Starting phenix.real_space_refine on Mon Sep 14 23:09:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w5x_32323/09_2026/7w5x_32323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5x_32323/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w5x_32323/09_2026/7w5x_32323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5x_32323/09_2026/7w5x_32323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w5x_32323/09_2026/7w5x_32323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5x_32323/09_2026/7w5x_32323.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.72, 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 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: 3.53 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: 7.67 Time building geometry restraints manager: 3.56 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: 46645 2.15 - 4.31: 1251 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=" C3' DG 2 20 " pdb=" O3' DG 2 20 " pdb=" P DT 2 21 " ideal model delta sigma weight residual 119.70 125.43 -5.73 1.20e+00 6.94e-01 2.28e+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 ... (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: 0.900 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.380 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- 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 : 0.831 10.766 48039 Z= 0.527 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 0.83079 / 0.53 (48039) hydrogen bonds : bond 0.32242 / 35.87 ( 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 : 1.135 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: 0.6923 (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: 0.7010 (mmtp) 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: 0.7515 (p90) REVERT: D 892 PHE cc_start: 0.7670 (m-80) cc_final: 0.7022 (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: 0.7878 (mt) REVERT: F 509 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8406 (t) REVERT: B 139 SER cc_start: 0.5387 (t) cc_final: 0.5012 (p) outliers start: 12 outliers final: 6 residues processed: 447 average time/residue: 0.2573 time to fit residues: 173.5335 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 : 1.154 ------------------------------------------------------------------------------- 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 = 0.181116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144812 restraints weight = 49108.500| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.91 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35095 Z= 0.136 Angle : 0.590 8.032 48039 Z= 0.331 Chirality : 0.044 0.235 5479 Planarity : 0.005 0.074 5736 Dihedral : 17.279 176.383 6004 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 1.39 % Allowed : 11.24 % Favored : 87.38 % 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 0.010 0.000 ARG C 371 TYR 0.017 0.001 TYR B 152 PHE 0.013 0.001 PHE D 620 TRP 0.010 0.001 TRP D 33 HIS 0.008 0.001 HIS F 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (35095) covalent geometry : angle 0.58959 / 0.33 (48039) hydrogen bonds : bond 0.06442 / 7.27 ( 1032) hydrogen bonds : angle 5.98310 / 8.04 ( 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 358 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 311 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: C 484 LEU cc_start: 0.4915 (mm) cc_final: 0.4672 (mm) REVERT: C 941 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7761 (mttm) REVERT: D 29 MET cc_start: 0.7795 (tpp) cc_final: 0.7530 (ttm) REVERT: D 304 ASP cc_start: 0.6442 (m-30) cc_final: 0.6006 (m-30) REVERT: D 652 GLU cc_start: 0.7023 (mp0) cc_final: 0.6212 (tm-30) REVERT: D 698 MET cc_start: 0.6591 (mmm) cc_final: 0.6295 (mmm) REVERT: D 892 PHE cc_start: 0.7638 (m-80) cc_final: 0.7252 (t80) REVERT: F 111 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7557 (pp) REVERT: F 317 ASN cc_start: 0.4547 (p0) cc_final: 0.4320 (p0) REVERT: F 561 MET cc_start: 0.6414 (mmm) cc_final: 0.6130 (mmp) REVERT: K 78 MET cc_start: 0.0936 (tpp) cc_final: 0.0526 (tpp) outliers start: 47 outliers final: 17 residues processed: 351 average time/residue: 0.2148 time to fit residues: 122.2492 Evaluate side-chains 286 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 391 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 363 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 B 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.179528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146712 restraints weight = 49050.753| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.58 r_work: 0.3390 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35095 Z= 0.157 Angle : 0.570 8.685 48039 Z= 0.313 Chirality : 0.044 0.263 5479 Planarity : 0.004 0.051 5736 Dihedral : 17.255 168.458 6003 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 1.98 % Allowed : 12.98 % Favored : 85.05 % 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: -2.86 (0.12), residues: 3929 helix: -2.22 (0.11), residues: 1481 sheet: -0.81 (0.26), residues: 385 loop : -1.82 (0.12), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 535 TYR 0.014 0.001 TYR C1231 PHE 0.016 0.001 PHE D 620 TRP 0.011 0.001 TRP K 36 HIS 0.008 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (35095) covalent geometry : angle 0.57022 / 0.31 (48039) hydrogen bonds : bond 0.04911 / 5.57 ( 1032) hydrogen bonds : angle 5.23383 / 7.04 ( 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 346 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7431 (ptt) cc_final: 0.7024 (ptm) REVERT: C 651 ASP cc_start: 0.8120 (t0) cc_final: 0.7853 (t0) REVERT: C 941 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7765 (mttm) REVERT: D 304 ASP cc_start: 0.6875 (m-30) cc_final: 0.6402 (m-30) REVERT: D 652 GLU cc_start: 0.7236 (mp0) cc_final: 0.6477 (tm-30) REVERT: D 698 MET cc_start: 0.7100 (mmm) cc_final: 0.6808 (mmm) REVERT: D 700 ASN cc_start: 0.7550 (t0) cc_final: 0.7108 (t0) REVERT: D 892 PHE cc_start: 0.7944 (m-80) cc_final: 0.7325 (t80) REVERT: F 111 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7761 (pp) REVERT: F 487 MET cc_start: 0.6468 (mmm) cc_final: 0.6207 (ttm) REVERT: K 41 MET cc_start: 0.3167 (ptt) cc_final: 0.2865 (ptm) outliers start: 67 outliers final: 43 residues processed: 333 average time/residue: 0.1989 time to fit residues: 109.1653 Evaluate side-chains 313 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR 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 508 SER 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 342 LEU 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 877 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 1120 THR Chi-restraints excluded: chain D residue 1275 LEU 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 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: 10.0000 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 0.0170 chunk 134 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 255 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.180144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144700 restraints weight = 48819.897| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.75 r_work: 0.3321 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35095 Z= 0.132 Angle : 0.527 8.164 48039 Z= 0.291 Chirality : 0.043 0.267 5479 Planarity : 0.004 0.049 5736 Dihedral : 17.185 168.435 6002 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 1.98 % Allowed : 14.39 % Favored : 83.63 % 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: -2.41 (0.12), residues: 3929 helix: -1.68 (0.12), residues: 1471 sheet: -0.73 (0.26), residues: 390 loop : -1.66 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1290 TYR 0.014 0.001 TYR C 105 PHE 0.010 0.001 PHE D 620 TRP 0.013 0.001 TRP D1020 HIS 0.006 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (35095) covalent geometry : angle 0.52674 / 0.29 (48039) hydrogen bonds : bond 0.04176 / 4.71 ( 1032) hydrogen bonds : angle 4.97897 / 6.70 ( 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 336 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7310 (ptt) cc_final: 0.6953 (ptm) REVERT: C 651 ASP cc_start: 0.8165 (t0) cc_final: 0.7859 (t0) REVERT: C 941 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7742 (mttm) REVERT: D 304 ASP cc_start: 0.6847 (m-30) cc_final: 0.6377 (m-30) REVERT: D 372 MET cc_start: 0.9146 (ttm) cc_final: 0.8688 (ttp) REVERT: D 698 MET cc_start: 0.7069 (mmm) cc_final: 0.6759 (mmm) REVERT: D 700 ASN cc_start: 0.7534 (t0) cc_final: 0.7075 (t0) REVERT: D 892 PHE cc_start: 0.7993 (m-80) cc_final: 0.7272 (t80) REVERT: F 111 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7767 (pp) REVERT: F 288 MET cc_start: -0.0089 (mmt) cc_final: -0.0620 (mmp) REVERT: F 487 MET cc_start: 0.6535 (mmm) cc_final: 0.6191 (ttm) REVERT: K 41 MET cc_start: 0.3093 (ptt) cc_final: 0.2702 (ptm) REVERT: A 166 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7278 (mtm110) REVERT: A 183 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8429 (mt) REVERT: B 80 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: B 193 GLU cc_start: 0.5938 (pm20) cc_final: 0.5479 (pm20) outliers start: 67 outliers final: 47 residues processed: 327 average time/residue: 0.2021 time to fit residues: 108.7802 Evaluate side-chains 307 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 402 GLU 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 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 E residue 70 GLN 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 337 VAL Chi-restraints excluded: chain F residue 500 ILE 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 80 GLU Chi-restraints excluded: chain B residue 93 GLN 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: 6.9990 chunk 63 optimal weight: 0.3980 chunk 346 optimal weight: 8.9990 chunk 279 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 340 optimal weight: 0.0870 overall best weight: 1.6562 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.179142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153340 restraints weight = 48858.982| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.99 r_work: 0.3567 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 35095 Z= 0.112 Angle : 0.501 8.343 48039 Z= 0.277 Chirality : 0.042 0.266 5479 Planarity : 0.004 0.047 5736 Dihedral : 17.093 168.926 6001 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 2.51 % Allowed : 14.66 % Favored : 82.84 % 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: -2.07 (0.13), residues: 3929 helix: -1.29 (0.13), residues: 1487 sheet: -0.64 (0.26), residues: 399 loop : -1.54 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1290 TYR 0.011 0.001 TYR B 152 PHE 0.010 0.001 PHE C 405 TRP 0.010 0.001 TRP D1020 HIS 0.005 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (35095) covalent geometry : angle 0.50106 / 0.28 (48039) hydrogen bonds : bond 0.03688 / 4.17 ( 1032) hydrogen bonds : angle 4.73607 / 6.35 ( 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 361 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 276 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7325 (ptt) cc_final: 0.7007 (ptm) REVERT: C 484 LEU cc_start: 0.5262 (mm) cc_final: 0.4944 (mm) REVERT: C 651 ASP cc_start: 0.8000 (t0) cc_final: 0.7737 (t0) REVERT: C 941 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7980 (mttm) REVERT: D 304 ASP cc_start: 0.6957 (m-30) cc_final: 0.6509 (m-30) REVERT: D 698 MET cc_start: 0.7087 (mmm) cc_final: 0.6810 (mmm) REVERT: D 700 ASN cc_start: 0.7555 (t0) cc_final: 0.7175 (t0) REVERT: D 817 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.5807 (t-90) REVERT: D 864 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7714 (tt) REVERT: D 892 PHE cc_start: 0.7910 (m-80) cc_final: 0.7343 (t80) REVERT: F 111 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7733 (pp) REVERT: F 277 MET cc_start: 0.5716 (tmm) cc_final: 0.5471 (mmm) REVERT: K 41 MET cc_start: 0.3144 (ptt) cc_final: 0.2651 (ptm) REVERT: A 166 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7151 (mtm110) REVERT: A 183 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8410 (mt) REVERT: B 80 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: B 193 GLU cc_start: 0.5447 (pm20) cc_final: 0.5214 (pm20) outliers start: 85 outliers final: 57 residues processed: 348 average time/residue: 0.1998 time to fit residues: 114.4864 Evaluate side-chains 324 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 260 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 342 LEU 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 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 140 ILE 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: 0.6980 chunk 202 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 210 optimal weight: 0.0000 chunk 377 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.179957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152724 restraints weight = 48588.536| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.00 r_work: 0.3555 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2393 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= 0.116 Angle : 0.500 7.963 48039 Z= 0.275 Chirality : 0.042 0.268 5479 Planarity : 0.004 0.046 5736 Dihedral : 17.048 168.952 6001 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 2.45 % Allowed : 15.45 % Favored : 82.10 % 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: -1.83 (0.13), residues: 3929 helix: -1.02 (0.13), residues: 1488 sheet: -0.54 (0.26), residues: 409 loop : -1.46 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 260 TYR 0.012 0.001 TYR K 37 PHE 0.010 0.001 PHE C 405 TRP 0.012 0.001 TRP K 36 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (35095) covalent geometry : angle 0.49954 / 0.27 (48039) hydrogen bonds : bond 0.03515 / 3.99 ( 1032) hydrogen bonds : angle 4.58096 / 6.14 ( 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 347 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: C 484 LEU cc_start: 0.5222 (mm) cc_final: 0.4959 (mm) REVERT: C 651 ASP cc_start: 0.7993 (t0) cc_final: 0.7709 (t0) REVERT: C 941 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8019 (mttm) REVERT: D 304 ASP cc_start: 0.6998 (m-30) cc_final: 0.6580 (m-30) REVERT: D 698 MET cc_start: 0.7088 (mmm) cc_final: 0.6844 (mmm) REVERT: D 700 ASN cc_start: 0.7586 (t0) cc_final: 0.6901 (t0) REVERT: D 817 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.5816 (t-90) REVERT: D 864 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7635 (tt) REVERT: D 892 PHE cc_start: 0.7900 (m-80) cc_final: 0.7350 (t80) REVERT: F 111 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7727 (pp) REVERT: F 273 MET cc_start: 0.5395 (mmt) cc_final: 0.5188 (mmp) REVERT: A 51 MET cc_start: 0.8482 (mmp) cc_final: 0.8058 (mmp) REVERT: A 166 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6080 (mtm-85) REVERT: B 80 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: B 193 GLU cc_start: 0.5444 (pm20) cc_final: 0.5232 (pm20) outliers start: 83 outliers final: 59 residues processed: 338 average time/residue: 0.2113 time to fit residues: 118.8810 Evaluate side-chains 319 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR 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 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 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 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 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 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: 0.6980 chunk 266 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 39 optimal weight: 40.0000 chunk 268 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 250 optimal weight: 0.0970 chunk 122 optimal weight: 0.9980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.180449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.153306 restraints weight = 48725.771| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.04 r_work: 0.3558 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35095 Z= 0.110 Angle : 0.492 13.747 48039 Z= 0.270 Chirality : 0.042 0.270 5479 Planarity : 0.003 0.045 5736 Dihedral : 17.027 169.147 6001 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 2.36 % Allowed : 15.66 % Favored : 81.98 % 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: -1.65 (0.13), residues: 3929 helix: -0.78 (0.13), residues: 1491 sheet: -0.49 (0.26), residues: 421 loop : -1.43 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 40 TYR 0.010 0.001 TYR B 152 PHE 0.010 0.001 PHE C 405 TRP 0.008 0.001 TRP K 36 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (35095) covalent geometry : angle 0.49211 / 0.27 (48039) hydrogen bonds : bond 0.03337 / 3.77 ( 1032) hydrogen bonds : angle 4.45786 / 5.98 ( 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 341 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: C 332 ARG cc_start: 0.5067 (ttp-170) cc_final: 0.4697 (ptm160) REVERT: C 484 LEU cc_start: 0.5155 (mm) cc_final: 0.4891 (mm) REVERT: C 651 ASP cc_start: 0.7835 (t0) cc_final: 0.7620 (t0) REVERT: C 704 MET cc_start: 0.8770 (mmm) cc_final: 0.8384 (mtp) REVERT: C 737 ASN cc_start: 0.7375 (m-40) cc_final: 0.7169 (m-40) REVERT: D 304 ASP cc_start: 0.6803 (m-30) cc_final: 0.6378 (m-30) REVERT: D 698 MET cc_start: 0.6992 (mmm) cc_final: 0.6762 (mmm) REVERT: D 700 ASN cc_start: 0.7537 (t0) cc_final: 0.6905 (t0) REVERT: D 817 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5787 (t-90) REVERT: D 864 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7612 (tt) REVERT: D 892 PHE cc_start: 0.7852 (m-80) cc_final: 0.7209 (t80) REVERT: F 111 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7720 (pp) REVERT: F 141 ILE cc_start: 0.4270 (OUTLIER) cc_final: 0.4057 (tt) REVERT: F 277 MET cc_start: 0.5777 (tmm) cc_final: 0.5475 (mmm) REVERT: F 466 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8160 (mt) REVERT: K 41 MET cc_start: 0.4239 (ptm) cc_final: 0.3799 (ptt) REVERT: A 51 MET cc_start: 0.8387 (mmp) cc_final: 0.8008 (mmp) REVERT: A 166 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6048 (mtm-85) REVERT: B 80 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6838 (tp30) outliers start: 80 outliers final: 61 residues processed: 331 average time/residue: 0.2030 time to fit residues: 111.9804 Evaluate side-chains 313 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR 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 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 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 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 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 466 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 80 optimal weight: 0.6980 chunk 182 optimal weight: 0.6980 chunk 301 optimal weight: 5.9990 chunk 385 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 402 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 105 optimal weight: 0.0770 chunk 154 optimal weight: 0.0870 overall best weight: 1.1118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150723 restraints weight = 48306.894| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.11 r_work: 0.3506 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35095 Z= 0.097 Angle : 0.475 7.693 48039 Z= 0.263 Chirality : 0.041 0.268 5479 Planarity : 0.003 0.044 5736 Dihedral : 16.991 169.790 6001 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 2.09 % Allowed : 16.04 % Favored : 81.86 % 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: -0.57 (0.13), residues: 1489 sheet: -0.43 (0.26), residues: 421 loop : -1.36 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 260 TYR 0.015 0.001 TYR F 143 PHE 0.010 0.001 PHE C 405 TRP 0.009 0.001 TRP D1020 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.10 (35095) covalent geometry : angle 0.47498 / 0.26 (48039) hydrogen bonds : bond 0.03154 / 3.58 ( 1032) hydrogen bonds : angle 4.36349 / 5.84 ( 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 331 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: C 20 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7203 (pt0) REVERT: C 332 ARG cc_start: 0.4954 (ttp-170) cc_final: 0.4593 (ptm160) REVERT: C 484 LEU cc_start: 0.5090 (mm) cc_final: 0.4847 (mm) REVERT: C 651 ASP cc_start: 0.7833 (t0) cc_final: 0.7615 (t0) REVERT: C 704 MET cc_start: 0.8817 (mmm) cc_final: 0.8399 (mtp) REVERT: C 737 ASN cc_start: 0.7269 (m-40) cc_final: 0.7041 (m-40) REVERT: D 304 ASP cc_start: 0.6787 (m-30) cc_final: 0.6405 (m-30) REVERT: D 698 MET cc_start: 0.6805 (mmm) cc_final: 0.6567 (mmm) REVERT: D 700 ASN cc_start: 0.7554 (t0) cc_final: 0.6966 (t0) REVERT: D 817 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.5876 (t-90) REVERT: D 864 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7608 (tt) REVERT: D 892 PHE cc_start: 0.7857 (m-80) cc_final: 0.7249 (t80) REVERT: D 1291 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6316 (mm-30) REVERT: F 111 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7711 (pp) REVERT: F 273 MET cc_start: 0.5231 (mmt) cc_final: 0.4913 (mmp) REVERT: F 277 MET cc_start: 0.5802 (tmm) cc_final: 0.5547 (mmm) REVERT: F 369 GLU cc_start: 0.6992 (pp20) cc_final: 0.6680 (pt0) REVERT: K 41 MET cc_start: 0.3952 (ptm) cc_final: 0.3507 (ptt) REVERT: A 166 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.5984 (mtm-85) REVERT: B 80 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6803 (tp30) outliers start: 71 outliers final: 52 residues processed: 320 average time/residue: 0.1985 time to fit residues: 105.9629 Evaluate side-chains 306 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 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 839 VAL Chi-restraints excluded: chain C residue 844 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 210 SER 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 168 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 289 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 358 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 360 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.179473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151858 restraints weight = 48179.520| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.07 r_work: 0.3517 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35095 Z= 0.096 Angle : 0.472 8.263 48039 Z= 0.260 Chirality : 0.041 0.267 5479 Planarity : 0.003 0.053 5736 Dihedral : 16.944 170.047 6001 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 2.01 % Allowed : 16.25 % Favored : 81.75 % 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: -1.26 (0.13), residues: 3929 helix: -0.35 (0.14), residues: 1491 sheet: -0.28 (0.27), residues: 410 loop : -1.30 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 150 TYR 0.014 0.001 TYR K 82 PHE 0.010 0.001 PHE A 8 TRP 0.010 0.001 TRP D1020 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.10 (35095) covalent geometry : angle 0.47237 / 0.26 (48039) hydrogen bonds : bond 0.03073 / 3.48 ( 1032) hydrogen bonds : angle 4.26699 / 5.68 ( 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 320 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: C 20 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: C 58 PRO cc_start: 0.7344 (Cg_endo) cc_final: 0.7075 (Cg_exo) REVERT: C 332 ARG cc_start: 0.4941 (ttp-170) cc_final: 0.4638 (ptm160) REVERT: C 484 LEU cc_start: 0.5098 (mm) cc_final: 0.4826 (mm) REVERT: C 651 ASP cc_start: 0.7788 (t0) cc_final: 0.7583 (t0) REVERT: C 704 MET cc_start: 0.8794 (mmm) cc_final: 0.8383 (mtp) REVERT: D 298 MET cc_start: 0.8727 (mtm) cc_final: 0.8510 (mtm) REVERT: D 304 ASP cc_start: 0.6880 (m-30) cc_final: 0.6487 (m-30) REVERT: D 698 MET cc_start: 0.6826 (mmm) cc_final: 0.6619 (mmm) REVERT: D 700 ASN cc_start: 0.7549 (t0) cc_final: 0.6990 (t0) REVERT: D 817 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.5863 (t-90) REVERT: D 864 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7579 (tt) REVERT: D 892 PHE cc_start: 0.7846 (m-80) cc_final: 0.7194 (t80) REVERT: D 1291 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6280 (mm-30) REVERT: D 1349 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: F 111 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7714 (pp) REVERT: F 277 MET cc_start: 0.5730 (tmm) cc_final: 0.5454 (mmm) REVERT: F 369 GLU cc_start: 0.6949 (pp20) cc_final: 0.6745 (pt0) REVERT: K 41 MET cc_start: 0.4048 (ptm) cc_final: 0.3489 (ptt) REVERT: A 166 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.5974 (mtm-85) REVERT: B 80 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6777 (tp30) outliers start: 68 outliers final: 54 residues processed: 311 average time/residue: 0.1903 time to fit residues: 99.2506 Evaluate side-chains 310 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 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 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 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 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR 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 1349 GLU 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 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 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 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: 0.1980 chunk 389 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 370 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 354 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.148423 restraints weight = 48108.233| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.14 r_work: 0.3478 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2762 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= 0.122 Angle : 0.496 7.807 48039 Z= 0.271 Chirality : 0.042 0.272 5479 Planarity : 0.004 0.051 5736 Dihedral : 16.966 168.932 6001 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.01 % Allowed : 16.19 % 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: -1.25 (0.13), residues: 3929 helix: -0.33 (0.13), residues: 1503 sheet: -0.25 (0.27), residues: 408 loop : -1.31 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 58 TYR 0.012 0.001 TYR K 82 PHE 0.016 0.001 PHE D1037 TRP 0.011 0.001 TRP D1020 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (35095) covalent geometry : angle 0.49603 / 0.27 (48039) hydrogen bonds : bond 0.03295 / 3.73 ( 1032) hydrogen bonds : angle 4.29303 / 5.75 ( 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 323 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: C 20 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: C 332 ARG cc_start: 0.4968 (ttp-170) cc_final: 0.4649 (ptm160) REVERT: C 651 ASP cc_start: 0.7848 (t0) cc_final: 0.7618 (t0) REVERT: C 704 MET cc_start: 0.8800 (mmm) cc_final: 0.8406 (mtp) REVERT: D 304 ASP cc_start: 0.6898 (m-30) cc_final: 0.6492 (m-30) REVERT: D 698 MET cc_start: 0.6590 (mmm) cc_final: 0.6303 (mmm) REVERT: D 700 ASN cc_start: 0.7572 (t0) cc_final: 0.7002 (t0) REVERT: D 817 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.5867 (t-90) REVERT: D 864 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7620 (tt) REVERT: D 892 PHE cc_start: 0.7850 (m-80) cc_final: 0.7248 (t80) REVERT: D 1040 MET cc_start: 0.0584 (OUTLIER) cc_final: -0.0732 (mmt) REVERT: D 1291 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6270 (mm-30) REVERT: D 1349 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: F 111 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7737 (pp) REVERT: F 273 MET cc_start: 0.5439 (mmt) cc_final: 0.4921 (mmp) REVERT: F 369 GLU cc_start: 0.6992 (pp20) cc_final: 0.6688 (pt0) REVERT: K 41 MET cc_start: 0.3999 (ptm) cc_final: 0.3414 (ptt) REVERT: A 166 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.5999 (mtm-85) REVERT: B 80 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6836 (tp30) outliers start: 68 outliers final: 56 residues processed: 312 average time/residue: 0.1916 time to fit residues: 100.5464 Evaluate side-chains 310 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 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 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 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 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1040 MET 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 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 108 VAL Chi-restraints excluded: chain F residue 111 LEU 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 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 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: 0.0060 chunk 172 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 368 optimal weight: 0.4980 chunk 397 optimal weight: 0.3980 chunk 44 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 334 optimal weight: 0.0070 chunk 223 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 318 optimal weight: 4.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1324 ASN D 805 GLN F 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153408 restraints weight = 48199.597| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.11 r_work: 0.3516 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35095 Z= 0.087 Angle : 0.460 8.444 48039 Z= 0.254 Chirality : 0.040 0.264 5479 Planarity : 0.003 0.043 5736 Dihedral : 16.876 171.487 6001 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 16.90 % Favored : 81.45 % 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: -0.93 (0.13), residues: 3929 helix: -0.02 (0.14), residues: 1497 sheet: -0.14 (0.27), residues: 400 loop : -1.15 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 58 TYR 0.010 0.001 TYR C1231 PHE 0.009 0.001 PHE C 405 TRP 0.013 0.001 TRP D1020 HIS 0.002 0.000 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.09 (35095) covalent geometry : angle 0.46040 / 0.25 (48039) hydrogen bonds : bond 0.02830 / 3.23 ( 1032) hydrogen bonds : angle 4.14445 / 5.52 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.06 seconds wall clock time: 119 minutes 57.85 seconds (7197.85 seconds total)