 0.00269 ( 1) link_NAG-ASN : angle 1.30298 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8836 Ramachandran restraints generated. 4418 Oldfield, 0 Emsley, 4418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 677 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6990 (tpp) cc_final: 0.6572 (tpp) REVERT: A 81 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7356 (tt) REVERT: A 150 MET cc_start: 0.7298 (tpp) cc_final: 0.6924 (tpp) REVERT: A 176 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6793 (mm-30) REVERT: A 280 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7882 (tp30) REVERT: A 296 TRP cc_start: 0.7781 (p-90) cc_final: 0.7431 (p-90) REVERT: A 405 TYR cc_start: 0.7852 (p90) cc_final: 0.7395 (p90) REVERT: A 430 ASP cc_start: 0.8116 (m-30) cc_final: 0.7493 (t0) REVERT: A 442 PHE cc_start: 0.6300 (t80) cc_final: 0.5616 (p90) REVERT: A 602 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 894 ILE cc_start: 0.8709 (mm) cc_final: 0.8401 (tp) REVERT: A 963 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 1173 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7933 (mtt90) REVERT: A 1227 LEU cc_start: 0.8597 (mm) cc_final: 0.8186 (mm) REVERT: A 1244 MET cc_start: 0.7601 (mpp) cc_final: 0.6974 (mmt) REVERT: A 1471 GLN cc_start: 0.7080 (mt0) cc_final: 0.6621 (mt0) REVERT: A 1546 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7835 (mmmt) REVERT: A 1561 TYR cc_start: 0.6550 (t80) cc_final: 0.6302 (t80) REVERT: B 269 GLN cc_start: 0.8142 (mp10) cc_final: 0.7760 (mp10) REVERT: B 272 ASP cc_start: 0.8020 (m-30) cc_final: 0.7404 (t0) REVERT: B 302 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: B 315 GLN cc_start: 0.7899 (tt0) cc_final: 0.7636 (mt0) REVERT: D 228 MET cc_start: 0.7862 (pmm) cc_final: 0.7349 (ppp) REVERT: D 276 MET cc_start: 0.8343 (mmt) cc_final: 0.7726 (mtt) REVERT: D 812 MET cc_start: 0.9122 (tpp) cc_final: 0.8749 (mtt) REVERT: D 868 TYR cc_start: 0.8882 (m-80) cc_final: 0.8651 (m-10) REVERT: D 1062 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7601 (tt0) REVERT: D 1081 LYS cc_start: 0.7543 (pptt) cc_final: 0.7190 (pttp) REVERT: D 1171 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6693 (tm-30) REVERT: D 1303 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7649 (tttt) REVERT: D 2023 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8467 (mm) REVERT: D 2117 MET cc_start: 0.8278 (tpp) cc_final: 0.7913 (tpp) REVERT: D 2178 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7429 (mm-40) REVERT: D 2371 MET cc_start: 0.5639 (tpt) cc_final: 0.5339 (tpt) REVERT: D 2425 HIS cc_start: 0.7226 (t-90) cc_final: 0.7017 (t-90) REVERT: E 361 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6878 (t-90) REVERT: E 788 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8177 (mt) REVERT: E 792 MET cc_start: 0.8512 (mtp) cc_final: 0.8149 (mtp) REVERT: E 930 ASP cc_start: 0.8454 (m-30) cc_final: 0.8028 (m-30) REVERT: E 936 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8162 (mm-40) REVERT: E 1184 MET cc_start: 0.9095 (mmm) cc_final: 0.8423 (mpp) REVERT: E 1192 ASN cc_start: 0.8835 (t0) cc_final: 0.8561 (t0) REVERT: E 1343 MET cc_start: 0.8807 (mmm) cc_final: 0.8605 (mmp) REVERT: E 1453 TYR cc_start: 0.5435 (m-80) cc_final: 0.4551 (m-80) REVERT: E 1741 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7196 (tm-30) REVERT: E 1907 MET cc_start: 0.8711 (mmm) cc_final: 0.8345 (mmm) REVERT: E 2003 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7749 (tm-30) REVERT: E 2044 MET cc_start: 0.7265 (ttp) cc_final: 0.6980 (ttp) REVERT: E 2087 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8504 (mm110) REVERT: E 2157 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8809 (tp) REVERT: E 2198 ILE cc_start: 0.9216 (mm) cc_final: 0.9000 (mt) REVERT: E 2313 ASP cc_start: 0.8094 (t0) cc_final: 0.7893 (t70) REVERT: E 2366 MET cc_start: 0.9096 (mmp) cc_final: 0.8589 (mmp) REVERT: E 2494 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8448 (tt0) REVERT: E 2530 ASP cc_start: 0.8149 (m-30) cc_final: 0.7930 (m-30) REVERT: E 2535 MET cc_start: 0.8196 (tpp) cc_final: 0.7891 (tpt) REVERT: E 2646 MET cc_start: 0.6094 (pmm) cc_final: 0.5388 (pmm) REVERT: E 2804 CYS cc_start: 0.8439 (t) cc_final: 0.7845 (p) outliers start: 110 outliers final: 86 residues processed: 745 average time/residue: 0.2081 time to fit residues: 267.5065 Evaluate side-chains 758 residues out of total 4114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 664 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1048 ILE Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1101 GLU Chi-restraints excluded: chain D residue 1116 ASP Chi-restraints excluded: chain D residue 1385 CYS Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2045 LEU Chi-restraints excluded: chain D residue 2068 MET Chi-restraints excluded: chain D residue 2107 THR Chi-restraints excluded: chain D residue 2175 ASN Chi-restraints excluded: chain D residue 2235 LEU Chi-restraints excluded: chain D residue 2247 ARG Chi-restraints excluded: chain D residue 2281 LEU Chi-restraints excluded: chain D residue 2341 LEU Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2533 MET Chi-restraints excluded: chain D residue 2615 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 825 GLU Chi-restraints excluded: chain E residue 831 LEU Chi-restraints excluded: chain E residue 954 LEU Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1501 LEU Chi-restraints excluded: chain E residue 1764 TYR Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1956 THR Chi-restraints excluded: chain E residue 2061 ILE Chi-restraints excluded: chain E residue 2097 GLU Chi-restraints excluded: chain E residue 2157 LEU Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2302 ASP Chi-restraints excluded: chain E residue 2339 LEU Chi-restraints excluded: chain E residue 2351 VAL Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2496 LEU Chi-restraints excluded: chain E residue 2513 ILE Chi-restraints excluded: chain E residue 2516 ASN Chi-restraints excluded: chain E residue 2597 HIS Chi-restraints excluded: chain E residue 2615 ILE Chi-restraints excluded: chain E residue 2619 CYS Chi-restraints excluded: chain E residue 2634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 33 optimal weight: 6.9990 chunk 354 optimal weight: 0.0170 chunk 407 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 353 optimal weight: 0.7980 chunk 290 optimal weight: 0.0370 chunk 233 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 364 optimal weight: 0.0070 chunk 429 optimal weight: 2.9990 overall best weight: 0.7716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS B 338 GLN E 87 HIS E 933 GLN ** E1930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2597 HIS E2613 ASN E2633 HIS E2704 GLN E2742 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.181959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135928 restraints weight = 70505.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140482 restraints weight = 31373.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142423 restraints weight = 17192.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143124 restraints weight = 12884.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143345 restraints weight = 12009.317| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38349 Z= 0.125 Angle : 0.678 13.675 51938 Z= 0.325 Chirality : 0.041 0.366 6006 Planarity : 0.004 0.071 6423 Dihedral : 5.374 70.467 5235 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.02 % Allowed : 21.42 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 1.57 (0.13), residues: 4418 helix: 1.67 (0.09), residues: 3142 sheet: -0.84 (0.70), residues: 37 loop : -0.46 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D2110 TYR 0.019 0.001 TYR E1503 PHE 0.062 0.001 PHE D2478 TRP 0.050 0.001 TRP D2390 HIS 0.011 0.001 HIS E2597 Details of bonding type rmsd covalent geometry : bond 0.00273 (38338) covalent geometry : angle 0.67769 (51915) SS BOND : bond 0.00242 ( 10) SS BOND : angle 1.06663 ( 20) hydrogen bonds : bond 0.03705 ( 2343) hydrogen bonds : angle 4.05234 ( 6906) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 1.10310 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8996.08 seconds wall clock time: 154 minutes 42.20 seconds (9282.20 seconds total)