Starting phenix.real_space_refine on Tue Sep 15 03:19:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7beg_12157/09_2026/7beg_12157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7beg_12157/09_2026/7beg_12157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7beg_12157/09_2026/7beg_12157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7beg_12157/09_2026/7beg_12157.map" model { file = "/net/cci-nas-00/data/ceres_data/7beg_12157/09_2026/7beg_12157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7beg_12157/09_2026/7beg_12157.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 188 5.49 5 S 131 5.16 5 C 21529 2.51 5 N 6235 2.21 5 O 7163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35246 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2350 Classifications: {'peptide': 302} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10570 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} 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: "D" Number of atoms: 10548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10548 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1306} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 708 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3996 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1934 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "T" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1920 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "G" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 848 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 6.20, per 1000 atoms: 0.18 Number of scatterers: 35246 At special positions: 0 Unit cell: (192.045, 190.96, 235.445, 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 131 16.00 P 188 15.00 O 7163 8.00 N 6235 7.00 C 21529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 41 sheets defined 43.1% alpha, 8.7% beta 62 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.829A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.608A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.816A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.534A pdb=" N ASP A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.254A pdb=" N GLU A 273 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 274 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.646A pdb=" N ARG A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.011A pdb=" N ARG B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.656A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.580A 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 154 through 161 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.624A pdb=" N ALA B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.555A pdb=" N SER B 266 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA B 267 " --> pdb=" O VAL B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 267' Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.599A pdb=" N ALA B 272 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 273 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 274' Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.302A pdb=" N GLU B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.543A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.665A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 removed outlier: 4.161A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.552A pdb=" N ILE C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.640A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.241A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.748A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.764A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 4.138A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.652A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.593A pdb=" N ASP C 491 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 492' Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.646A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.638A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 628 removed outlier: 3.812A pdb=" N GLY C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS C 628 " --> pdb=" O GLU C 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 624 through 628' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.661A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.950A pdb=" N ALA C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 709 removed outlier: 3.765A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 704 through 709' Processing helix chain 'C' and resid 820 through 825 removed outlier: 4.259A pdb=" N GLN C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 820 through 825' Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 945 through 955 Processing helix chain 'C' and resid 957 through 983 removed outlier: 3.635A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1039 removed outlier: 3.868A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.770A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 4.085A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.728A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.523A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.954A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.527A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.553A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.861A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 118' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 170 removed outlier: 3.695A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.796A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 3.798A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.168A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.802A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.802A pdb=" N GLY D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.743A pdb=" N ALA D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 387 removed outlier: 4.259A pdb=" N LEU D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.772A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.504A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.738A pdb=" N GLY D 433 " --> pdb=" O HIS D 430 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 434' Processing helix chain 'D' and resid 450 through 454 removed outlier: 3.674A pdb=" N CYS D 454 " --> pdb=" O PRO D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 482 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.730A pdb=" N GLY D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.507A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 4.394A pdb=" N VAL D 592 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.684A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.726A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 669 removed outlier: 4.289A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 768 through 803 removed outlier: 3.555A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.588A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.590A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 934 removed outlier: 3.530A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 4.975A pdb=" N MET D 932 " --> pdb=" O THR D 928 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 934 " --> pdb=" O LEU D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1146 Proline residue: D1139 - end of helix Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.784A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.791A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.304A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 3.693A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1309 through 1314' Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.775A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1353 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 1375 removed outlier: 3.666A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 33 removed outlier: 4.201A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.755A pdb=" N ALA E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.357A pdb=" N THR E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.590A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.589A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 136 removed outlier: 3.998A pdb=" N ILE F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.932A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.505A 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 213 through 233 removed outlier: 5.017A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 Processing helix chain 'F' and resid 262 through 295 Processing helix chain 'F' and resid 299 through 309 removed outlier: 4.198A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.681A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS F 329 " --> pdb=" O TRP F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.131A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN F 342 " --> pdb=" O HIS F 338 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 3.608A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 417 removed outlier: 4.020A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 444 removed outlier: 4.018A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.903A pdb=" N LEU F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 530 through 551 removed outlier: 3.501A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 removed outlier: 4.069A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 584 through 599 Processing helix chain 'F' and resid 608 through 612 removed outlier: 4.152A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.633A pdb=" N VAL G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 30 removed outlier: 3.849A pdb=" N ARG G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 46 removed outlier: 3.689A pdb=" N ARG G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU G 42 " --> pdb=" O HIS G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 67 removed outlier: 3.520A pdb=" N ARG G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.551A pdb=" N ILE G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 73 through 78' Processing helix chain 'G' and resid 85 through 90 removed outlier: 3.567A pdb=" N PHE G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 100 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.853A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 28 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 206 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 104 removed outlier: 4.100A pdb=" N VAL A 98 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 146 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 102 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.795A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.429A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.640A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 104 removed outlier: 3.532A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.364A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.566A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.549A pdb=" N ILE C 138 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 148 through 151 removed outlier: 3.747A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 4.334A pdb=" N PHE C 156 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C 175 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 158 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.611A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 529 through 530 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.634A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.501A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 615 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 636 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 722 through 723 Processing sheet with id=AC2, first strand: chain 'C' and resid 731 through 732 removed outlier: 3.849A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 798 through 801 removed outlier: 3.725A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1075 through 1076 Processing sheet with id=AC5, first strand: chain 'C' and resid 833 through 836 removed outlier: 3.596A pdb=" N GLN C 834 " --> pdb=" O LEU C1054 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C1052 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 876 through 877 removed outlier: 3.941A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 889 removed outlier: 3.662A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1336 through 1337 Processing sheet with id=AC9, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.004A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.750A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.518A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 350 through 352 Processing sheet with id=AD4, first strand: chain 'D' and resid 355 through 357 removed outlier: 6.446A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.347A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.687A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 826 through 827 removed outlier: 3.786A pdb=" N GLU D 827 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 956 through 957 removed outlier: 4.347A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 960 through 961 removed outlier: 4.138A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.677A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.636A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE4, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.591A pdb=" N VAL D1176 " --> pdb=" O SER D1164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.567A pdb=" N THR D1265 " --> pdb=" O SER D1303 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 9.15 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9851 1.34 - 1.46: 9319 1.46 - 1.59: 16424 1.59 - 1.71: 351 1.71 - 1.84: 232 Bond restraints: 36177 Sorted by residual: bond pdb=" C4' DT N 7 " pdb=" O4' DT N 7 " ideal model delta sigma weight residual 1.446 1.654 -0.208 1.00e-02 1.00e+04 4.32e+02 bond pdb=" O3' DA N -15 " pdb=" P DT N -14 " ideal model delta sigma weight residual 1.607 1.410 0.197 1.20e-02 6.94e+03 2.69e+02 bond pdb=" O3' DC N 1 " pdb=" P DC N 2 " ideal model delta sigma weight residual 1.607 1.417 0.190 1.20e-02 6.94e+03 2.52e+02 bond pdb=" C4' DA N 6 " pdb=" O4' DA N 6 " ideal model delta sigma weight residual 1.446 1.590 -0.144 1.00e-02 1.00e+04 2.06e+02 bond pdb=" O3' DT N -40 " pdb=" P DA N -39 " ideal model delta sigma weight residual 1.607 1.440 0.167 1.20e-02 6.94e+03 1.94e+02 ... (remaining 36172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.63: 49408 5.63 - 11.27: 233 11.27 - 16.90: 27 16.90 - 22.54: 11 22.54 - 28.17: 1 Bond angle restraints: 49680 Sorted by residual: angle pdb=" N ASP A 199 " pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 108.24 128.37 -20.13 1.32e+00 5.74e-01 2.32e+02 angle pdb=" C3' DA T -4 " pdb=" O3' DA T -4 " pdb=" P DT T -3 " ideal model delta sigma weight residual 119.70 137.08 -17.38 1.20e+00 6.94e-01 2.10e+02 angle pdb=" C3' DA N -15 " pdb=" O3' DA N -15 " pdb=" P DT N -14 " ideal model delta sigma weight residual 119.70 136.43 -16.73 1.20e+00 6.94e-01 1.94e+02 angle pdb=" C3' DC N 1 " pdb=" O3' DC N 1 " pdb=" P DC N 2 " ideal model delta sigma weight residual 119.70 135.41 -15.71 1.20e+00 6.94e-01 1.71e+02 angle pdb=" O3' DT N -63 " pdb=" P DA N -62 " pdb=" O5' DA N -62 " ideal model delta sigma weight residual 104.00 125.76 -21.76 1.90e+00 2.77e-01 1.31e+02 ... (remaining 49675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 20842 33.68 - 67.35: 926 67.35 - 101.03: 30 101.03 - 134.71: 2 134.71 - 168.38: 3 Dihedral angle restraints: 21803 sinusoidal: 10279 harmonic: 11524 Sorted by residual: dihedral pdb=" CA ARG D1242 " pdb=" C ARG D1242 " pdb=" N LEU D1243 " pdb=" CA LEU D1243 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 0.00 -28.58 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE D 381 " pdb=" C ILE D 381 " pdb=" N TYR D 382 " pdb=" CA TYR D 382 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 21800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 5599 0.214 - 0.429: 55 0.429 - 0.643: 9 0.643 - 0.858: 2 0.858 - 1.072: 1 Chirality restraints: 5666 Sorted by residual: chirality pdb=" C4' DT N -63 " pdb=" C5' DT N -63 " pdb=" O4' DT N -63 " pdb=" C3' DT N -63 " both_signs ideal model delta sigma weight residual False -2.53 -1.46 -1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" C4' DC N 1 " pdb=" C5' DC N 1 " pdb=" O4' DC N 1 " pdb=" C3' DC N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.76 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C4' DA N -15 " pdb=" C5' DA N -15 " pdb=" O4' DA N -15 " pdb=" C3' DA N -15 " both_signs ideal model delta sigma weight residual False -2.53 -1.82 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 5663 not shown) Planarity restraints: 5826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T -2 " 0.016 2.00e-02 2.50e+03 6.60e-02 1.31e+02 pdb=" N9 DG T -2 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG T -2 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DG T -2 " 0.108 2.00e-02 2.50e+03 pdb=" C5 DG T -2 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG T -2 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DG T -2 " -0.002 2.00e-02 2.50e+03 pdb=" N1 DG T -2 " -0.078 2.00e-02 2.50e+03 pdb=" C2 DG T -2 " 0.117 2.00e-02 2.50e+03 pdb=" N2 DG T -2 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG T -2 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DG T -2 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -54 " -0.114 2.00e-02 2.50e+03 4.94e-02 7.31e+01 pdb=" N9 DG N -54 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG N -54 " 0.055 2.00e-02 2.50e+03 pdb=" N7 DG N -54 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG N -54 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG N -54 " -0.081 2.00e-02 2.50e+03 pdb=" O6 DG N -54 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG N -54 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG N -54 " 0.022 2.00e-02 2.50e+03 pdb=" N2 DG N -54 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG N -54 " 0.029 2.00e-02 2.50e+03 pdb=" C4 DG N -54 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 4 " -0.125 2.00e-02 2.50e+03 5.35e-02 7.17e+01 pdb=" N1 DT N 4 " 0.066 2.00e-02 2.50e+03 pdb=" C2 DT N 4 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DT N 4 " 0.036 2.00e-02 2.50e+03 pdb=" N3 DT N 4 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT N 4 " -0.020 2.00e-02 2.50e+03 pdb=" O4 DT N 4 " -0.054 2.00e-02 2.50e+03 pdb=" C5 DT N 4 " 0.015 2.00e-02 2.50e+03 pdb=" C7 DT N 4 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT N 4 " 0.053 2.00e-02 2.50e+03 ... (remaining 5823 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3931 2.76 - 3.29: 31199 3.29 - 3.83: 56061 3.83 - 4.36: 62081 4.36 - 4.90: 103795 Nonbonded interactions: 257067 Sorted by model distance: nonbonded pdb=" N1 DG N -17 " pdb=" O2 DC T 17 " model vdw 2.222 3.120 nonbonded pdb=" OP2 DT N -55 " pdb=" O2 DT N -55 " model vdw 2.235 3.040 nonbonded pdb=" N6 DA N 6 " pdb=" N3 DT T -6 " model vdw 2.251 3.200 nonbonded pdb=" NZ LYS C 163 " pdb=" OP1 DA N 5 " model vdw 2.278 3.120 nonbonded pdb=" O4 DT N 7 " pdb=" N1 DA T -7 " model vdw 2.280 2.496 ... (remaining 257062 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 249 through 322)) selection = (chain 'B' and (resid 6 through 297 or (resid 298 and (name N or name CA or name \ C or name O or name CB )) or resid 299 through 322)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.770 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 0.208 36177 Z= 0.515 Angle : 1.087 28.173 49680 Z= 0.685 Chirality : 0.066 1.072 5666 Planarity : 0.006 0.070 5826 Dihedral : 15.611 168.383 14371 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.09 % Favored : 92.59 % Rotamer: Outliers : 0.53 % Allowed : 4.99 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.10), residues: 3979 helix: -2.65 (0.09), residues: 1516 sheet: -1.58 (0.30), residues: 285 loop : -2.81 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1355 TYR 0.026 0.001 TYR D 382 PHE 0.030 0.001 PHE C 804 TRP 0.029 0.001 TRP D 33 HIS 0.019 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.52 (36177) covalent geometry : angle 1.08744 / 0.68 (49680) hydrogen bonds : bond 0.17090 / 11.75 ( 1279) hydrogen bonds : angle 7.49245 / 5.09 ( 3572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 574 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.6251 (p90) cc_final: 0.5745 (p90) REVERT: B 32 GLU cc_start: 0.6600 (mm-30) cc_final: 0.5116 (mp0) REVERT: B 142 MET cc_start: 0.8975 (pmm) cc_final: 0.8730 (pmm) REVERT: B 316 MET cc_start: 0.8824 (tmm) cc_final: 0.8484 (pmm) REVERT: C 503 LYS cc_start: 0.8977 (pttt) cc_final: 0.8623 (tmtt) REVERT: C 805 MET cc_start: 0.7369 (pp-130) cc_final: 0.7130 (ppp) REVERT: C 1238 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7782 (mm) REVERT: D 361 LEU cc_start: 0.5415 (mt) cc_final: 0.5133 (mt) REVERT: D 429 LEU cc_start: 0.8727 (pp) cc_final: 0.8410 (pp) REVERT: D 626 TYR cc_start: 0.7252 (m-10) cc_final: 0.6685 (m-10) REVERT: D 686 TRP cc_start: 0.9469 (m100) cc_final: 0.8393 (m100) REVERT: D 698 MET cc_start: 0.9371 (tpp) cc_final: 0.9086 (tmm) REVERT: D 724 MET cc_start: 0.7529 (mmt) cc_final: 0.7011 (tpp) REVERT: D 725 MET cc_start: 0.8116 (tmm) cc_final: 0.7903 (tmm) REVERT: D 738 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8657 (mmm160) REVERT: D 743 MET cc_start: 0.5886 (mmt) cc_final: 0.5218 (tpp) REVERT: D 792 ASN cc_start: 0.8948 (m-40) cc_final: 0.8511 (t0) REVERT: D 796 LEU cc_start: 0.9213 (tp) cc_final: 0.8945 (tt) REVERT: D 929 GLN cc_start: 0.1997 (OUTLIER) cc_final: 0.0603 (mm110) REVERT: D 981 GLU cc_start: 0.9717 (mt-10) cc_final: 0.9502 (tm-30) REVERT: D 1040 MET cc_start: 0.4428 (mtp) cc_final: 0.4033 (ttt) REVERT: E 45 LYS cc_start: 0.3584 (pttt) cc_final: 0.3278 (pttt) REVERT: E 48 VAL cc_start: 0.6998 (t) cc_final: 0.6783 (m) REVERT: E 49 ILE cc_start: 0.6783 (mt) cc_final: 0.6563 (pt) REVERT: E 54 ILE cc_start: 0.8182 (mt) cc_final: 0.7848 (pt) REVERT: F 100 MET cc_start: 0.8832 (mtp) cc_final: 0.8367 (mtt) REVERT: F 143 TYR cc_start: 0.9476 (m-80) cc_final: 0.8947 (t80) REVERT: F 297 MET cc_start: 0.4344 (ttm) cc_final: 0.4032 (ttt) REVERT: F 533 ASP cc_start: 0.9127 (m-30) cc_final: 0.8533 (t0) REVERT: G 39 LEU cc_start: 0.8960 (mt) cc_final: 0.8686 (pp) REVERT: G 62 LEU cc_start: 0.5360 (tp) cc_final: 0.4460 (pp) REVERT: G 68 ARG cc_start: 0.5697 (mtt90) cc_final: 0.5302 (mmt180) outliers start: 18 outliers final: 3 residues processed: 590 average time/residue: 0.2425 time to fit residues: 222.7156 Evaluate side-chains 308 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 303 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 overall best weight: 4.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN B 66 HIS B 84 ASN B 103 ASN B 283 GLN C 36 GLN C 120 GLN C 165 HIS C 330 HIS C 343 HIS C 450 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 832 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1116 HIS C1244 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN D 229 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN D1227 HIS ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1268 ASN D1350 ASN E 31 GLN F 242 HIS F 301 ASN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.088753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.068293 restraints weight = 292080.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.067584 restraints weight = 219913.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.067586 restraints weight = 176947.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.067731 restraints weight = 170787.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.067708 restraints weight = 150023.641| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 36177 Z= 0.289 Angle : 0.859 15.223 49680 Z= 0.453 Chirality : 0.050 0.281 5666 Planarity : 0.006 0.098 5826 Dihedral : 19.542 177.765 6504 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.21 % Favored : 92.64 % Rotamer: Outliers : 0.26 % Allowed : 2.85 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.12), residues: 3979 helix: -0.84 (0.12), residues: 1559 sheet: -1.31 (0.27), residues: 328 loop : -2.30 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG C 996 TYR 0.025 0.002 TYR D 360 PHE 0.025 0.002 PHE C 804 TRP 0.028 0.002 TRP D 33 HIS 0.017 0.002 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.29 (36177) covalent geometry : angle 0.85927 / 0.45 (49680) hydrogen bonds : bond 0.05967 / 4.07 ( 1279) hydrogen bonds : angle 5.08478 / 3.52 ( 3572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 319 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 503 LYS cc_start: 0.9238 (pttt) cc_final: 0.8968 (tmtt) REVERT: C 741 MET cc_start: 0.8413 (tpp) cc_final: 0.7972 (tpp) REVERT: C 1269 ARG cc_start: 0.7209 (ptm160) cc_final: 0.6931 (ptm160) REVERT: D 135 ILE cc_start: 0.9283 (mt) cc_final: 0.8793 (mt) REVERT: D 686 TRP cc_start: 0.9274 (m100) cc_final: 0.8452 (m100) REVERT: D 792 ASN cc_start: 0.9034 (m-40) cc_final: 0.8716 (t0) REVERT: D 796 LEU cc_start: 0.9366 (tp) cc_final: 0.9121 (tp) REVERT: D 1040 MET cc_start: 0.1018 (mtp) cc_final: -0.0572 (ttt) REVERT: E 60 ASN cc_start: 0.8855 (m-40) cc_final: 0.8629 (m-40) REVERT: F 100 MET cc_start: 0.8453 (mtp) cc_final: 0.8248 (mtt) REVERT: F 297 MET cc_start: 0.1795 (ttm) cc_final: 0.1361 (ttt) REVERT: F 533 ASP cc_start: 0.9055 (m-30) cc_final: 0.8748 (t0) REVERT: F 567 MET cc_start: 0.8472 (ptp) cc_final: 0.7790 (ptp) REVERT: G 68 ARG cc_start: 0.6598 (mtt90) cc_final: 0.6310 (mmt180) outliers start: 9 outliers final: 2 residues processed: 327 average time/residue: 0.2315 time to fit residues: 118.6143 Evaluate side-chains 226 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 18 optimal weight: 5.9990 chunk 347 optimal weight: 0.9990 chunk 159 optimal weight: 0.0980 chunk 308 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN B 283 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 419 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 594 GLN D 651 HIS D 805 GLN D 865 HIS D 921 GLN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 309 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.090021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.070310 restraints weight = 296325.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.068897 restraints weight = 233274.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.069015 restraints weight = 216538.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.069144 restraints weight = 174739.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.069017 restraints weight = 152479.019| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36177 Z= 0.128 Angle : 0.624 10.586 49680 Z= 0.336 Chirality : 0.043 0.276 5666 Planarity : 0.005 0.121 5826 Dihedral : 19.450 179.495 6504 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.18 % Favored : 93.69 % Rotamer: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 3979 helix: -0.17 (0.13), residues: 1558 sheet: -0.88 (0.29), residues: 296 loop : -2.07 (0.12), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 24 TYR 0.018 0.001 TYR D 144 PHE 0.033 0.001 PHE C 972 TRP 0.022 0.001 TRP G 37 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (36177) covalent geometry : angle 0.62399 / 0.34 (49680) hydrogen bonds : bond 0.04410 / 2.95 ( 1279) hydrogen bonds : angle 4.46184 / 3.10 ( 3572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 271 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7839 (tpp) cc_final: 0.7598 (tpt) REVERT: C 403 MET cc_start: 0.9001 (tmm) cc_final: 0.8752 (tmm) REVERT: C 503 LYS cc_start: 0.9227 (pttt) cc_final: 0.8910 (tmtt) REVERT: C 685 MET cc_start: 0.8232 (tpp) cc_final: 0.7941 (tpp) REVERT: C 944 ARG cc_start: 0.6273 (mmm160) cc_final: 0.6026 (mmm160) REVERT: C 1227 VAL cc_start: 0.7925 (t) cc_final: 0.7702 (m) REVERT: D 342 LEU cc_start: 0.8185 (tp) cc_final: 0.7969 (tp) REVERT: D 360 TYR cc_start: 0.6268 (t80) cc_final: 0.6004 (t80) REVERT: D 686 TRP cc_start: 0.9269 (m100) cc_final: 0.8343 (m100) REVERT: D 792 ASN cc_start: 0.9149 (m-40) cc_final: 0.8761 (t0) REVERT: D 796 LEU cc_start: 0.9350 (tp) cc_final: 0.9080 (tt) REVERT: D 1040 MET cc_start: 0.1430 (mtp) cc_final: -0.0074 (ttt) REVERT: F 297 MET cc_start: 0.1769 (ttm) cc_final: 0.1286 (ttt) REVERT: F 533 ASP cc_start: 0.8994 (m-30) cc_final: 0.8651 (t0) REVERT: F 567 MET cc_start: 0.8497 (ptp) cc_final: 0.7826 (ptp) REVERT: G 60 LEU cc_start: -0.1961 (mt) cc_final: -0.2172 (mt) REVERT: G 68 ARG cc_start: 0.6661 (mtt90) cc_final: 0.6396 (mmt180) outliers start: 5 outliers final: 1 residues processed: 275 average time/residue: 0.2215 time to fit residues: 97.9704 Evaluate side-chains 216 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 343 optimal weight: 0.8980 chunk 341 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 573 ASN C 686 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS D 276 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN E 72 GLN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.087255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.067219 restraints weight = 299449.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.066212 restraints weight = 230998.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.066279 restraints weight = 184358.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.066445 restraints weight = 161869.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.066397 restraints weight = 151111.522| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 36177 Z= 0.197 Angle : 0.690 13.898 49680 Z= 0.364 Chirality : 0.045 0.616 5666 Planarity : 0.005 0.117 5826 Dihedral : 19.458 175.902 6504 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.16 % Favored : 92.69 % Rotamer: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 3979 helix: 0.26 (0.13), residues: 1581 sheet: -0.67 (0.28), residues: 306 loop : -1.92 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C1269 TYR 0.032 0.002 TYR A 68 PHE 0.023 0.002 PHE D 437 TRP 0.024 0.002 TRP D 33 HIS 0.011 0.002 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (36177) covalent geometry : angle 0.68988 / 0.36 (49680) hydrogen bonds : bond 0.04578 / 3.14 ( 1279) hydrogen bonds : angle 4.36960 / 3.06 ( 3572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 503 LYS cc_start: 0.9243 (pttt) cc_final: 0.8961 (tmtt) REVERT: C 741 MET cc_start: 0.8476 (tpp) cc_final: 0.7898 (tpp) REVERT: C 1170 MET cc_start: 0.8497 (mmt) cc_final: 0.8143 (mmt) REVERT: D 334 LYS cc_start: 0.6000 (tttt) cc_final: 0.5732 (ptmm) REVERT: D 342 LEU cc_start: 0.8209 (tp) cc_final: 0.7986 (tt) REVERT: D 360 TYR cc_start: 0.6692 (t80) cc_final: 0.6437 (t80) REVERT: D 484 MET cc_start: 0.8546 (mmt) cc_final: 0.8138 (mmm) REVERT: D 581 MET cc_start: 0.8942 (ppp) cc_final: 0.8701 (ppp) REVERT: D 686 TRP cc_start: 0.9250 (m100) cc_final: 0.8373 (m100) REVERT: D 792 ASN cc_start: 0.9060 (m-40) cc_final: 0.8747 (t0) REVERT: D 796 LEU cc_start: 0.9302 (tp) cc_final: 0.9088 (tp) REVERT: D 1040 MET cc_start: 0.0998 (mtp) cc_final: -0.0642 (ttt) REVERT: E 60 ASN cc_start: 0.8994 (m-40) cc_final: 0.8774 (m-40) REVERT: F 100 MET cc_start: 0.8453 (mtt) cc_final: 0.8194 (mtt) REVERT: F 297 MET cc_start: 0.1716 (ttm) cc_final: 0.1288 (ttt) REVERT: F 516 ASP cc_start: 0.6527 (t70) cc_final: 0.6271 (m-30) REVERT: F 533 ASP cc_start: 0.8948 (m-30) cc_final: 0.8700 (t0) REVERT: G 60 LEU cc_start: -0.1450 (mt) cc_final: -0.1703 (mt) REVERT: G 61 LEU cc_start: 0.5376 (pp) cc_final: 0.4786 (pp) REVERT: G 62 LEU cc_start: -0.0738 (pp) cc_final: -0.1014 (pt) REVERT: G 68 ARG cc_start: 0.6686 (mtt90) cc_final: 0.6366 (mmt180) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.2264 time to fit residues: 89.7018 Evaluate side-chains 187 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 258 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 410 optimal weight: 30.0000 chunk 160 optimal weight: 0.3980 chunk 233 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 325 optimal weight: 0.8980 chunk 42 optimal weight: 0.0030 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.087839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.067704 restraints weight = 298344.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.066484 restraints weight = 229679.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.066485 restraints weight = 209908.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066468 restraints weight = 199356.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066509 restraints weight = 167169.006| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36177 Z= 0.128 Angle : 0.605 13.404 49680 Z= 0.322 Chirality : 0.043 0.291 5666 Planarity : 0.004 0.101 5826 Dihedral : 19.398 176.745 6504 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3979 helix: 0.47 (0.13), residues: 1582 sheet: -0.82 (0.28), residues: 317 loop : -1.80 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.014 0.001 TYR D 512 PHE 0.019 0.001 PHE C 804 TRP 0.018 0.001 TRP D 33 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (36177) covalent geometry : angle 0.60528 / 0.32 (49680) hydrogen bonds : bond 0.03874 / 2.61 ( 1279) hydrogen bonds : angle 4.17807 / 2.92 ( 3572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.6425 (p90) cc_final: 0.6015 (p90) REVERT: C 503 LYS cc_start: 0.9241 (pttt) cc_final: 0.8957 (tmtt) REVERT: C 741 MET cc_start: 0.8527 (tpp) cc_final: 0.7868 (tpp) REVERT: C 951 MET cc_start: 0.8660 (tpt) cc_final: 0.8245 (tpp) REVERT: C 1170 MET cc_start: 0.8445 (mmt) cc_final: 0.8090 (mmt) REVERT: C 1304 MET cc_start: 0.8215 (tmm) cc_final: 0.7980 (tmm) REVERT: C 1308 ILE cc_start: 0.8675 (mm) cc_final: 0.8323 (mm) REVERT: D 334 LYS cc_start: 0.5972 (tttt) cc_final: 0.5675 (ptmm) REVERT: D 360 TYR cc_start: 0.6315 (t80) cc_final: 0.6083 (t80) REVERT: D 686 TRP cc_start: 0.9258 (m100) cc_final: 0.8339 (m100) REVERT: D 743 MET cc_start: 0.7264 (tpp) cc_final: 0.6859 (tpt) REVERT: D 792 ASN cc_start: 0.9027 (m-40) cc_final: 0.8732 (t0) REVERT: D 796 LEU cc_start: 0.9280 (tp) cc_final: 0.9044 (tt) REVERT: D 1040 MET cc_start: 0.1325 (mtp) cc_final: -0.0184 (ttt) REVERT: E 60 ASN cc_start: 0.9005 (m-40) cc_final: 0.8789 (m-40) REVERT: F 100 MET cc_start: 0.8414 (mtt) cc_final: 0.8116 (mtt) REVERT: F 297 MET cc_start: 0.1886 (ttm) cc_final: 0.1445 (ttt) REVERT: F 516 ASP cc_start: 0.6582 (t70) cc_final: 0.6327 (m-30) REVERT: F 522 PHE cc_start: 0.7375 (m-10) cc_final: 0.7073 (m-80) REVERT: F 533 ASP cc_start: 0.8857 (m-30) cc_final: 0.8635 (t0) REVERT: G 68 ARG cc_start: 0.6776 (mtt90) cc_final: 0.6477 (mmt180) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.2144 time to fit residues: 83.2666 Evaluate side-chains 189 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 358 optimal weight: 40.0000 chunk 108 optimal weight: 0.0270 chunk 242 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 279 optimal weight: 0.7980 chunk 164 optimal weight: 0.0020 chunk 291 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 overall best weight: 0.9650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN C 120 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 594 GLN D 736 GLN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.088009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.067861 restraints weight = 297663.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066443 restraints weight = 227570.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.066687 restraints weight = 194792.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.066418 restraints weight = 192594.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.066459 restraints weight = 165053.841| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 36177 Z= 0.114 Angle : 0.589 13.148 49680 Z= 0.313 Chirality : 0.042 0.250 5666 Planarity : 0.004 0.096 5826 Dihedral : 19.339 178.224 6504 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3979 helix: 0.62 (0.14), residues: 1582 sheet: -0.74 (0.28), residues: 306 loop : -1.72 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C1269 TYR 0.016 0.001 TYR D 512 PHE 0.020 0.001 PHE C 804 TRP 0.016 0.001 TRP D 33 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (36177) covalent geometry : angle 0.58888 / 0.31 (49680) hydrogen bonds : bond 0.03595 / 2.43 ( 1279) hydrogen bonds : angle 4.10689 / 2.88 ( 3572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.6415 (p90) cc_final: 0.5967 (p90) REVERT: C 503 LYS cc_start: 0.9223 (pttt) cc_final: 0.8953 (tmtt) REVERT: C 741 MET cc_start: 0.8541 (tpp) cc_final: 0.7849 (tpp) REVERT: C 1170 MET cc_start: 0.8404 (mmt) cc_final: 0.8086 (mmt) REVERT: C 1232 MET cc_start: 0.7416 (ptp) cc_final: 0.7191 (ptp) REVERT: C 1304 MET cc_start: 0.8239 (tmm) cc_final: 0.7972 (tmm) REVERT: C 1308 ILE cc_start: 0.8688 (mm) cc_final: 0.8326 (mm) REVERT: D 334 LYS cc_start: 0.5976 (tttt) cc_final: 0.5684 (ptmm) REVERT: D 686 TRP cc_start: 0.9231 (m100) cc_final: 0.8355 (m100) REVERT: D 792 ASN cc_start: 0.9058 (m-40) cc_final: 0.8751 (t0) REVERT: D 796 LEU cc_start: 0.9314 (tp) cc_final: 0.9089 (tt) REVERT: D 1040 MET cc_start: 0.1441 (mtp) cc_final: -0.0017 (ttt) REVERT: F 102 MET cc_start: 0.9001 (mtm) cc_final: 0.8677 (mtm) REVERT: F 297 MET cc_start: 0.1967 (ttm) cc_final: 0.1520 (ttt) REVERT: G 60 LEU cc_start: -0.1405 (mt) cc_final: -0.1694 (mt) REVERT: G 68 ARG cc_start: 0.6810 (mtt90) cc_final: 0.6511 (mmt180) outliers start: 4 outliers final: 3 residues processed: 231 average time/residue: 0.2245 time to fit residues: 83.9302 Evaluate side-chains 189 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 32 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 393 optimal weight: 40.0000 chunk 162 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 415 optimal weight: 30.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.087234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.066775 restraints weight = 298065.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.065706 restraints weight = 227070.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.065590 restraints weight = 188083.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.065624 restraints weight = 176410.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.065613 restraints weight = 158457.170| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36177 Z= 0.136 Angle : 0.611 13.081 49680 Z= 0.322 Chirality : 0.042 0.247 5666 Planarity : 0.004 0.051 5826 Dihedral : 19.347 179.133 6504 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3979 helix: 0.70 (0.14), residues: 1580 sheet: -0.83 (0.27), residues: 321 loop : -1.64 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C1269 TYR 0.021 0.001 TYR D 360 PHE 0.023 0.001 PHE D1274 TRP 0.017 0.001 TRP D 33 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (36177) covalent geometry : angle 0.61080 / 0.32 (49680) hydrogen bonds : bond 0.03672 / 2.49 ( 1279) hydrogen bonds : angle 4.09197 / 2.87 ( 3572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 503 LYS cc_start: 0.9228 (pttt) cc_final: 0.8962 (tmtt) REVERT: C 741 MET cc_start: 0.8472 (tpp) cc_final: 0.7818 (tpp) REVERT: C 1170 MET cc_start: 0.8346 (mmt) cc_final: 0.8063 (mmt) REVERT: C 1304 MET cc_start: 0.8217 (tmm) cc_final: 0.7970 (tmm) REVERT: C 1308 ILE cc_start: 0.8677 (mm) cc_final: 0.8323 (mm) REVERT: D 484 MET cc_start: 0.8675 (mmt) cc_final: 0.8312 (mmm) REVERT: D 686 TRP cc_start: 0.9277 (m100) cc_final: 0.8400 (m100) REVERT: D 792 ASN cc_start: 0.9043 (m-40) cc_final: 0.8758 (t0) REVERT: D 796 LEU cc_start: 0.9306 (tp) cc_final: 0.9088 (tt) REVERT: D 1040 MET cc_start: 0.1613 (mtp) cc_final: 0.0230 (ttt) REVERT: E 60 ASN cc_start: 0.8973 (m-40) cc_final: 0.8752 (m-40) REVERT: F 102 MET cc_start: 0.8944 (mtm) cc_final: 0.8648 (mtm) REVERT: F 273 MET cc_start: 0.9542 (ppp) cc_final: 0.9334 (ppp) REVERT: F 297 MET cc_start: 0.1987 (ttm) cc_final: 0.1537 (ttt) REVERT: F 522 PHE cc_start: 0.7320 (m-10) cc_final: 0.7048 (m-80) REVERT: G 60 LEU cc_start: -0.1095 (mt) cc_final: -0.1457 (mt) REVERT: G 68 ARG cc_start: 0.6748 (mtt90) cc_final: 0.6449 (mmt180) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.2235 time to fit residues: 83.2034 Evaluate side-chains 186 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 157 optimal weight: 7.9990 chunk 368 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 369 optimal weight: 0.0040 chunk 67 optimal weight: 0.7980 chunk 246 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 371 optimal weight: 10.0000 chunk 372 optimal weight: 0.0470 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 450 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 736 GLN E 72 GLN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.087997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.068076 restraints weight = 295733.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.066939 restraints weight = 227644.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.066869 restraints weight = 194441.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.066872 restraints weight = 177740.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.066949 restraints weight = 157468.739| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36177 Z= 0.106 Angle : 0.589 13.742 49680 Z= 0.309 Chirality : 0.042 0.258 5666 Planarity : 0.004 0.078 5826 Dihedral : 19.294 179.044 6504 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 0.03 % Allowed : 0.97 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 3979 helix: 0.76 (0.14), residues: 1582 sheet: -0.63 (0.28), residues: 304 loop : -1.55 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1269 TYR 0.015 0.001 TYR D 512 PHE 0.038 0.001 PHE D 763 TRP 0.013 0.001 TRP D 580 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (36177) covalent geometry : angle 0.58900 / 0.31 (49680) hydrogen bonds : bond 0.03278 / 2.21 ( 1279) hydrogen bonds : angle 3.99949 / 2.81 ( 3572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 503 LYS cc_start: 0.9206 (pttt) cc_final: 0.8922 (tmtt) REVERT: C 741 MET cc_start: 0.8579 (tpp) cc_final: 0.7870 (tpp) REVERT: C 1170 MET cc_start: 0.8411 (mmt) cc_final: 0.8142 (mmt) REVERT: C 1243 MET cc_start: 0.7476 (tmm) cc_final: 0.7166 (tmm) REVERT: C 1254 VAL cc_start: 0.8546 (t) cc_final: 0.8321 (t) REVERT: C 1304 MET cc_start: 0.8304 (tmm) cc_final: 0.8032 (tmm) REVERT: C 1308 ILE cc_start: 0.8803 (mm) cc_final: 0.8436 (mm) REVERT: D 360 TYR cc_start: 0.6630 (t80) cc_final: 0.6370 (t80) REVERT: D 484 MET cc_start: 0.8631 (mmt) cc_final: 0.8297 (mmm) REVERT: D 686 TRP cc_start: 0.9226 (m100) cc_final: 0.8385 (m100) REVERT: D 725 MET cc_start: 0.7644 (tmm) cc_final: 0.7443 (tmm) REVERT: D 792 ASN cc_start: 0.9110 (m-40) cc_final: 0.8804 (t0) REVERT: D 796 LEU cc_start: 0.9384 (tp) cc_final: 0.9181 (tt) REVERT: D 1040 MET cc_start: 0.1594 (mtp) cc_final: 0.0281 (ttt) REVERT: E 4 VAL cc_start: 0.6336 (p) cc_final: 0.5948 (p) REVERT: F 102 MET cc_start: 0.8936 (mtm) cc_final: 0.8664 (mtm) REVERT: F 297 MET cc_start: 0.1971 (ttm) cc_final: 0.1530 (ttt) REVERT: F 522 PHE cc_start: 0.7407 (m-10) cc_final: 0.7043 (m-80) REVERT: G 60 LEU cc_start: -0.1285 (mt) cc_final: -0.1488 (mt) REVERT: G 68 ARG cc_start: 0.6720 (mtt90) cc_final: 0.6433 (mmt180) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.2189 time to fit residues: 84.4765 Evaluate side-chains 193 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 362 optimal weight: 30.0000 chunk 320 optimal weight: 0.0980 chunk 297 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 200 optimal weight: 0.0040 chunk 123 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.086305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.066342 restraints weight = 294547.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.065047 restraints weight = 224374.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.065088 restraints weight = 191230.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.065249 restraints weight = 166846.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.065216 restraints weight = 152725.674| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 36177 Z= 0.154 Angle : 0.630 13.884 49680 Z= 0.330 Chirality : 0.042 0.245 5666 Planarity : 0.004 0.066 5826 Dihedral : 19.342 177.374 6504 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.34 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3979 helix: 0.81 (0.14), residues: 1580 sheet: -0.88 (0.26), residues: 345 loop : -1.54 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 481 TYR 0.015 0.001 TYR D 512 PHE 0.023 0.001 PHE D 437 TRP 0.026 0.001 TRP D 33 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (36177) covalent geometry : angle 0.63045 / 0.33 (49680) hydrogen bonds : bond 0.03767 / 2.56 ( 1279) hydrogen bonds : angle 4.08120 / 2.86 ( 3572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.6556 (p90) cc_final: 0.5838 (p90) REVERT: B 316 MET cc_start: 0.6215 (pmm) cc_final: 0.5975 (pmm) REVERT: C 503 LYS cc_start: 0.9250 (pttt) cc_final: 0.8960 (tmtt) REVERT: C 741 MET cc_start: 0.8545 (tpp) cc_final: 0.7925 (tpp) REVERT: C 1243 MET cc_start: 0.7614 (tmm) cc_final: 0.7345 (tmm) REVERT: C 1254 VAL cc_start: 0.8660 (t) cc_final: 0.8424 (t) REVERT: C 1304 MET cc_start: 0.8406 (tmm) cc_final: 0.7930 (tmm) REVERT: C 1308 ILE cc_start: 0.8717 (mm) cc_final: 0.8028 (mm) REVERT: D 360 TYR cc_start: 0.6730 (t80) cc_final: 0.6411 (t80) REVERT: D 686 TRP cc_start: 0.9166 (m100) cc_final: 0.8413 (m100) REVERT: D 725 MET cc_start: 0.7594 (tmm) cc_final: 0.7368 (tmm) REVERT: D 743 MET cc_start: 0.6983 (tpp) cc_final: 0.6300 (tpt) REVERT: D 760 THR cc_start: 0.8236 (m) cc_final: 0.8035 (m) REVERT: D 792 ASN cc_start: 0.9106 (m-40) cc_final: 0.8790 (t0) REVERT: D 1040 MET cc_start: 0.1562 (mtp) cc_final: 0.0262 (ttt) REVERT: E 60 ASN cc_start: 0.8992 (m-40) cc_final: 0.8759 (m-40) REVERT: F 102 MET cc_start: 0.8977 (mtm) cc_final: 0.8674 (mtm) REVERT: F 273 MET cc_start: 0.9505 (ppp) cc_final: 0.9297 (ppp) REVERT: F 297 MET cc_start: 0.2008 (ttm) cc_final: 0.1563 (ttt) REVERT: F 507 MET cc_start: 0.7958 (tpt) cc_final: 0.7699 (tpt) REVERT: F 522 PHE cc_start: 0.7622 (m-10) cc_final: 0.7331 (m-80) REVERT: G 68 ARG cc_start: 0.6560 (mtt90) cc_final: 0.6271 (mmt180) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2222 time to fit residues: 80.5516 Evaluate side-chains 181 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 252 optimal weight: 3.9990 chunk 404 optimal weight: 40.0000 chunk 320 optimal weight: 0.9980 chunk 372 optimal weight: 0.9990 chunk 375 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 179 optimal weight: 0.0370 chunk 354 optimal weight: 8.9990 chunk 213 optimal weight: 0.0770 chunk 327 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN E 72 GLN F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.087406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.066879 restraints weight = 293177.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066083 restraints weight = 221265.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.065777 restraints weight = 201514.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.065956 restraints weight = 193352.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065909 restraints weight = 163391.824| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 36177 Z= 0.107 Angle : 0.599 14.197 49680 Z= 0.313 Chirality : 0.042 0.260 5666 Planarity : 0.004 0.064 5826 Dihedral : 19.309 177.345 6504 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.33 % Favored : 93.57 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3979 helix: 0.85 (0.14), residues: 1575 sheet: -0.81 (0.27), residues: 325 loop : -1.45 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 362 TYR 0.012 0.001 TYR A 152 PHE 0.022 0.001 PHE C 804 TRP 0.016 0.001 TRP D 580 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (36177) covalent geometry : angle 0.59939 / 0.31 (49680) hydrogen bonds : bond 0.03211 / 2.18 ( 1279) hydrogen bonds : angle 4.01423 / 2.82 ( 3572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.6414 (pmm) cc_final: 0.6140 (pmm) REVERT: C 503 LYS cc_start: 0.9169 (pttt) cc_final: 0.8931 (tmtt) REVERT: C 741 MET cc_start: 0.8572 (tpp) cc_final: 0.7909 (tpp) REVERT: C 951 MET cc_start: 0.8573 (tpt) cc_final: 0.8214 (tpp) REVERT: C 1243 MET cc_start: 0.7765 (tmm) cc_final: 0.7464 (tmm) REVERT: C 1254 VAL cc_start: 0.8491 (t) cc_final: 0.8285 (t) REVERT: C 1269 ARG cc_start: 0.7445 (ttt180) cc_final: 0.6667 (ttt180) REVERT: C 1304 MET cc_start: 0.8251 (tmm) cc_final: 0.8039 (tmm) REVERT: C 1308 ILE cc_start: 0.8707 (mm) cc_final: 0.8366 (mm) REVERT: D 360 TYR cc_start: 0.6330 (t80) cc_final: 0.6083 (t80) REVERT: D 686 TRP cc_start: 0.9133 (m100) cc_final: 0.8376 (m100) REVERT: D 743 MET cc_start: 0.7134 (tpp) cc_final: 0.6905 (tpp) REVERT: D 792 ASN cc_start: 0.9020 (m-40) cc_final: 0.8706 (t0) REVERT: D 796 LEU cc_start: 0.9344 (tp) cc_final: 0.9068 (tt) REVERT: D 1040 MET cc_start: 0.1720 (mtp) cc_final: 0.0497 (ttt) REVERT: F 102 MET cc_start: 0.8947 (mtm) cc_final: 0.8650 (mtm) REVERT: F 297 MET cc_start: 0.2110 (ttm) cc_final: 0.1660 (ttt) REVERT: F 522 PHE cc_start: 0.7629 (m-10) cc_final: 0.7289 (m-80) REVERT: G 60 LEU cc_start: -0.1452 (mt) cc_final: -0.1692 (mt) REVERT: G 68 ARG cc_start: 0.6663 (mtt90) cc_final: 0.6342 (mmt180) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.2055 time to fit residues: 77.9733 Evaluate side-chains 186 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 293 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 405 optimal weight: 70.0000 chunk 402 optimal weight: 50.0000 chunk 254 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.086518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.066223 restraints weight = 293112.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.064816 restraints weight = 228615.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064808 restraints weight = 203121.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064757 restraints weight = 208440.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.064869 restraints weight = 171206.964| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36177 Z= 0.126 Angle : 0.597 13.181 49680 Z= 0.313 Chirality : 0.042 0.250 5666 Planarity : 0.004 0.061 5826 Dihedral : 19.334 177.081 6504 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.01 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3979 helix: 0.90 (0.14), residues: 1580 sheet: -0.78 (0.27), residues: 325 loop : -1.40 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 103 TYR 0.014 0.001 TYR D 512 PHE 0.036 0.001 PHE C 972 TRP 0.018 0.001 TRP D 33 HIS 0.009 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (36177) covalent geometry : angle 0.59683 / 0.31 (49680) hydrogen bonds : bond 0.03385 / 2.31 ( 1279) hydrogen bonds : angle 4.03841 / 2.83 ( 3572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6097.07 seconds wall clock time: 105 minutes 46.50 seconds (6346.50 seconds total)