Starting phenix.real_space_refine on Sun Jun 29 04:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w5x_32323/06_2025/7w5x_32323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5x_32323/06_2025/7w5x_32323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w5x_32323/06_2025/7w5x_32323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5x_32323/06_2025/7w5x_32323.map" model { file = "/net/cci-nas-00/data/ceres_data/7w5x_32323/06_2025/7w5x_32323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5x_32323/06_2025/7w5x_32323.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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: 22.28, per 1000 atoms: 0.65 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: 8.59 Conformation dependent library (CDL) restraints added in 5.4 seconds 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7378 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 45 sheets defined 40.4% alpha, 13.8% beta 21 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 12.16 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: 16.69 Time building geometry restraints manager: 10.00 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=" C LYS C 496 " pdb=" N PRO C 497 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" C LYS F 324 " pdb=" N PRO F 325 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.85e+00 bond pdb=" CB VAL D1255 " pdb=" CG1 VAL D1255 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" C3' DG 2 43 " pdb=" O3' DG 2 43 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.42e+00 ... (remaining 35090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 46803 2.15 - 4.31: 1094 4.31 - 6.46: 108 6.46 - 8.61: 27 8.61 - 10.77: 7 Bond angle restraints: 48039 Sorted by residual: angle pdb=" N GLY D1103 " pdb=" CA GLY D1103 " pdb=" C GLY D1103 " ideal model delta sigma weight residual 112.33 119.02 -6.69 1.10e+00 8.26e-01 3.70e+01 angle pdb=" C ASN D 320 " pdb=" N LYS D 321 " pdb=" CA LYS D 321 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C PRO D 859 " pdb=" N ARG D 860 " pdb=" CA ARG D 860 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" O3' DA 1 79 " pdb=" C3' DA 1 79 " pdb=" C2' DA 1 79 " ideal model delta sigma weight residual 111.50 104.42 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" N SER B 266 " pdb=" CA SER B 266 " pdb=" C SER B 266 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+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: 4874 0.078 - 0.156: 552 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: 15.170 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: 0.050 Extract box with map and model: 1.330 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 87.870 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.170 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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= 0.244 Angle : 0.802 10.766 48039 Z= 0.452 Chirality : 0.052 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP C 997 HIS 0.014 0.002 HIS C 554 PHE 0.033 0.002 PHE D 338 TYR 0.017 0.002 TYR C 105 ARG 0.006 0.001 ARG D 780 Details of bonding type rmsd hydrogen bonds : bond 0.32242 ( 1032) hydrogen bonds : angle 10.40902 ( 2916) covalent geometry : bond 0.00558 (35095) covalent geometry : angle 0.80242 (48039) *********************** 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 : 3.435 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7305 (Cg_endo) cc_final: 0.7044 (Cg_exo) REVERT: C 315 MET cc_start: 0.7239 (ttm) cc_final: 0.6924 (ttp) REVERT: C 484 LEU cc_start: 0.5642 (mm) cc_final: 0.5416 (mm) REVERT: C 496 LYS cc_start: 0.7304 (mmtp) cc_final: 0.7009 (mmtp) REVERT: C 542 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6981 (mtp-110) REVERT: D 562 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7150 (tt0) REVERT: D 566 LYS cc_start: 0.8079 (ptmt) cc_final: 0.7800 (ptpt) REVERT: D 865 HIS cc_start: 0.7784 (p90) cc_final: 0.7514 (p90) REVERT: D 892 PHE cc_start: 0.7670 (m-80) cc_final: 0.7023 (t80) REVERT: D 1174 ARG cc_start: 0.5007 (mtt180) cc_final: 0.4676 (mtp180) REVERT: D 1220 ILE cc_start: 0.8128 (mm) cc_final: 0.7877 (mt) REVERT: F 509 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 139 SER cc_start: 0.5387 (t) cc_final: 0.5011 (p) outliers start: 12 outliers final: 6 residues processed: 447 average time/residue: 0.6909 time to fit residues: 470.7435 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 : 3.878 ------------------------------------------------------------------------------- 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 343 optimal weight: 10.0000 chunk 308 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 237 optimal weight: 0.1980 chunk 369 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 C1090 ASN C1157 GLN C1313 HIS D 294 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 560 ASN D 805 GLN 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.182154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145678 restraints weight = 48972.966| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.83 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35095 Z= 0.123 Angle : 0.539 7.433 48039 Z= 0.299 Chirality : 0.041 0.154 5479 Planarity : 0.005 0.056 5736 Dihedral : 17.209 177.263 6004 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 1.42 % Allowed : 10.97 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.11), residues: 3929 helix: -3.32 (0.09), residues: 1471 sheet: -1.13 (0.26), residues: 384 loop : -2.00 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.008 0.001 HIS F 545 PHE 0.012 0.001 PHE D 620 TYR 0.017 0.001 TYR D1282 ARG 0.013 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.05116 ( 1032) hydrogen bonds : angle 5.65044 ( 2916) covalent geometry : bond 0.00250 (35095) covalent geometry : angle 0.53915 (48039) *********************** 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 373 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 3.634 Fit side-chains REVERT: C 58 PRO cc_start: 0.7224 (Cg_endo) cc_final: 0.6952 (Cg_exo) REVERT: C 239 MET cc_start: 0.7094 (ptt) cc_final: 0.6728 (ptm) REVERT: C 941 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7861 (mttm) REVERT: D 29 MET cc_start: 0.7754 (tpp) cc_final: 0.7498 (ttm) REVERT: D 304 ASP cc_start: 0.6439 (m-30) cc_final: 0.5983 (m-30) REVERT: D 698 MET cc_start: 0.6616 (mmm) cc_final: 0.6338 (mmm) REVERT: D 700 ASN cc_start: 0.7134 (t0) cc_final: 0.6730 (t0) REVERT: D 892 PHE cc_start: 0.7652 (m-80) cc_final: 0.7183 (t80) REVERT: F 111 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7481 (pp) REVERT: F 561 MET cc_start: 0.6260 (mmm) cc_final: 0.6037 (mmp) REVERT: F 582 VAL cc_start: 0.6041 (OUTLIER) cc_final: 0.5827 (t) REVERT: K 78 MET cc_start: 0.0841 (tpp) cc_final: 0.0418 (tpp) REVERT: B 188 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6798 (mt-10) outliers start: 48 outliers final: 20 residues processed: 365 average time/residue: 0.5066 time to fit residues: 301.1001 Evaluate side-chains 290 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 493 ILE 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 805 GLN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 331 optimal weight: 6.9990 chunk 336 optimal weight: 0.5980 chunk 252 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 363 optimal weight: 0.0010 chunk 270 optimal weight: 5.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C1090 ASN C1157 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 75 GLN B 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.179816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150499 restraints weight = 48860.140| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.24 r_work: 0.3515 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35095 Z= 0.115 Angle : 0.503 8.134 48039 Z= 0.276 Chirality : 0.041 0.203 5479 Planarity : 0.004 0.050 5736 Dihedral : 16.994 175.041 6001 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 1.53 % Allowed : 12.59 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.12), residues: 3929 helix: -2.20 (0.11), residues: 1472 sheet: -0.95 (0.26), residues: 402 loop : -1.72 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 33 HIS 0.005 0.001 HIS K 47 PHE 0.012 0.001 PHE D 620 TYR 0.012 0.001 TYR C1231 ARG 0.007 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1032) hydrogen bonds : angle 4.95052 ( 2916) covalent geometry : bond 0.00256 (35095) covalent geometry : angle 0.50320 (48039) *********************** 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 349 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 3.710 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7343 (Cg_endo) cc_final: 0.7059 (Cg_exo) REVERT: C 239 MET cc_start: 0.7245 (ptt) cc_final: 0.6885 (ptm) REVERT: C 651 ASP cc_start: 0.7976 (t0) cc_final: 0.7732 (t0) REVERT: C 941 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7791 (mttm) REVERT: D 304 ASP cc_start: 0.6867 (m-30) cc_final: 0.6392 (m-30) REVERT: D 698 MET cc_start: 0.7053 (mmm) cc_final: 0.6787 (mmm) REVERT: D 700 ASN cc_start: 0.7490 (t0) cc_final: 0.6760 (t0) REVERT: D 892 PHE cc_start: 0.7826 (m-80) cc_final: 0.7308 (t80) REVERT: F 111 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7635 (pp) REVERT: B 78 ILE cc_start: 0.7800 (mm) cc_final: 0.7494 (tt) REVERT: B 188 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7347 (mt-10) outliers start: 52 outliers final: 29 residues processed: 338 average time/residue: 0.4846 time to fit residues: 266.5340 Evaluate side-chains 306 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 508 SER Chi-restraints excluded: chain C residue 615 VAL 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 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 639 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 D residue 1305 ASP 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 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 312 optimal weight: 0.5980 chunk 219 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 390 optimal weight: 1.9990 chunk 318 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1090 ASN D 951 GLN F 265 GLN B 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.179982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147375 restraints weight = 49001.609| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.61 r_work: 0.3382 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35095 Z= 0.148 Angle : 0.529 8.141 48039 Z= 0.286 Chirality : 0.042 0.152 5479 Planarity : 0.004 0.048 5736 Dihedral : 17.005 174.383 6001 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 2.21 % Allowed : 14.04 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.12), residues: 3929 helix: -1.60 (0.12), residues: 1478 sheet: -0.71 (0.26), residues: 400 loop : -1.59 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1193 HIS 0.007 0.001 HIS C 554 PHE 0.013 0.001 PHE D 620 TYR 0.013 0.001 TYR C1231 ARG 0.003 0.000 ARG K 55 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 1032) hydrogen bonds : angle 4.73844 ( 2916) covalent geometry : bond 0.00348 (35095) covalent geometry : angle 0.52890 (48039) *********************** 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 345 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 270 time to evaluate : 3.667 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7318 (ptt) cc_final: 0.6973 (ptm) REVERT: C 484 LEU cc_start: 0.5310 (mm) cc_final: 0.5098 (mm) REVERT: C 514 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 651 ASP cc_start: 0.8127 (t0) cc_final: 0.7849 (t0) REVERT: D 304 ASP cc_start: 0.6843 (m-30) cc_final: 0.6438 (m-30) REVERT: D 698 MET cc_start: 0.7067 (mmm) cc_final: 0.6780 (mmm) REVERT: D 700 ASN cc_start: 0.7528 (t0) cc_final: 0.6792 (t0) REVERT: D 817 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.5953 (t-90) REVERT: D 892 PHE cc_start: 0.7919 (m-80) cc_final: 0.7246 (t80) REVERT: D 951 GLN cc_start: 0.4637 (OUTLIER) cc_final: 0.4332 (tt0) REVERT: F 111 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7665 (pp) REVERT: K 41 MET cc_start: 0.3098 (ptt) cc_final: 0.2827 (ptm) REVERT: A 166 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7153 (mtm110) REVERT: B 188 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 215 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7680 (tm-30) outliers start: 75 outliers final: 53 residues processed: 335 average time/residue: 0.4962 time to fit residues: 270.9504 Evaluate side-chains 309 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 3.389 ------------------------------------------------------------------------------- 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 208 ILE 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 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 196 GLN 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 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 951 GLN Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain 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 595 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 282 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 362 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 395 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.176285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149718 restraints weight = 48351.669| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.03 r_work: 0.3486 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35095 Z= 0.163 Angle : 0.537 8.330 48039 Z= 0.290 Chirality : 0.042 0.157 5479 Planarity : 0.004 0.047 5736 Dihedral : 17.051 174.347 6001 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 2.62 % Allowed : 15.16 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 3929 helix: -1.30 (0.13), residues: 1489 sheet: -0.59 (0.26), residues: 400 loop : -1.54 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 36 HIS 0.007 0.001 HIS D 113 PHE 0.013 0.001 PHE D 620 TYR 0.014 0.001 TYR C 105 ARG 0.005 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 1032) hydrogen bonds : angle 4.69194 ( 2916) covalent geometry : bond 0.00389 (35095) covalent geometry : angle 0.53696 (48039) *********************** 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 349 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 260 time to evaluate : 3.777 Fit side-chains REVERT: C 239 MET cc_start: 0.7389 (ptt) cc_final: 0.7039 (ptm) REVERT: C 514 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7805 (t80) REVERT: C 651 ASP cc_start: 0.7956 (t0) cc_final: 0.7728 (t0) REVERT: C 704 MET cc_start: 0.8767 (mmm) cc_final: 0.8464 (mtp) REVERT: D 304 ASP cc_start: 0.6860 (m-30) cc_final: 0.6473 (m-30) REVERT: D 545 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.8098 (p90) REVERT: D 698 MET cc_start: 0.6994 (mmm) cc_final: 0.6739 (mmm) REVERT: D 700 ASN cc_start: 0.7554 (t0) cc_final: 0.6917 (t0) REVERT: D 817 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.5863 (t-90) REVERT: D 892 PHE cc_start: 0.7774 (m-80) cc_final: 0.7339 (t80) REVERT: D 1291 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6195 (mm-30) REVERT: F 111 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7799 (pp) REVERT: K 41 MET cc_start: 0.3279 (ptt) cc_final: 0.3053 (ptm) REVERT: A 51 MET cc_start: 0.8354 (mmp) cc_final: 0.8015 (mmp) REVERT: A 166 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7033 (mtm110) REVERT: B 188 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7353 (mt-10) REVERT: B 215 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7592 (tm-30) outliers start: 89 outliers final: 61 residues processed: 337 average time/residue: 0.4670 time to fit residues: 261.2425 Evaluate side-chains 320 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 3.555 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 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 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1115 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 176 PHE Chi-restraints excluded: chain D residue 180 MET 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 501 VAL Chi-restraints excluded: chain D residue 545 HIS 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 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU 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 B residue 59 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 378 optimal weight: 10.0000 chunk 26 optimal weight: 0.0020 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 0.6980 chunk 210 optimal weight: 0.5980 chunk 211 optimal weight: 4.9990 chunk 99 optimal weight: 0.0570 chunk 324 optimal weight: 0.3980 chunk 242 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1324 ASN D 805 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.180037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155155 restraints weight = 48390.692| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.96 r_work: 0.3568 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35095 Z= 0.090 Angle : 0.464 8.722 48039 Z= 0.253 Chirality : 0.040 0.192 5479 Planarity : 0.003 0.044 5736 Dihedral : 16.812 177.981 6001 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.71 % Allowed : 16.25 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3929 helix: -0.75 (0.13), residues: 1490 sheet: -0.41 (0.26), residues: 404 loop : -1.32 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1020 HIS 0.004 0.000 HIS K 47 PHE 0.020 0.001 PHE F 256 TYR 0.009 0.001 TYR B 152 ARG 0.008 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 1032) hydrogen bonds : angle 4.30538 ( 2916) covalent geometry : bond 0.00192 (35095) covalent geometry : angle 0.46415 (48039) *********************** 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 339 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 281 time to evaluate : 3.418 Fit side-chains REVERT: C 58 PRO cc_start: 0.7279 (Cg_endo) cc_final: 0.7033 (Cg_exo) REVERT: C 285 ILE cc_start: 0.7164 (mm) cc_final: 0.6856 (mt) REVERT: C 651 ASP cc_start: 0.7783 (t0) cc_final: 0.7573 (t0) REVERT: C 704 MET cc_start: 0.8726 (mmm) cc_final: 0.8382 (mtp) REVERT: D 304 ASP cc_start: 0.6711 (m-30) cc_final: 0.6337 (m-30) REVERT: D 700 ASN cc_start: 0.7479 (t0) cc_final: 0.6942 (t0) REVERT: D 713 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.4096 (tt0) REVERT: D 817 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5796 (t-90) REVERT: D 892 PHE cc_start: 0.7774 (m-80) cc_final: 0.7173 (t80) REVERT: D 1291 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6248 (mm-30) REVERT: F 111 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7692 (pp) REVERT: F 255 VAL cc_start: 0.5111 (p) cc_final: 0.4898 (t) REVERT: F 273 MET cc_start: 0.5492 (mmt) cc_final: 0.5124 (mmp) REVERT: B 80 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: B 188 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7250 (mt-10) outliers start: 58 outliers final: 40 residues processed: 331 average time/residue: 0.4616 time to fit residues: 249.0083 Evaluate side-chains 299 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR 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 1156 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU 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 805 GLN Chi-restraints excluded: chain D residue 817 HIS 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 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 K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 0.0030 chunk 164 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN D 805 GLN B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.154458 restraints weight = 48291.675| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.85 r_work: 0.3523 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35095 Z= 0.141 Angle : 0.509 7.962 48039 Z= 0.274 Chirality : 0.041 0.147 5479 Planarity : 0.004 0.045 5736 Dihedral : 16.913 175.290 6001 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 2.12 % Allowed : 16.46 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3929 helix: -0.70 (0.13), residues: 1497 sheet: -0.33 (0.27), residues: 402 loop : -1.34 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1020 HIS 0.006 0.001 HIS D 113 PHE 0.015 0.001 PHE C 80 TYR 0.012 0.001 TYR C1231 ARG 0.011 0.000 ARG F 596 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 1032) hydrogen bonds : angle 4.38773 ( 2916) covalent geometry : bond 0.00335 (35095) covalent geometry : angle 0.50889 (48039) *********************** 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 327 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 255 time to evaluate : 3.384 Fit side-chains revert: symmetry clash REVERT: C 79 VAL cc_start: 0.9005 (m) cc_final: 0.8733 (m) REVERT: C 651 ASP cc_start: 0.7820 (t0) cc_final: 0.7617 (t0) REVERT: C 704 MET cc_start: 0.8795 (mmm) cc_final: 0.8432 (mtp) REVERT: D 298 MET cc_start: 0.8706 (mtm) cc_final: 0.8418 (mtm) REVERT: D 304 ASP cc_start: 0.6760 (m-30) cc_final: 0.6408 (m-30) REVERT: D 700 ASN cc_start: 0.7635 (t0) cc_final: 0.7099 (t0) REVERT: D 817 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.5841 (t-90) REVERT: D 892 PHE cc_start: 0.7758 (m-80) cc_final: 0.7318 (t80) REVERT: D 1291 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6130 (mm-30) REVERT: F 111 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7762 (pp) REVERT: F 255 VAL cc_start: 0.5179 (p) cc_final: 0.4972 (t) REVERT: F 323 ASN cc_start: 0.1009 (OUTLIER) cc_final: 0.0076 (t0) REVERT: K 41 MET cc_start: 0.4110 (ptm) cc_final: 0.3623 (ptt) REVERT: A 166 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7017 (mtm110) REVERT: B 80 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: B 188 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7417 (mt-10) outliers start: 72 outliers final: 56 residues processed: 317 average time/residue: 0.4729 time to fit residues: 248.1548 Evaluate side-chains 307 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 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 D residue 48 THR 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 805 GLN Chi-restraints excluded: chain D residue 817 HIS 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 1287 ILE Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP 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 323 ASN Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU 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 252 ILE 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 93 GLN Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 236 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 373 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 400 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN D 805 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149667 restraints weight = 48181.748| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.08 r_work: 0.3486 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35095 Z= 0.159 Angle : 0.527 11.238 48039 Z= 0.282 Chirality : 0.042 0.188 5479 Planarity : 0.004 0.045 5736 Dihedral : 16.968 175.155 6001 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.86 % Rotamer: Outliers : 2.36 % Allowed : 16.43 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3929 helix: -0.72 (0.13), residues: 1506 sheet: -0.44 (0.26), residues: 413 loop : -1.34 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.007 0.001 HIS D 113 PHE 0.013 0.001 PHE D1037 TYR 0.013 0.001 TYR C 105 ARG 0.009 0.000 ARG K 58 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1032) hydrogen bonds : angle 4.44171 ( 2916) covalent geometry : bond 0.00382 (35095) covalent geometry : angle 0.52739 (48039) *********************** 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: 80 poor density : 251 time to evaluate : 3.852 Fit side-chains REVERT: C 484 LEU cc_start: 0.5053 (mm) cc_final: 0.4839 (mm) REVERT: C 704 MET cc_start: 0.8866 (mmm) cc_final: 0.8478 (mtp) REVERT: D 298 MET cc_start: 0.8730 (mtm) cc_final: 0.8437 (mtm) REVERT: D 304 ASP cc_start: 0.6855 (m-30) cc_final: 0.6488 (m-30) REVERT: D 700 ASN cc_start: 0.7669 (t0) cc_final: 0.7103 (t0) REVERT: D 817 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.5864 (t-90) REVERT: D 864 LEU cc_start: 0.8540 (mt) cc_final: 0.8334 (mt) REVERT: D 892 PHE cc_start: 0.7781 (m-80) cc_final: 0.7207 (t80) REVERT: D 1040 MET cc_start: 0.0497 (OUTLIER) cc_final: -0.1020 (mmt) REVERT: D 1243 LEU cc_start: 0.8378 (tt) cc_final: 0.8151 (tp) REVERT: D 1291 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6180 (mm-30) REVERT: F 111 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7797 (pp) REVERT: F 255 VAL cc_start: 0.5484 (p) cc_final: 0.5217 (t) REVERT: F 273 MET cc_start: 0.5375 (mmt) cc_final: 0.5134 (mmp) REVERT: F 323 ASN cc_start: 0.0934 (OUTLIER) cc_final: -0.0020 (t0) REVERT: F 388 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8945 (tt) REVERT: K 41 MET cc_start: 0.4015 (ptm) cc_final: 0.3536 (ptt) REVERT: A 166 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7033 (mtm110) REVERT: B 80 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6814 (tp30) REVERT: B 188 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7330 (mt-10) outliers start: 80 outliers final: 60 residues processed: 317 average time/residue: 0.5649 time to fit residues: 300.5588 Evaluate side-chains 316 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ILE 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 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 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 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 805 GLN Chi-restraints excluded: chain D residue 817 HIS 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 1040 MET 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 1287 ILE Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 8 ASP 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 137 TYR Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 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 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 Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 52 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 367 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 385 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN D 805 GLN D 979 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.175253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152396 restraints weight = 48466.487| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.86 r_work: 0.3496 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35095 Z= 0.197 Angle : 0.572 8.642 48039 Z= 0.305 Chirality : 0.043 0.177 5479 Planarity : 0.004 0.045 5736 Dihedral : 17.112 173.786 6001 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.58 % Rotamer: Outliers : 2.21 % Allowed : 16.57 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3929 helix: -0.83 (0.13), residues: 1510 sheet: -0.33 (0.27), residues: 398 loop : -1.42 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 868 HIS 0.009 0.001 HIS D 113 PHE 0.012 0.001 PHE D 377 TYR 0.015 0.001 TYR C 105 ARG 0.008 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 1032) hydrogen bonds : angle 4.60586 ( 2916) covalent geometry : bond 0.00478 (35095) covalent geometry : angle 0.57205 (48039) *********************** 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 328 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 253 time to evaluate : 3.646 Fit side-chains REVERT: C 514 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7839 (t80) REVERT: C 704 MET cc_start: 0.8836 (mmm) cc_final: 0.8412 (mtp) REVERT: C 1230 MET cc_start: 0.8620 (ttm) cc_final: 0.8102 (ttm) REVERT: D 304 ASP cc_start: 0.6842 (m-30) cc_final: 0.6463 (m-30) REVERT: D 700 ASN cc_start: 0.7725 (t0) cc_final: 0.7500 (t0) REVERT: D 817 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.5848 (t-90) REVERT: D 892 PHE cc_start: 0.7788 (m-80) cc_final: 0.7322 (t80) REVERT: D 1040 MET cc_start: 0.0413 (OUTLIER) cc_final: -0.1056 (mmt) REVERT: D 1287 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7512 (mm) REVERT: D 1291 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6179 (mm-30) REVERT: F 111 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7913 (pp) REVERT: F 323 ASN cc_start: 0.1275 (OUTLIER) cc_final: 0.0140 (t0) REVERT: F 388 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8974 (tt) REVERT: K 41 MET cc_start: 0.4194 (ptm) cc_final: 0.3695 (ptt) REVERT: A 166 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7050 (mtm110) REVERT: B 80 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: B 188 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7417 (mt-10) outliers start: 75 outliers final: 58 residues processed: 316 average time/residue: 0.4593 time to fit residues: 240.8459 Evaluate side-chains 315 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ILE 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 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 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 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 180 MET Chi-restraints excluded: chain D residue 201 LEU 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 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 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP 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 8 ASP 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 323 ASN Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU 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 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 Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 167 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 219 optimal weight: 30.0000 chunk 61 optimal weight: 0.0000 chunk 316 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 371 optimal weight: 0.1980 overall best weight: 2.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN F 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148027 restraints weight = 48061.076| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.19 r_work: 0.3465 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2872 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= 0.139 Angle : 0.520 8.472 48039 Z= 0.280 Chirality : 0.041 0.146 5479 Planarity : 0.004 0.044 5736 Dihedral : 17.012 175.416 6001 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.09 % Rotamer: Outliers : 2.09 % Allowed : 16.69 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3929 helix: -0.64 (0.13), residues: 1506 sheet: -0.30 (0.26), residues: 409 loop : -1.34 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 13 HIS 0.006 0.001 HIS D 113 PHE 0.011 0.001 PHE F 256 TYR 0.011 0.001 TYR C1231 ARG 0.008 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1032) hydrogen bonds : angle 4.45992 ( 2916) covalent geometry : bond 0.00328 (35095) covalent geometry : angle 0.51965 (48039) ********************** 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 319 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 248 time to evaluate : 3.872 Fit side-chains REVERT: C 651 ASP cc_start: 0.7826 (t0) cc_final: 0.7608 (t0) REVERT: C 704 MET cc_start: 0.8853 (mmm) cc_final: 0.8449 (mtp) REVERT: C 1230 MET cc_start: 0.8563 (ttm) cc_final: 0.8114 (ttt) REVERT: D 298 MET cc_start: 0.8740 (mtm) cc_final: 0.8447 (mtm) REVERT: D 304 ASP cc_start: 0.6878 (m-30) cc_final: 0.6513 (m-30) REVERT: D 700 ASN cc_start: 0.7716 (t0) cc_final: 0.7155 (t0) REVERT: D 817 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.5836 (t-90) REVERT: D 892 PHE cc_start: 0.7841 (m-80) cc_final: 0.7226 (t80) REVERT: D 1040 MET cc_start: 0.0714 (OUTLIER) cc_final: -0.0821 (mmt) REVERT: D 1287 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7442 (mm) REVERT: D 1291 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6114 (mm-30) REVERT: F 111 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7899 (pp) REVERT: F 273 MET cc_start: 0.5495 (mmt) cc_final: 0.5132 (mmp) REVERT: F 323 ASN cc_start: 0.1208 (OUTLIER) cc_final: 0.0185 (t0) REVERT: F 388 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8957 (tt) REVERT: K 41 MET cc_start: 0.4075 (ptm) cc_final: 0.3585 (ptt) REVERT: A 166 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7095 (mtm110) REVERT: B 80 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6857 (tp30) REVERT: B 188 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7361 (mt-10) outliers start: 71 outliers final: 57 residues processed: 307 average time/residue: 0.4714 time to fit residues: 240.3375 Evaluate side-chains 311 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 246 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ILE 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 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 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 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU 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 805 GLN Chi-restraints excluded: chain D residue 817 HIS 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 1040 MET Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP 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 323 ASN Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU 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 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 Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 104 optimal weight: 8.9990 chunk 331 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 262 optimal weight: 0.0040 chunk 143 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN D 805 GLN F 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.179512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.157307 restraints weight = 48355.122| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.85 r_work: 0.3572 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35095 Z= 0.091 Angle : 0.465 8.296 48039 Z= 0.252 Chirality : 0.040 0.139 5479 Planarity : 0.003 0.042 5736 Dihedral : 16.782 177.588 6001 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 1.68 % Allowed : 17.16 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3929 helix: -0.23 (0.14), residues: 1504 sheet: -0.21 (0.26), residues: 421 loop : -1.15 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1020 HIS 0.004 0.001 HIS C 554 PHE 0.012 0.001 PHE F 256 TYR 0.010 0.001 TYR C1231 ARG 0.008 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.02747 ( 1032) hydrogen bonds : angle 4.15731 ( 2916) covalent geometry : bond 0.00198 (35095) covalent geometry : angle 0.46484 (48039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15165.55 seconds wall clock time: 264 minutes 59.37 seconds (15899.37 seconds total)