Starting phenix.real_space_refine on Mon Jul 6 08:10:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w5x_32323/07_2026/7w5x_32323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5x_32323/07_2026/7w5x_32323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w5x_32323/07_2026/7w5x_32323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5x_32323/07_2026/7w5x_32323.map" model { file = "/net/cci-nas-00/data/ceres_data/7w5x_32323/07_2026/7w5x_32323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5x_32323/07_2026/7w5x_32323.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 135 5.16 5 C 21016 2.51 5 N 6086 2.21 5 O 6879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34265 Number of models: 1 Model: "" Number of chains: 9 Chain: "1" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1548 Classifications: {'DNA': 75} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 74} Chain: "2" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1537 Classifications: {'DNA': 75} Link IDs: {'rna3p': 74} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10560 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 10369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10369 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3979 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 479} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 912 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2334 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2399 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Time building chain proxies: 6.87, per 1000 atoms: 0.20 Number of scatterers: 34265 At special positions: 0 Unit cell: (174.9, 227.7, 169.4, 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 135 16.00 P 149 15.00 O 6879 8.00 N 6086 7.00 C 21016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7378 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 45 sheets defined 40.4% alpha, 13.8% beta 21 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.767A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.501A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.546A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.995A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.666A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.255A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.641A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.557A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.740A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 3.668A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.690A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 removed outlier: 3.806A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.780A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.695A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.853A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.562A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.676A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.520A pdb=" N ARG C 903 " --> pdb=" O GLU C 899 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 959 removed outlier: 3.566A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 966 removed outlier: 3.542A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 981 removed outlier: 3.859A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1027 removed outlier: 3.822A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1034 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.541A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.813A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1121 Processing helix chain 'C' and resid 1121 through 1134 removed outlier: 3.913A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1148 Processing helix chain 'C' and resid 1165 through 1176 removed outlier: 3.506A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.502A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.501A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.507A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 removed outlier: 3.531A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.808A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C1305 " --> pdb=" O ARG C1301 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 removed outlier: 3.500A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.508A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.850A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.703A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.409A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.663A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 202 removed outlier: 3.659A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.897A pdb=" N ASN D 206 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.953A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.685A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 308 removed outlier: 3.655A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.179A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.723A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.929A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.520A pdb=" N ALA D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.581A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.528A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.914A pdb=" N ASN D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.654A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 660 removed outlier: 3.804A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 removed outlier: 3.543A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 697 removed outlier: 3.928A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.620A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.679A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 788 removed outlier: 3.503A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 removed outlier: 3.688A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.672A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.926A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 924 removed outlier: 3.703A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.210A pdb=" N THR D 928 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.660A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1237 removed outlier: 3.817A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D1232 " --> pdb=" O ALA D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1237 through 1244 removed outlier: 3.803A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1258 removed outlier: 4.196A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 removed outlier: 3.642A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 3.602A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 removed outlier: 3.559A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.529A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.528A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.999A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.570A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 79 removed outlier: 3.633A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 89 removed outlier: 3.866A pdb=" N SER F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.550A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.774A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 4.030A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 152 " --> pdb=" O TYR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.730A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 164' Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.697A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.720A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 291 removed outlier: 3.575A pdb=" N SER F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.658A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 removed outlier: 3.967A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 318 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA F 319 " --> pdb=" O TRP F 315 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.871A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.677A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 383 removed outlier: 3.782A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.916A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 401 through 419 removed outlier: 3.790A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.792A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 424 " --> pdb=" O TYR F 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 420 through 424' Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.001A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.842A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 3.559A pdb=" N ALA F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET F 487 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.510A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 539 removed outlier: 3.947A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 548 removed outlier: 3.654A pdb=" N HIS F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 551 No H-bonds generated for 'chain 'F' and resid 549 through 551' Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.566A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.567A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 599 removed outlier: 3.519A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 4.491A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 613 removed outlier: 3.816A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP F 613 " --> pdb=" O PHE F 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 609 through 613' Processing helix chain 'K' and resid 2 through 11 Processing helix chain 'K' and resid 23 through 28 Processing helix chain 'K' and resid 29 through 32 removed outlier: 3.708A pdb=" N GLY K 32 " --> pdb=" O LYS K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 29 through 32' Processing helix chain 'K' and resid 36 through 47 removed outlier: 3.911A pdb=" N ARG K 40 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET K 41 " --> pdb=" O TYR K 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG K 43 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR K 44 " --> pdb=" O ARG K 40 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL K 45 " --> pdb=" O MET K 41 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR K 46 " --> pdb=" O PHE K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 65 Processing helix chain 'K' and resid 72 through 77 removed outlier: 3.609A pdb=" N ILE K 76 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA K 77 " --> pdb=" O ILE K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 77' Processing helix chain 'K' and resid 84 through 89 removed outlier: 4.228A pdb=" N PHE K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.505A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.732A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.731A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.955A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.877A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.520A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.515A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 4.033A pdb=" N LYS A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.060A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.678A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.705A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.628A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.558A pdb=" N LEU B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.852A pdb=" N ALA B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.820A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.644A pdb=" N ILE B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.490A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.507A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.380A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 161 removed outlier: 3.847A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.073A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.928A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.161A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.622A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.679A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.755A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.471A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.719A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.934A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.138A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.564A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.443A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.505A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AC7, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.635A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AC9, first strand: chain 'D' and resid 821 through 822 Processing sheet with id=AD1, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.798A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.939A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D1009 " --> pdb=" O ILE D 958 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1028 through 1029 removed outlier: 3.510A pdb=" N THR D1029 " --> pdb=" O ASP D1119 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D1119 " --> pdb=" O THR D1029 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 1080 through 1081 Processing sheet with id=AD5, first strand: chain 'D' and resid 1047 through 1049 removed outlier: 3.576A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.571A pdb=" N ILE D1162 " --> pdb=" O THR D1178 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1263 through 1265 Processing sheet with id=AD8, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.811A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.811A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.553A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.550A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE4, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AE5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AE6, first strand: chain 'B' and resid 12 through 17 removed outlier: 5.352A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.910A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AE9, first strand: chain 'B' and resid 109 through 110 994 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 8.16 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9722 1.33 - 1.45: 5855 1.45 - 1.57: 18983 1.57 - 1.69: 298 1.69 - 1.81: 237 Bond restraints: 35095 Sorted by residual: bond pdb=" CA THR D 152 " pdb=" C THR D 152 " ideal model delta sigma weight residual 1.522 1.620 -0.099 1.72e-02 3.38e+03 3.29e+01 bond pdb=" C1' DT 2 60 " pdb=" N1 DT 2 60 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" C3' DG 1 71 " pdb=" C2' DG 1 71 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.62e+01 bond pdb=" C3' DG 2 20 " pdb=" C2' DG 2 20 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.61e+01 bond pdb=" C1' DC 1 17 " pdb=" N1 DC 1 17 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.45e+01 ... (remaining 35090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 46648 2.15 - 4.31: 1248 4.31 - 6.46: 110 6.46 - 8.61: 26 8.61 - 10.77: 7 Bond angle restraints: 48039 Sorted by residual: angle pdb=" N GLY D1103 " pdb=" CA GLY D1103 " pdb=" C GLY D1103 " ideal model delta sigma weight residual 112.33 119.02 -6.69 1.10e+00 8.26e-01 3.70e+01 angle pdb=" C ASN D 320 " pdb=" N LYS D 321 " pdb=" CA LYS D 321 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C PRO D 859 " pdb=" N ARG D 860 " pdb=" CA ARG D 860 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" O4' DC 2 27 " pdb=" C4' DC 2 27 " pdb=" C3' DC 2 27 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DA 2 12 " pdb=" C4' DA 2 12 " pdb=" C3' DA 2 12 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 ... (remaining 48034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 20260 35.10 - 70.20: 899 70.20 - 105.31: 45 105.31 - 140.41: 1 140.41 - 175.51: 3 Dihedral angle restraints: 21208 sinusoidal: 9780 harmonic: 11428 Sorted by residual: dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA THR F 527 " pdb=" C THR F 527 " pdb=" N LEU F 528 " pdb=" CA LEU F 528 " ideal model delta harmonic sigma weight residual -180.00 -153.79 -26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 21205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4807 0.078 - 0.156: 619 0.156 - 0.234: 44 0.234 - 0.312: 7 0.312 - 0.390: 2 Chirality restraints: 5479 Sorted by residual: chirality pdb=" CB VAL A 287 " pdb=" CA VAL A 287 " pdb=" CG1 VAL A 287 " pdb=" CG2 VAL A 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB VAL D 421 " pdb=" CA VAL D 421 " pdb=" CG1 VAL D 421 " pdb=" CG2 VAL D 421 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5476 not shown) Planarity restraints: 5736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 992 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 993 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 993 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 993 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 209 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C GLY A 209 " 0.044 2.00e-02 2.50e+03 pdb=" O GLY A 209 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 210 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO C 190 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.035 5.00e-02 4.00e+02 ... (remaining 5733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7681 2.79 - 3.31: 27707 3.31 - 3.84: 54172 3.84 - 4.37: 65833 4.37 - 4.90: 109125 Nonbonded interactions: 264518 Sorted by model distance: nonbonded pdb=" O GLU K 65 " pdb=" OG1 THR K 69 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU C 876 " pdb=" OG1 THR C 927 " model vdw 2.297 3.040 nonbonded pdb=" OG SER C 759 " pdb=" OG1 THR C 763 " model vdw 2.303 3.040 nonbonded pdb=" OG SER D 949 " pdb=" OG1 THR D1016 " model vdw 2.306 3.040 nonbonded pdb=" OE1 GLU D 811 " pdb=" OG1 THR D 890 " model vdw 2.308 3.040 ... (remaining 264513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 233 or resid 250 through 324)) selection = (chain 'B' and (resid 6 through 233 or resid 250 through 264 or (resid 265 and ( \ name N or name CA or name C or name O or name CB )) or resid 266 through 294 or \ resid 299 through 324)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 34.400 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.006 0.099 35095 Z= 0.333 Angle : 0.830 10.766 48039 Z= 0.525 Chirality : 0.054 0.390 5479 Planarity : 0.006 0.071 5736 Dihedral : 17.753 175.509 13830 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 0.35 % Allowed : 8.43 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.10), residues: 3929 helix: -4.86 (0.05), residues: 1420 sheet: -1.85 (0.24), residues: 424 loop : -2.46 (0.11), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 780 TYR 0.017 0.002 TYR C 105 PHE 0.033 0.002 PHE D 338 TRP 0.014 0.002 TRP C 997 HIS 0.014 0.002 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.33 (35095) covalent geometry : angle 0.82970 / 0.53 (48039) hydrogen bonds : bond 0.32242 / 35.67 ( 1032) hydrogen bonds : angle 10.40902 / 13.83 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 436 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7305 (Cg_endo) cc_final: 0.7045 (Cg_exo) REVERT: C 315 MET cc_start: 0.7239 (ttm) cc_final: 0.6924 (ttp) REVERT: C 484 LEU cc_start: 0.5642 (mm) cc_final: 0.5416 (mm) REVERT: C 496 LYS cc_start: 0.7304 (mmtp) cc_final: 0.7009 (mmtp) REVERT: C 542 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6981 (mtp-110) REVERT: D 562 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7150 (tt0) REVERT: D 566 LYS cc_start: 0.8079 (ptmt) cc_final: 0.7800 (ptpt) REVERT: D 865 HIS cc_start: 0.7784 (p90) cc_final: 0.7514 (p90) REVERT: D 892 PHE cc_start: 0.7670 (m-80) cc_final: 0.7023 (t80) REVERT: D 1174 ARG cc_start: 0.5007 (mtt180) cc_final: 0.4676 (mtp180) REVERT: D 1220 ILE cc_start: 0.8128 (mm) cc_final: 0.7877 (mt) REVERT: F 509 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 139 SER cc_start: 0.5387 (t) cc_final: 0.5011 (p) outliers start: 12 outliers final: 6 residues processed: 447 average time/residue: 0.2534 time to fit residues: 171.2629 Evaluate side-chains 291 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 284 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain A residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.2980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 447 HIS C 510 GLN C 513 GLN C 622 ASN C 737 ASN C 952 GLN C 965 GLN C1313 HIS D 294 ASN D 477 GLN D 560 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS D1084 GLN D1108 GLN D1227 HIS D1235 ASN D1366 HIS D1367 GLN F 210 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN F 362 ASN F 383 ASN F 455 HIS F 461 ASN F 545 HIS K 3 HIS K 20 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147532 restraints weight = 49025.132| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.78 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35095 Z= 0.136 Angle : 0.592 8.054 48039 Z= 0.331 Chirality : 0.044 0.210 5479 Planarity : 0.005 0.068 5736 Dihedral : 17.292 176.508 6004 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 1.42 % Allowed : 11.24 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.11), residues: 3929 helix: -3.28 (0.09), residues: 1475 sheet: -1.07 (0.26), residues: 389 loop : -2.06 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 371 TYR 0.017 0.001 TYR B 152 PHE 0.011 0.001 PHE D 620 TRP 0.011 0.001 TRP D 33 HIS 0.010 0.001 HIS F 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (35095) covalent geometry : angle 0.59193 / 0.33 (48039) hydrogen bonds : bond 0.06306 / 7.09 ( 1032) hydrogen bonds : angle 5.96957 / 8.02 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: C 484 LEU cc_start: 0.4732 (mm) cc_final: 0.4507 (mm) REVERT: C 941 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7743 (mttm) REVERT: D 29 MET cc_start: 0.7870 (tpp) cc_final: 0.7615 (ttm) REVERT: D 304 ASP cc_start: 0.6517 (m-30) cc_final: 0.6053 (m-30) REVERT: D 652 GLU cc_start: 0.6947 (mp0) cc_final: 0.6202 (tm-30) REVERT: D 698 MET cc_start: 0.6581 (mmm) cc_final: 0.6300 (mmm) REVERT: D 892 PHE cc_start: 0.7605 (m-80) cc_final: 0.7243 (t80) REVERT: F 111 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7563 (pp) REVERT: F 317 ASN cc_start: 0.4523 (p0) cc_final: 0.4289 (p0) REVERT: F 561 MET cc_start: 0.6312 (mmm) cc_final: 0.6032 (mmp) REVERT: K 78 MET cc_start: 0.1117 (tpp) cc_final: 0.0681 (tpp) outliers start: 48 outliers final: 19 residues processed: 352 average time/residue: 0.2089 time to fit residues: 118.1750 Evaluate side-chains 289 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 140 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 50 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 391 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C1070 HIS C1090 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D 907 HIS F 265 GLN A 147 GLN B 75 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152243 restraints weight = 48679.088| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.93 r_work: 0.3530 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35095 Z= 0.187 Angle : 0.593 8.652 48039 Z= 0.326 Chirality : 0.045 0.248 5479 Planarity : 0.005 0.053 5736 Dihedral : 17.309 167.288 6003 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.71 % Rotamer: Outliers : 1.89 % Allowed : 13.24 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.12), residues: 3929 helix: -2.33 (0.11), residues: 1467 sheet: -0.84 (0.26), residues: 386 loop : -1.87 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 535 TYR 0.013 0.001 TYR C1231 PHE 0.016 0.002 PHE D 620 TRP 0.011 0.001 TRP K 36 HIS 0.009 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (35095) covalent geometry : angle 0.59307 / 0.33 (48039) hydrogen bonds : bond 0.05337 / 6.02 ( 1032) hydrogen bonds : angle 5.39633 / 7.26 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.7474 (ptt) cc_final: 0.7131 (ptm) REVERT: C 514 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7747 (t80) REVERT: C 941 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7931 (mttm) REVERT: D 304 ASP cc_start: 0.6900 (m-30) cc_final: 0.6487 (m-30) REVERT: D 652 GLU cc_start: 0.7151 (mp0) cc_final: 0.6492 (tm-30) REVERT: D 698 MET cc_start: 0.7155 (mmm) cc_final: 0.6873 (mmm) REVERT: D 700 ASN cc_start: 0.7567 (t0) cc_final: 0.7167 (t0) REVERT: D 892 PHE cc_start: 0.7879 (m-80) cc_final: 0.7385 (t80) REVERT: F 111 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7807 (pp) REVERT: K 41 MET cc_start: 0.3392 (ptt) cc_final: 0.3060 (ptm) REVERT: K 78 MET cc_start: 0.1382 (tpp) cc_final: 0.0924 (tpp) outliers start: 64 outliers final: 44 residues processed: 324 average time/residue: 0.2163 time to fit residues: 114.8430 Evaluate side-chains 309 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1090 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 98 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152246 restraints weight = 48459.949| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.98 r_work: 0.3544 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35095 Z= 0.133 Angle : 0.529 8.134 48039 Z= 0.293 Chirality : 0.043 0.252 5479 Planarity : 0.004 0.049 5736 Dihedral : 17.223 166.567 6002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 2.12 % Allowed : 14.39 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.47 (0.12), residues: 3929 helix: -1.76 (0.12), residues: 1478 sheet: -0.69 (0.27), residues: 385 loop : -1.70 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1290 TYR 0.014 0.001 TYR C 105 PHE 0.010 0.001 PHE D 227 TRP 0.015 0.001 TRP D1020 HIS 0.006 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (35095) covalent geometry : angle 0.52901 / 0.29 (48039) hydrogen bonds : bond 0.04245 / 4.77 ( 1032) hydrogen bonds : angle 5.02204 / 6.75 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7391 (ptt) cc_final: 0.7063 (ptm) REVERT: C 651 ASP cc_start: 0.8032 (t0) cc_final: 0.7782 (t0) REVERT: C 941 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7927 (mttm) REVERT: D 304 ASP cc_start: 0.6977 (m-30) cc_final: 0.6516 (m-30) REVERT: D 698 MET cc_start: 0.7145 (mmm) cc_final: 0.6869 (mmm) REVERT: D 700 ASN cc_start: 0.7556 (t0) cc_final: 0.7172 (t0) REVERT: D 817 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.5749 (t-90) REVERT: D 892 PHE cc_start: 0.7892 (m-80) cc_final: 0.7343 (t80) REVERT: F 111 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7753 (pp) REVERT: K 41 MET cc_start: 0.3241 (ptt) cc_final: 0.2916 (ptm) REVERT: A 166 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7156 (mtm110) REVERT: B 80 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6958 (tp30) outliers start: 72 outliers final: 50 residues processed: 337 average time/residue: 0.2161 time to fit residues: 118.8635 Evaluate side-chains 312 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 367 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 327 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 346 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151864 restraints weight = 48719.303| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.98 r_work: 0.3544 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35095 Z= 0.142 Angle : 0.530 8.232 48039 Z= 0.291 Chirality : 0.043 0.255 5479 Planarity : 0.004 0.052 5736 Dihedral : 17.171 165.687 6002 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 2.65 % Allowed : 14.80 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.15 (0.13), residues: 3929 helix: -1.36 (0.13), residues: 1479 sheet: -0.62 (0.27), residues: 390 loop : -1.60 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1290 TYR 0.012 0.001 TYR B 152 PHE 0.010 0.001 PHE C 405 TRP 0.010 0.001 TRP D1020 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (35095) covalent geometry : angle 0.53046 / 0.29 (48039) hydrogen bonds : bond 0.03992 / 4.50 ( 1032) hydrogen bonds : angle 4.82708 / 6.49 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 269 time to evaluate : 1.391 Fit side-chains REVERT: C 239 MET cc_start: 0.7350 (ptt) cc_final: 0.7023 (ptm) REVERT: C 484 LEU cc_start: 0.5173 (mm) cc_final: 0.4875 (mm) REVERT: C 514 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 651 ASP cc_start: 0.7908 (t0) cc_final: 0.7685 (t0) REVERT: C 737 ASN cc_start: 0.7453 (m-40) cc_final: 0.7245 (m-40) REVERT: C 941 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7934 (mttm) REVERT: D 304 ASP cc_start: 0.6825 (m-30) cc_final: 0.6373 (m-30) REVERT: D 698 MET cc_start: 0.7087 (mmm) cc_final: 0.6818 (mmm) REVERT: D 700 ASN cc_start: 0.7535 (t0) cc_final: 0.7175 (t0) REVERT: D 817 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.5853 (t-90) REVERT: D 892 PHE cc_start: 0.7835 (m-80) cc_final: 0.7331 (t80) REVERT: F 111 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7716 (pp) REVERT: F 277 MET cc_start: 0.5716 (tmm) cc_final: 0.5461 (mmm) REVERT: F 388 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8928 (tt) REVERT: K 41 MET cc_start: 0.3257 (ptt) cc_final: 0.2767 (ptm) REVERT: A 166 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7112 (mtm110) REVERT: B 80 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6847 (tp30) outliers start: 90 outliers final: 63 residues processed: 348 average time/residue: 0.2004 time to fit residues: 114.3396 Evaluate side-chains 325 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 350 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 241 optimal weight: 30.0000 chunk 27 optimal weight: 0.9990 chunk 210 optimal weight: 0.0970 chunk 377 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152365 restraints weight = 48509.285| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.01 r_work: 0.3547 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35095 Z= 0.125 Angle : 0.511 8.098 48039 Z= 0.282 Chirality : 0.042 0.256 5479 Planarity : 0.004 0.049 5736 Dihedral : 17.126 165.638 6001 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 2.45 % Allowed : 15.75 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.97 (0.13), residues: 3929 helix: -1.17 (0.13), residues: 1488 sheet: -0.48 (0.27), residues: 390 loop : -1.54 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1290 TYR 0.011 0.001 TYR C1231 PHE 0.010 0.001 PHE C 405 TRP 0.009 0.001 TRP K 36 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (35095) covalent geometry : angle 0.51106 / 0.28 (48039) hydrogen bonds : bond 0.03716 / 4.19 ( 1032) hydrogen bonds : angle 4.69959 / 6.30 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 259 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7349 (ptt) cc_final: 0.7024 (ptm) REVERT: C 484 LEU cc_start: 0.5195 (mm) cc_final: 0.4924 (mm) REVERT: C 651 ASP cc_start: 0.7880 (t0) cc_final: 0.7641 (t0) REVERT: C 737 ASN cc_start: 0.7426 (m-40) cc_final: 0.7211 (m-40) REVERT: C 941 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7976 (mttm) REVERT: D 304 ASP cc_start: 0.6839 (m-30) cc_final: 0.6403 (m-30) REVERT: D 698 MET cc_start: 0.7044 (mmm) cc_final: 0.6787 (mmm) REVERT: D 700 ASN cc_start: 0.7539 (t0) cc_final: 0.6852 (t0) REVERT: D 817 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5814 (t-90) REVERT: D 864 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7691 (tt) REVERT: D 892 PHE cc_start: 0.7831 (m-80) cc_final: 0.7324 (t80) REVERT: F 111 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7692 (pp) REVERT: K 41 MET cc_start: 0.3149 (ptt) cc_final: 0.2945 (ptm) REVERT: A 166 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7081 (mtm110) REVERT: B 80 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6856 (tp30) outliers start: 83 outliers final: 61 residues processed: 333 average time/residue: 0.1964 time to fit residues: 107.6308 Evaluate side-chains 313 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 1 optimal weight: 50.0000 chunk 326 optimal weight: 0.0970 chunk 266 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS D 805 GLN B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144070 restraints weight = 48994.773| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.78 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35095 Z= 0.189 Angle : 0.574 11.815 48039 Z= 0.310 Chirality : 0.044 0.269 5479 Planarity : 0.004 0.055 5736 Dihedral : 17.204 163.068 6001 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 2.77 % Allowed : 16.25 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.98 (0.13), residues: 3929 helix: -1.14 (0.13), residues: 1486 sheet: -0.44 (0.27), residues: 390 loop : -1.60 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1290 TYR 0.013 0.001 TYR C1231 PHE 0.013 0.001 PHE D 377 TRP 0.010 0.001 TRP K 36 HIS 0.009 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (35095) covalent geometry : angle 0.57385 / 0.31 (48039) hydrogen bonds : bond 0.04148 / 4.66 ( 1032) hydrogen bonds : angle 4.74925 / 6.40 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 250 time to evaluate : 1.174 Fit side-chains REVERT: C 239 MET cc_start: 0.7243 (ptt) cc_final: 0.6924 (ptm) REVERT: C 484 LEU cc_start: 0.4916 (mm) cc_final: 0.4617 (mm) REVERT: C 514 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7678 (t80) REVERT: C 641 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6275 (pp20) REVERT: C 941 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7882 (mttm) REVERT: D 304 ASP cc_start: 0.6385 (m-30) cc_final: 0.6024 (m-30) REVERT: D 698 MET cc_start: 0.6551 (mmm) cc_final: 0.6294 (mmm) REVERT: D 700 ASN cc_start: 0.7290 (t0) cc_final: 0.7017 (t0) REVERT: D 817 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.5583 (t-90) REVERT: D 864 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7594 (tt) REVERT: D 892 PHE cc_start: 0.7686 (m-80) cc_final: 0.7349 (t80) REVERT: F 111 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7770 (pp) REVERT: F 141 ILE cc_start: 0.4279 (OUTLIER) cc_final: 0.4044 (tt) REVERT: K 41 MET cc_start: 0.2866 (ptt) cc_final: 0.2620 (ptm) REVERT: B 80 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6549 (tp30) outliers start: 94 outliers final: 67 residues processed: 331 average time/residue: 0.2070 time to fit residues: 113.3343 Evaluate side-chains 318 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 80 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 385 optimal weight: 0.0570 chunk 148 optimal weight: 8.9990 chunk 402 optimal weight: 0.2980 chunk 316 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.177735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149277 restraints weight = 48177.997| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.14 r_work: 0.3481 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35095 Z= 0.102 Angle : 0.500 7.889 48039 Z= 0.277 Chirality : 0.042 0.258 5479 Planarity : 0.004 0.047 5736 Dihedral : 17.111 164.611 6001 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 2.06 % Allowed : 16.75 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.70 (0.13), residues: 3929 helix: -0.86 (0.13), residues: 1493 sheet: -0.34 (0.27), residues: 402 loop : -1.46 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1290 TYR 0.011 0.001 TYR B 152 PHE 0.009 0.001 PHE C 405 TRP 0.009 0.001 TRP D1020 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (35095) covalent geometry : angle 0.50039 / 0.28 (48039) hydrogen bonds : bond 0.03387 / 3.81 ( 1032) hydrogen bonds : angle 4.54612 / 6.08 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: C 20 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: C 332 ARG cc_start: 0.5085 (ttp-170) cc_final: 0.4700 (ptm160) REVERT: C 484 LEU cc_start: 0.4874 (mm) cc_final: 0.4608 (mm) REVERT: C 651 ASP cc_start: 0.7878 (t0) cc_final: 0.7652 (t0) REVERT: D 304 ASP cc_start: 0.6765 (m-30) cc_final: 0.6340 (m-30) REVERT: D 698 MET cc_start: 0.6902 (mmm) cc_final: 0.6649 (mmm) REVERT: D 700 ASN cc_start: 0.7586 (t0) cc_final: 0.6953 (t0) REVERT: D 817 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5798 (t-90) REVERT: D 864 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7690 (tt) REVERT: D 892 PHE cc_start: 0.7864 (m-80) cc_final: 0.7227 (t80) REVERT: F 111 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7746 (pp) REVERT: K 41 MET cc_start: 0.3197 (ptt) cc_final: 0.2940 (ptm) REVERT: B 80 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6796 (tp30) REVERT: B 205 MET cc_start: 0.7786 (ttm) cc_final: 0.7533 (ttt) outliers start: 70 outliers final: 53 residues processed: 318 average time/residue: 0.1966 time to fit residues: 103.1213 Evaluate side-chains 305 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 168 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 326 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 289 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 358 optimal weight: 0.0570 chunk 191 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 360 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 799 ASN C1324 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN B 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150600 restraints weight = 48115.247| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.12 r_work: 0.3505 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35095 Z= 0.095 Angle : 0.483 7.737 48039 Z= 0.268 Chirality : 0.041 0.253 5479 Planarity : 0.004 0.050 5736 Dihedral : 17.045 165.684 6001 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 1.98 % Allowed : 16.81 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.46 (0.13), residues: 3929 helix: -0.61 (0.13), residues: 1495 sheet: -0.35 (0.26), residues: 414 loop : -1.34 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1290 TYR 0.011 0.001 TYR K 82 PHE 0.018 0.001 PHE C 80 TRP 0.012 0.001 TRP D1020 HIS 0.002 0.000 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (35095) covalent geometry : angle 0.48307 / 0.27 (48039) hydrogen bonds : bond 0.03149 / 3.55 ( 1032) hydrogen bonds : angle 4.41701 / 5.88 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 264 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: C 20 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: C 79 VAL cc_start: 0.8987 (m) cc_final: 0.8717 (m) REVERT: C 332 ARG cc_start: 0.4929 (ttp-170) cc_final: 0.4538 (ptm160) REVERT: C 484 LEU cc_start: 0.4830 (mm) cc_final: 0.4565 (mm) REVERT: C 651 ASP cc_start: 0.7801 (t0) cc_final: 0.7588 (t0) REVERT: D 304 ASP cc_start: 0.6800 (m-30) cc_final: 0.6416 (m-30) REVERT: D 698 MET cc_start: 0.6727 (mmm) cc_final: 0.6479 (mmm) REVERT: D 700 ASN cc_start: 0.7627 (t0) cc_final: 0.7058 (t0) REVERT: D 817 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.5771 (t-90) REVERT: D 864 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7654 (tt) REVERT: D 892 PHE cc_start: 0.7844 (m-80) cc_final: 0.7275 (t80) REVERT: D 1040 MET cc_start: -0.1173 (mmt) cc_final: -0.1403 (ptp) REVERT: D 1291 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6048 (mm-30) REVERT: F 111 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7755 (pp) REVERT: F 273 MET cc_start: 0.5308 (mmt) cc_final: 0.4960 (mmp) REVERT: K 41 MET cc_start: 0.3125 (ptt) cc_final: 0.2867 (ptm) REVERT: B 80 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6771 (tp30) REVERT: B 205 MET cc_start: 0.7818 (ttm) cc_final: 0.7565 (ttt) outliers start: 67 outliers final: 49 residues processed: 321 average time/residue: 0.2143 time to fit residues: 114.2129 Evaluate side-chains 306 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 107 optimal weight: 0.9990 chunk 389 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 370 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 chunk 340 optimal weight: 40.0000 chunk 83 optimal weight: 8.9990 chunk 285 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 799 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149769 restraints weight = 48094.542| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.07 r_work: 0.3486 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35095 Z= 0.125 Angle : 0.507 7.933 48039 Z= 0.277 Chirality : 0.042 0.258 5479 Planarity : 0.004 0.069 5736 Dihedral : 17.079 164.719 6001 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 1.80 % Allowed : 16.90 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.44 (0.13), residues: 3929 helix: -0.58 (0.13), residues: 1504 sheet: -0.34 (0.27), residues: 413 loop : -1.35 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1290 TYR 0.015 0.001 TYR K 82 PHE 0.011 0.001 PHE C 405 TRP 0.010 0.001 TRP D1020 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (35095) covalent geometry : angle 0.50710 / 0.28 (48039) hydrogen bonds : bond 0.03429 / 3.86 ( 1032) hydrogen bonds : angle 4.41473 / 5.90 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: C 20 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: C 332 ARG cc_start: 0.4994 (ttp-170) cc_final: 0.4582 (ptm160) REVERT: C 484 LEU cc_start: 0.4994 (mm) cc_final: 0.4779 (mm) REVERT: C 514 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7730 (t80) REVERT: C 651 ASP cc_start: 0.7952 (t0) cc_final: 0.7732 (t0) REVERT: C 704 MET cc_start: 0.8948 (mmm) cc_final: 0.8707 (mtp) REVERT: D 304 ASP cc_start: 0.6767 (m-30) cc_final: 0.6413 (m-30) REVERT: D 698 MET cc_start: 0.6786 (mmm) cc_final: 0.6544 (mmm) REVERT: D 700 ASN cc_start: 0.7724 (t0) cc_final: 0.7160 (t0) REVERT: D 817 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.5870 (t-90) REVERT: D 864 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7735 (tt) REVERT: D 892 PHE cc_start: 0.7929 (m-80) cc_final: 0.7286 (t80) REVERT: D 1040 MET cc_start: -0.1136 (mmt) cc_final: -0.1350 (ptp) REVERT: D 1291 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6004 (mm-30) REVERT: F 111 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7792 (pp) REVERT: F 388 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8970 (tt) REVERT: K 41 MET cc_start: 0.3089 (ptt) cc_final: 0.2790 (ptm) REVERT: B 80 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6926 (tp30) outliers start: 61 outliers final: 52 residues processed: 305 average time/residue: 0.2131 time to fit residues: 108.1535 Evaluate side-chains 307 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 299 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 397 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 334 optimal weight: 0.5980 chunk 223 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148420 restraints weight = 47960.977| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.16 r_work: 0.3488 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.204 35095 Z= 0.157 Angle : 0.619 59.093 48039 Z= 0.357 Chirality : 0.044 1.020 5479 Planarity : 0.004 0.066 5736 Dihedral : 17.084 164.702 6001 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 1.89 % Allowed : 17.10 % Favored : 81.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3929 helix: -0.58 (0.13), residues: 1504 sheet: -0.38 (0.27), residues: 413 loop : -1.35 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.016 0.001 TYR F 137 PHE 0.011 0.001 PHE C 405 TRP 0.009 0.001 TRP D1020 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (35095) covalent geometry : angle 0.61858 / 0.36 (48039) hydrogen bonds : bond 0.03457 / 3.89 ( 1032) hydrogen bonds : angle 4.41536 / 5.90 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6824.65 seconds wall clock time: 117 minutes 56.94 seconds (7076.94 seconds total)