Starting phenix.real_space_refine on Tue Aug 26 05:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w5x_32323/08_2025/7w5x_32323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5x_32323/08_2025/7w5x_32323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w5x_32323/08_2025/7w5x_32323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5x_32323/08_2025/7w5x_32323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w5x_32323/08_2025/7w5x_32323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5x_32323/08_2025/7w5x_32323.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 135 5.16 5 C 21016 2.51 5 N 6086 2.21 5 O 6879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34265 Number of models: 1 Model: "" Number of chains: 9 Chain: "1" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1548 Classifications: {'DNA': 75} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 74} Chain: "2" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1537 Classifications: {'DNA': 75} Link IDs: {'rna3p': 74} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10560 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 10369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10369 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3979 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 479} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 912 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2334 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2399 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Time building chain proxies: 8.17, per 1000 atoms: 0.24 Number of scatterers: 34265 At special positions: 0 Unit cell: (174.9, 227.7, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 149 15.00 O 6879 8.00 N 6086 7.00 C 21016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7378 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 45 sheets defined 40.4% alpha, 13.8% beta 21 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.767A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.501A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.546A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.995A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.666A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.255A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.641A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.557A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.740A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 3.668A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.690A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 removed outlier: 3.806A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.780A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.695A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.853A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.562A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.676A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.520A pdb=" N ARG C 903 " --> pdb=" O GLU C 899 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 959 removed outlier: 3.566A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 966 removed outlier: 3.542A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 981 removed outlier: 3.859A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1027 removed outlier: 3.822A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1034 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.541A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.813A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1121 Processing helix chain 'C' and resid 1121 through 1134 removed outlier: 3.913A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1148 Processing helix chain 'C' and resid 1165 through 1176 removed outlier: 3.506A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.502A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.501A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.507A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 removed outlier: 3.531A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.808A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C1305 " --> pdb=" O ARG C1301 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 removed outlier: 3.500A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.508A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.850A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.703A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.409A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.663A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 202 removed outlier: 3.659A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.897A pdb=" N ASN D 206 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.953A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.685A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 308 removed outlier: 3.655A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.179A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.723A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.929A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.520A pdb=" N ALA D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.581A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.528A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.914A pdb=" N ASN D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.654A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 660 removed outlier: 3.804A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 removed outlier: 3.543A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 697 removed outlier: 3.928A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.620A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.679A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 788 removed outlier: 3.503A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 removed outlier: 3.688A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.672A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.926A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 924 removed outlier: 3.703A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.210A pdb=" N THR D 928 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.660A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1237 removed outlier: 3.817A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D1232 " --> pdb=" O ALA D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1237 through 1244 removed outlier: 3.803A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1258 removed outlier: 4.196A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 removed outlier: 3.642A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 3.602A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 removed outlier: 3.559A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.529A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.528A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.999A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.570A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 79 removed outlier: 3.633A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 89 removed outlier: 3.866A pdb=" N SER F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.550A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.774A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 4.030A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 152 " --> pdb=" O TYR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.730A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 164' Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.697A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.720A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 291 removed outlier: 3.575A pdb=" N SER F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.658A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 removed outlier: 3.967A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 318 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA F 319 " --> pdb=" O TRP F 315 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.871A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.677A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 383 removed outlier: 3.782A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.916A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 401 through 419 removed outlier: 3.790A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.792A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 424 " --> pdb=" O TYR F 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 420 through 424' Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.001A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.842A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 3.559A pdb=" N ALA F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET F 487 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.510A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 539 removed outlier: 3.947A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 548 removed outlier: 3.654A pdb=" N HIS F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 551 No H-bonds generated for 'chain 'F' and resid 549 through 551' Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.566A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.567A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 599 removed outlier: 3.519A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 4.491A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 613 removed outlier: 3.816A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP F 613 " --> pdb=" O PHE F 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 609 through 613' Processing helix chain 'K' and resid 2 through 11 Processing helix chain 'K' and resid 23 through 28 Processing helix chain 'K' and resid 29 through 32 removed outlier: 3.708A pdb=" N GLY K 32 " --> pdb=" O LYS K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 29 through 32' Processing helix chain 'K' and resid 36 through 47 removed outlier: 3.911A pdb=" N ARG K 40 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET K 41 " --> pdb=" O TYR K 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG K 43 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR K 44 " --> pdb=" O ARG K 40 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL K 45 " --> pdb=" O MET K 41 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR K 46 " --> pdb=" O PHE K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 65 Processing helix chain 'K' and resid 72 through 77 removed outlier: 3.609A pdb=" N ILE K 76 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA K 77 " --> pdb=" O ILE K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 77' Processing helix chain 'K' and resid 84 through 89 removed outlier: 4.228A pdb=" N PHE K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.505A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.732A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.731A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.955A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.877A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.520A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.515A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 4.033A pdb=" N LYS A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.060A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.678A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.705A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.628A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.558A pdb=" N LEU B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.852A pdb=" N ALA B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.820A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.644A pdb=" N ILE B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.490A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.507A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.380A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 161 removed outlier: 3.847A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.073A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.928A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.161A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.622A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.679A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.755A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.471A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.719A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.934A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.138A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.564A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.443A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.505A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AC7, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.635A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AC9, first strand: chain 'D' and resid 821 through 822 Processing sheet with id=AD1, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.798A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.939A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D1009 " --> pdb=" O ILE D 958 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1028 through 1029 removed outlier: 3.510A pdb=" N THR D1029 " --> pdb=" O ASP D1119 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D1119 " --> pdb=" O THR D1029 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 1080 through 1081 Processing sheet with id=AD5, first strand: chain 'D' and resid 1047 through 1049 removed outlier: 3.576A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.571A pdb=" N ILE D1162 " --> pdb=" O THR D1178 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1263 through 1265 Processing sheet with id=AD8, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.811A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.811A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.553A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.550A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE4, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AE5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AE6, first strand: chain 'B' and resid 12 through 17 removed outlier: 5.352A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.910A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AE9, first strand: chain 'B' and resid 109 through 110 994 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 9.54 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9722 1.33 - 1.45: 5855 1.45 - 1.57: 18983 1.57 - 1.69: 298 1.69 - 1.81: 237 Bond restraints: 35095 Sorted by residual: bond pdb=" CA THR D 152 " pdb=" C THR D 152 " ideal model delta sigma weight residual 1.522 1.620 -0.099 1.72e-02 3.38e+03 3.29e+01 bond pdb=" C LYS C 496 " pdb=" N PRO C 497 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" C LYS F 324 " pdb=" N PRO F 325 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.85e+00 bond pdb=" CB VAL D1255 " pdb=" CG1 VAL D1255 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" C3' DG 2 43 " pdb=" O3' DG 2 43 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.42e+00 ... (remaining 35090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 46803 2.15 - 4.31: 1094 4.31 - 6.46: 108 6.46 - 8.61: 27 8.61 - 10.77: 7 Bond angle restraints: 48039 Sorted by residual: angle pdb=" N GLY D1103 " pdb=" CA GLY D1103 " pdb=" C GLY D1103 " ideal model delta sigma weight residual 112.33 119.02 -6.69 1.10e+00 8.26e-01 3.70e+01 angle pdb=" C ASN D 320 " pdb=" N LYS D 321 " pdb=" CA LYS D 321 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C PRO D 859 " pdb=" N ARG D 860 " pdb=" CA ARG D 860 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" O3' DA 1 79 " pdb=" C3' DA 1 79 " pdb=" C2' DA 1 79 " ideal model delta sigma weight residual 111.50 104.42 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" N SER B 266 " pdb=" CA SER B 266 " pdb=" C SER B 266 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 ... (remaining 48034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 20260 35.10 - 70.20: 899 70.20 - 105.31: 45 105.31 - 140.41: 1 140.41 - 175.51: 3 Dihedral angle restraints: 21208 sinusoidal: 9780 harmonic: 11428 Sorted by residual: dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA THR F 527 " pdb=" C THR F 527 " pdb=" N LEU F 528 " pdb=" CA LEU F 528 " ideal model delta harmonic sigma weight residual -180.00 -153.79 -26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 21205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4874 0.078 - 0.156: 552 0.156 - 0.234: 44 0.234 - 0.312: 7 0.312 - 0.390: 2 Chirality restraints: 5479 Sorted by residual: chirality pdb=" CB VAL A 287 " pdb=" CA VAL A 287 " pdb=" CG1 VAL A 287 " pdb=" CG2 VAL A 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB VAL D 421 " pdb=" CA VAL D 421 " pdb=" CG1 VAL D 421 " pdb=" CG2 VAL D 421 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5476 not shown) Planarity restraints: 5736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 992 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 993 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 993 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 993 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 209 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C GLY A 209 " 0.044 2.00e-02 2.50e+03 pdb=" O GLY A 209 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 210 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO C 190 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.035 5.00e-02 4.00e+02 ... (remaining 5733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7681 2.79 - 3.31: 27707 3.31 - 3.84: 54172 3.84 - 4.37: 65833 4.37 - 4.90: 109125 Nonbonded interactions: 264518 Sorted by model distance: nonbonded pdb=" O GLU K 65 " pdb=" OG1 THR K 69 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU C 876 " pdb=" OG1 THR C 927 " model vdw 2.297 3.040 nonbonded pdb=" OG SER C 759 " pdb=" OG1 THR C 763 " model vdw 2.303 3.040 nonbonded pdb=" OG SER D 949 " pdb=" OG1 THR D1016 " model vdw 2.306 3.040 nonbonded pdb=" OE1 GLU D 811 " pdb=" OG1 THR D 890 " model vdw 2.308 3.040 ... (remaining 264513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 233 or resid 250 through 324)) selection = (chain 'B' and (resid 6 through 233 or resid 250 through 264 or (resid 265 and ( \ name N or name CA or name C or name O or name CB )) or resid 266 through 294 or \ resid 299 through 324)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 38.670 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 35095 Z= 0.244 Angle : 0.802 10.766 48039 Z= 0.452 Chirality : 0.052 0.390 5479 Planarity : 0.006 0.071 5736 Dihedral : 17.753 175.509 13830 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 0.35 % Allowed : 8.43 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.01 (0.10), residues: 3929 helix: -4.86 (0.05), residues: 1420 sheet: -1.85 (0.24), residues: 424 loop : -2.46 (0.11), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 780 TYR 0.017 0.002 TYR C 105 PHE 0.033 0.002 PHE D 338 TRP 0.014 0.002 TRP C 997 HIS 0.014 0.002 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00558 (35095) covalent geometry : angle 0.80242 (48039) hydrogen bonds : bond 0.32242 ( 1032) hydrogen bonds : angle 10.40902 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 436 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7305 (Cg_endo) cc_final: 0.7044 (Cg_exo) REVERT: C 315 MET cc_start: 0.7239 (ttm) cc_final: 0.6924 (ttp) REVERT: C 484 LEU cc_start: 0.5642 (mm) cc_final: 0.5416 (mm) REVERT: C 496 LYS cc_start: 0.7304 (mmtp) cc_final: 0.7009 (mmtp) REVERT: C 542 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6981 (mtp-110) REVERT: D 562 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7150 (tt0) REVERT: D 566 LYS cc_start: 0.8079 (ptmt) cc_final: 0.7800 (ptpt) REVERT: D 865 HIS cc_start: 0.7784 (p90) cc_final: 0.7514 (p90) REVERT: D 892 PHE cc_start: 0.7670 (m-80) cc_final: 0.7023 (t80) REVERT: D 1174 ARG cc_start: 0.5007 (mtt180) cc_final: 0.4676 (mtp180) REVERT: D 1220 ILE cc_start: 0.8128 (mm) cc_final: 0.7877 (mt) REVERT: F 509 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 139 SER cc_start: 0.5387 (t) cc_final: 0.5011 (p) outliers start: 12 outliers final: 6 residues processed: 447 average time/residue: 0.2893 time to fit residues: 193.4866 Evaluate side-chains 291 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 284 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain A residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.2980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 447 HIS C 510 GLN C 513 GLN C 622 ASN C 737 ASN C 952 GLN C 965 GLN C1090 ASN C1157 GLN C1313 HIS D 294 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 560 ASN D 805 GLN D 907 HIS D1084 GLN D1108 GLN D1227 HIS D1235 ASN D1366 HIS D1367 GLN F 210 ASN F 265 GLN F 271 ASN F 362 ASN F 383 ASN F 455 HIS F 461 ASN F 545 HIS K 3 HIS K 20 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.181985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147867 restraints weight = 49122.271| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.81 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35095 Z= 0.116 Angle : 0.540 7.387 48039 Z= 0.299 Chirality : 0.041 0.151 5479 Planarity : 0.005 0.055 5736 Dihedral : 17.224 177.242 6004 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 1.53 % Allowed : 11.09 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.11), residues: 3929 helix: -3.25 (0.09), residues: 1471 sheet: -1.11 (0.26), residues: 384 loop : -1.99 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 371 TYR 0.015 0.001 TYR B 152 PHE 0.011 0.001 PHE D 620 TRP 0.011 0.001 TRP D 33 HIS 0.009 0.001 HIS F 545 Details of bonding type rmsd covalent geometry : bond 0.00249 (35095) covalent geometry : angle 0.53987 (48039) hydrogen bonds : bond 0.04895 ( 1032) hydrogen bonds : angle 5.62290 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7233 (Cg_endo) cc_final: 0.6957 (Cg_exo) REVERT: C 239 MET cc_start: 0.7049 (ptt) cc_final: 0.6705 (ptm) REVERT: C 484 LEU cc_start: 0.4857 (mm) cc_final: 0.4609 (mm) REVERT: C 941 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7856 (mttm) REVERT: D 29 MET cc_start: 0.7790 (tpp) cc_final: 0.7561 (ttm) REVERT: D 304 ASP cc_start: 0.6900 (m-30) cc_final: 0.6425 (m-30) REVERT: D 698 MET cc_start: 0.6617 (mmm) cc_final: 0.6345 (mmm) REVERT: D 700 ASN cc_start: 0.7077 (t0) cc_final: 0.6713 (t0) REVERT: D 892 PHE cc_start: 0.7641 (m-80) cc_final: 0.7213 (t80) REVERT: F 111 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7484 (pp) REVERT: F 265 GLN cc_start: 0.4128 (OUTLIER) cc_final: 0.3915 (pp30) REVERT: F 582 VAL cc_start: 0.6116 (OUTLIER) cc_final: 0.5904 (t) REVERT: K 78 MET cc_start: 0.0986 (tpp) cc_final: 0.0545 (tpp) REVERT: B 188 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6804 (mt-10) outliers start: 52 outliers final: 21 residues processed: 366 average time/residue: 0.2325 time to fit residues: 137.7665 Evaluate side-chains 295 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 50 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 391 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 363 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C1090 ASN C1157 GLN D 865 HIS A 147 GLN B 75 GLN B 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145848 restraints weight = 49236.805| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.82 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35095 Z= 0.111 Angle : 0.499 8.247 48039 Z= 0.273 Chirality : 0.041 0.226 5479 Planarity : 0.004 0.050 5736 Dihedral : 17.003 174.964 6001 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 1.59 % Allowed : 12.47 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.12), residues: 3929 helix: -2.13 (0.11), residues: 1471 sheet: -0.94 (0.26), residues: 402 loop : -1.72 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 535 TYR 0.012 0.001 TYR C1231 PHE 0.012 0.001 PHE D 620 TRP 0.009 0.001 TRP K 36 HIS 0.005 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00248 (35095) covalent geometry : angle 0.49922 (48039) hydrogen bonds : bond 0.03942 ( 1032) hydrogen bonds : angle 4.96185 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7225 (Cg_endo) cc_final: 0.6946 (Cg_exo) REVERT: C 239 MET cc_start: 0.7084 (ptt) cc_final: 0.6720 (ptm) REVERT: C 941 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7783 (mttm) REVERT: D 304 ASP cc_start: 0.6338 (m-30) cc_final: 0.5906 (m-30) REVERT: D 698 MET cc_start: 0.6676 (mmm) cc_final: 0.6412 (mmm) REVERT: D 700 ASN cc_start: 0.7180 (t0) cc_final: 0.6450 (t0) REVERT: D 892 PHE cc_start: 0.7643 (m-80) cc_final: 0.7263 (t80) REVERT: F 111 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7490 (pp) REVERT: F 487 MET cc_start: 0.5966 (mmm) cc_final: 0.5761 (ttm) REVERT: F 582 VAL cc_start: 0.6036 (OUTLIER) cc_final: 0.5833 (t) REVERT: B 188 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6766 (mt-10) outliers start: 54 outliers final: 31 residues processed: 341 average time/residue: 0.2351 time to fit residues: 129.3931 Evaluate side-chains 305 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1090 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN B 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142304 restraints weight = 48458.543| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.74 r_work: 0.3286 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35095 Z= 0.195 Angle : 0.579 8.427 48039 Z= 0.311 Chirality : 0.043 0.179 5479 Planarity : 0.004 0.049 5736 Dihedral : 17.134 172.688 6001 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 2.30 % Allowed : 14.27 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.12), residues: 3929 helix: -1.70 (0.12), residues: 1481 sheet: -0.75 (0.26), residues: 398 loop : -1.66 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 798 TYR 0.015 0.002 TYR C 105 PHE 0.016 0.001 PHE D 620 TRP 0.010 0.001 TRP D1193 HIS 0.009 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00467 (35095) covalent geometry : angle 0.57906 (48039) hydrogen bonds : bond 0.04328 ( 1032) hydrogen bonds : angle 4.91084 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 267 time to evaluate : 1.301 Fit side-chains REVERT: C 239 MET cc_start: 0.7404 (ptt) cc_final: 0.7032 (ptm) REVERT: C 514 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7785 (t80) REVERT: C 651 ASP cc_start: 0.8164 (t0) cc_final: 0.7856 (t0) REVERT: C 737 ASN cc_start: 0.7704 (m-40) cc_final: 0.7477 (m-40) REVERT: D 304 ASP cc_start: 0.6999 (m-30) cc_final: 0.6581 (m-30) REVERT: D 698 MET cc_start: 0.7206 (mmm) cc_final: 0.6923 (mmm) REVERT: D 700 ASN cc_start: 0.7591 (t0) cc_final: 0.7176 (t0) REVERT: D 817 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.5985 (t-90) REVERT: D 892 PHE cc_start: 0.8002 (m-80) cc_final: 0.7307 (t80) REVERT: F 111 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7833 (pp) REVERT: F 273 MET cc_start: 0.5862 (mmt) cc_final: 0.5429 (mmp) REVERT: F 487 MET cc_start: 0.6321 (mmm) cc_final: 0.6061 (ttm) REVERT: K 41 MET cc_start: 0.3234 (ptt) cc_final: 0.2874 (ptm) REVERT: A 166 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7218 (mtm110) REVERT: B 188 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7545 (mt-10) outliers start: 78 outliers final: 56 residues processed: 334 average time/residue: 0.2316 time to fit residues: 125.2473 Evaluate side-chains 314 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 367 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 327 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 chunk 340 optimal weight: 30.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1324 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.181871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149461 restraints weight = 49308.453| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.65 r_work: 0.3397 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35095 Z= 0.100 Angle : 0.474 7.861 48039 Z= 0.259 Chirality : 0.040 0.140 5479 Planarity : 0.003 0.045 5736 Dihedral : 16.880 176.928 6001 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 2.15 % Allowed : 15.04 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.13), residues: 3929 helix: -1.17 (0.13), residues: 1490 sheet: -0.64 (0.26), residues: 407 loop : -1.46 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 175 TYR 0.010 0.001 TYR B 152 PHE 0.009 0.001 PHE A 231 TRP 0.010 0.001 TRP D1020 HIS 0.003 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00221 (35095) covalent geometry : angle 0.47404 (48039) hydrogen bonds : bond 0.03115 ( 1032) hydrogen bonds : angle 4.49384 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7416 (Cg_endo) cc_final: 0.7129 (Cg_exo) REVERT: C 651 ASP cc_start: 0.8046 (t0) cc_final: 0.7787 (t0) REVERT: C 704 MET cc_start: 0.8875 (mmm) cc_final: 0.8532 (mtp) REVERT: C 737 ASN cc_start: 0.7589 (m-40) cc_final: 0.7344 (m-40) REVERT: C 941 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8007 (mttm) REVERT: D 304 ASP cc_start: 0.6825 (m-30) cc_final: 0.6412 (m-30) REVERT: D 698 MET cc_start: 0.7097 (mmm) cc_final: 0.6848 (mmm) REVERT: D 700 ASN cc_start: 0.7604 (t0) cc_final: 0.6948 (t0) REVERT: D 817 HIS cc_start: 0.6898 (OUTLIER) cc_final: 0.5867 (t-90) REVERT: D 892 PHE cc_start: 0.7973 (m-80) cc_final: 0.7080 (t80) REVERT: D 1291 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6233 (mm-30) REVERT: F 111 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7711 (pp) REVERT: F 141 ILE cc_start: 0.4617 (OUTLIER) cc_final: 0.4387 (tt) REVERT: F 487 MET cc_start: 0.6276 (mmm) cc_final: 0.5989 (ttm) REVERT: K 41 MET cc_start: 0.3056 (ptt) cc_final: 0.2803 (ptm) REVERT: B 188 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7445 (mt-10) outliers start: 73 outliers final: 47 residues processed: 342 average time/residue: 0.2064 time to fit residues: 114.7814 Evaluate side-chains 306 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1156 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 350 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 241 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.175761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148164 restraints weight = 48093.141| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.10 r_work: 0.3454 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35095 Z= 0.188 Angle : 0.561 8.312 48039 Z= 0.301 Chirality : 0.043 0.177 5479 Planarity : 0.004 0.046 5736 Dihedral : 17.072 173.683 6001 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.53 % Rotamer: Outliers : 2.62 % Allowed : 15.87 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.13), residues: 3929 helix: -1.11 (0.13), residues: 1493 sheet: -0.46 (0.27), residues: 388 loop : -1.51 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 596 TYR 0.015 0.002 TYR C 105 PHE 0.023 0.001 PHE F 256 TRP 0.008 0.001 TRP D1193 HIS 0.008 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00454 (35095) covalent geometry : angle 0.56109 (48039) hydrogen bonds : bond 0.03954 ( 1032) hydrogen bonds : angle 4.64614 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.7438 (ptt) cc_final: 0.7117 (ptm) REVERT: C 484 LEU cc_start: 0.5297 (mm) cc_final: 0.5070 (mm) REVERT: C 514 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7804 (t80) REVERT: C 651 ASP cc_start: 0.8078 (t0) cc_final: 0.7842 (t0) REVERT: C 704 MET cc_start: 0.8949 (mmm) cc_final: 0.8507 (mtp) REVERT: D 304 ASP cc_start: 0.6851 (m-30) cc_final: 0.6459 (m-30) REVERT: D 698 MET cc_start: 0.6879 (mmm) cc_final: 0.6603 (mmm) REVERT: D 700 ASN cc_start: 0.7624 (t0) cc_final: 0.6991 (t0) REVERT: D 817 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.5956 (t-90) REVERT: D 892 PHE cc_start: 0.7922 (m-80) cc_final: 0.7412 (t80) REVERT: D 1291 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6192 (mm-30) REVERT: F 111 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7821 (pp) REVERT: F 273 MET cc_start: 0.5796 (mmp) cc_final: 0.5593 (mmt) REVERT: K 41 MET cc_start: 0.3260 (ptt) cc_final: 0.2999 (ptm) REVERT: A 166 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7113 (mtm110) REVERT: B 80 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: B 188 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7484 (mt-10) outliers start: 89 outliers final: 66 residues processed: 327 average time/residue: 0.2009 time to fit residues: 107.5088 Evaluate side-chains 316 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 1 optimal weight: 30.0000 chunk 326 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 275 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 378 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.151105 restraints weight = 48299.604| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.86 r_work: 0.3503 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 35095 Z= 0.250 Angle : 0.631 9.645 48039 Z= 0.336 Chirality : 0.046 0.216 5479 Planarity : 0.005 0.048 5736 Dihedral : 17.325 171.898 6001 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.13 % Favored : 93.84 % Rotamer: Outliers : 2.62 % Allowed : 16.37 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.13), residues: 3929 helix: -1.30 (0.13), residues: 1503 sheet: -0.48 (0.27), residues: 396 loop : -1.64 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 596 TYR 0.017 0.002 TYR C 105 PHE 0.015 0.002 PHE F 256 TRP 0.009 0.002 TRP K 36 HIS 0.011 0.002 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00606 (35095) covalent geometry : angle 0.63120 (48039) hydrogen bonds : bond 0.04480 ( 1032) hydrogen bonds : angle 4.90666 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 1.166 Fit side-chains REVERT: C 239 MET cc_start: 0.7598 (ptt) cc_final: 0.7305 (ptm) REVERT: C 514 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7899 (t80) REVERT: C 704 MET cc_start: 0.8959 (mmm) cc_final: 0.8532 (mtp) REVERT: D 304 ASP cc_start: 0.7088 (m-30) cc_final: 0.6692 (m-30) REVERT: D 321 LYS cc_start: 0.7272 (ptmt) cc_final: 0.6946 (ttmm) REVERT: D 698 MET cc_start: 0.6959 (mmm) cc_final: 0.6720 (mmm) REVERT: D 700 ASN cc_start: 0.7708 (t0) cc_final: 0.7458 (t0) REVERT: D 817 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.5909 (t-90) REVERT: D 892 PHE cc_start: 0.7912 (m-80) cc_final: 0.7253 (t80) REVERT: D 1040 MET cc_start: 0.1243 (ptp) cc_final: -0.0288 (mmt) REVERT: D 1291 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6218 (mm-30) REVERT: F 111 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7911 (pp) REVERT: K 41 MET cc_start: 0.3371 (ptt) cc_final: 0.3075 (ptm) REVERT: A 166 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7099 (mtm110) REVERT: B 80 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6964 (tp30) REVERT: B 188 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7577 (mt-10) outliers start: 89 outliers final: 67 residues processed: 325 average time/residue: 0.1960 time to fit residues: 104.7309 Evaluate side-chains 321 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 249 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 80 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 402 optimal weight: 8.9990 chunk 316 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 284 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1135 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153254 restraints weight = 48161.948| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.79 r_work: 0.3519 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35095 Z= 0.165 Angle : 0.547 9.295 48039 Z= 0.294 Chirality : 0.042 0.170 5479 Planarity : 0.004 0.046 5736 Dihedral : 17.149 174.380 6001 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 2.39 % Allowed : 16.93 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.13), residues: 3929 helix: -1.06 (0.13), residues: 1499 sheet: -0.45 (0.27), residues: 402 loop : -1.54 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.011 0.001 TYR C 105 PHE 0.018 0.001 PHE F 256 TRP 0.009 0.001 TRP D 868 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00396 (35095) covalent geometry : angle 0.54721 (48039) hydrogen bonds : bond 0.03765 ( 1032) hydrogen bonds : angle 4.68054 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 1.251 Fit side-chains REVERT: C 239 MET cc_start: 0.7570 (ptt) cc_final: 0.7286 (ptm) REVERT: C 641 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.6802 (pp20) REVERT: C 651 ASP cc_start: 0.7950 (t0) cc_final: 0.7724 (t0) REVERT: C 704 MET cc_start: 0.8901 (mmm) cc_final: 0.8473 (mtp) REVERT: D 304 ASP cc_start: 0.6811 (m-30) cc_final: 0.6421 (m-30) REVERT: D 698 MET cc_start: 0.6892 (mmm) cc_final: 0.6670 (mmm) REVERT: D 700 ASN cc_start: 0.7677 (t0) cc_final: 0.7450 (t0) REVERT: D 817 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.5935 (t-90) REVERT: D 892 PHE cc_start: 0.7945 (m-80) cc_final: 0.7264 (t80) REVERT: D 1040 MET cc_start: 0.0967 (ptp) cc_final: -0.0521 (mmt) REVERT: D 1287 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7397 (mm) REVERT: D 1291 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6173 (mm-30) REVERT: F 111 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7929 (pp) REVERT: F 466 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8292 (mp) REVERT: K 41 MET cc_start: 0.3400 (ptt) cc_final: 0.3114 (ptm) REVERT: A 166 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7057 (mtm110) REVERT: B 80 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: B 188 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7476 (mt-10) outliers start: 81 outliers final: 64 residues processed: 321 average time/residue: 0.1845 time to fit residues: 98.1468 Evaluate side-chains 317 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1156 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 193 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 168 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 165 optimal weight: 1.9990 chunk 358 optimal weight: 0.0040 chunk 191 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 360 optimal weight: 6.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1135 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.178689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150545 restraints weight = 48154.922| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.18 r_work: 0.3488 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35095 Z= 0.098 Angle : 0.475 7.745 48039 Z= 0.259 Chirality : 0.040 0.139 5479 Planarity : 0.003 0.044 5736 Dihedral : 16.885 177.656 6001 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 1.92 % Allowed : 17.43 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.13), residues: 3929 helix: -0.61 (0.13), residues: 1502 sheet: -0.28 (0.26), residues: 412 loop : -1.35 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 542 TYR 0.010 0.001 TYR F 137 PHE 0.017 0.001 PHE F 256 TRP 0.011 0.001 TRP D1020 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00217 (35095) covalent geometry : angle 0.47547 (48039) hydrogen bonds : bond 0.02952 ( 1032) hydrogen bonds : angle 4.32427 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 651 ASP cc_start: 0.7936 (t0) cc_final: 0.7710 (t0) REVERT: C 704 MET cc_start: 0.8877 (mmm) cc_final: 0.8482 (mtp) REVERT: C 1230 MET cc_start: 0.8458 (ttm) cc_final: 0.8237 (ttm) REVERT: D 304 ASP cc_start: 0.6797 (m-30) cc_final: 0.6479 (m-30) REVERT: D 698 MET cc_start: 0.6890 (mmm) cc_final: 0.6666 (mmm) REVERT: D 700 ASN cc_start: 0.7716 (t0) cc_final: 0.7237 (t0) REVERT: D 817 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.5851 (t-90) REVERT: D 892 PHE cc_start: 0.7892 (m-80) cc_final: 0.7139 (t80) REVERT: D 1040 MET cc_start: 0.0976 (ptp) cc_final: -0.0444 (mmt) REVERT: D 1287 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7261 (mm) REVERT: D 1291 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6033 (mm-30) REVERT: E 44 ASP cc_start: 0.8304 (m-30) cc_final: 0.8101 (m-30) REVERT: F 111 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7864 (pp) REVERT: F 255 VAL cc_start: 0.5313 (p) cc_final: 0.5074 (t) REVERT: F 265 GLN cc_start: 0.3893 (pm20) cc_final: 0.3641 (pm20) REVERT: F 323 ASN cc_start: 0.1498 (OUTLIER) cc_final: 0.0544 (t0) REVERT: F 466 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8246 (mp) REVERT: K 41 MET cc_start: 0.3294 (ptt) cc_final: 0.3037 (ptm) REVERT: A 80 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7893 (mt-10) REVERT: A 166 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7052 (mtm110) REVERT: B 80 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: B 188 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7425 (mt-10) outliers start: 65 outliers final: 44 residues processed: 326 average time/residue: 0.1872 time to fit residues: 101.2669 Evaluate side-chains 310 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1156 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 107 optimal weight: 0.9990 chunk 389 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 370 optimal weight: 0.2980 chunk 250 optimal weight: 40.0000 chunk 60 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 chunk 340 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 285 optimal weight: 0.0770 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1135 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.179984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.152145 restraints weight = 48220.124| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.15 r_work: 0.3518 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 35095 Z= 0.090 Angle : 0.459 8.748 48039 Z= 0.250 Chirality : 0.040 0.147 5479 Planarity : 0.003 0.043 5736 Dihedral : 16.773 177.254 6001 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 1.59 % Allowed : 17.93 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3929 helix: -0.19 (0.14), residues: 1489 sheet: -0.22 (0.27), residues: 411 loop : -1.14 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 542 TYR 0.010 0.001 TYR F 137 PHE 0.016 0.001 PHE F 256 TRP 0.012 0.001 TRP D1020 HIS 0.002 0.000 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00199 (35095) covalent geometry : angle 0.45938 (48039) hydrogen bonds : bond 0.02735 ( 1032) hydrogen bonds : angle 4.12879 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 58 PRO cc_start: 0.7366 (Cg_endo) cc_final: 0.7118 (Cg_exo) REVERT: C 484 LEU cc_start: 0.5207 (mm) cc_final: 0.4940 (mm) REVERT: C 651 ASP cc_start: 0.7830 (t0) cc_final: 0.7621 (t0) REVERT: C 704 MET cc_start: 0.8841 (mmm) cc_final: 0.8456 (mtp) REVERT: C 1041 ASP cc_start: 0.7396 (t0) cc_final: 0.7178 (t0) REVERT: C 1230 MET cc_start: 0.8399 (ttm) cc_final: 0.8176 (ttm) REVERT: D 304 ASP cc_start: 0.6823 (m-30) cc_final: 0.6447 (m-30) REVERT: D 698 MET cc_start: 0.6630 (mmm) cc_final: 0.6366 (mmm) REVERT: D 700 ASN cc_start: 0.7552 (t0) cc_final: 0.6907 (t0) REVERT: D 713 GLU cc_start: 0.4713 (OUTLIER) cc_final: 0.4069 (tt0) REVERT: D 817 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.5881 (t-90) REVERT: D 892 PHE cc_start: 0.7851 (m-80) cc_final: 0.7182 (t80) REVERT: D 1040 MET cc_start: 0.1117 (ptp) cc_final: -0.0376 (mmt) REVERT: D 1287 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7280 (mm) REVERT: D 1291 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5961 (mm-30) REVERT: F 111 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7692 (pp) REVERT: F 255 VAL cc_start: 0.5416 (p) cc_final: 0.5172 (t) REVERT: F 265 GLN cc_start: 0.3863 (pm20) cc_final: 0.3581 (pm20) REVERT: F 273 MET cc_start: 0.5245 (mmp) cc_final: 0.4407 (mmp) REVERT: F 288 MET cc_start: 0.0271 (mmt) cc_final: 0.0018 (mmp) REVERT: F 323 ASN cc_start: 0.1509 (OUTLIER) cc_final: 0.0901 (t0) REVERT: F 466 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8143 (mp) REVERT: F 487 MET cc_start: 0.5898 (ttm) cc_final: 0.5563 (ttm) REVERT: K 41 MET cc_start: 0.3302 (ptt) cc_final: 0.3064 (ptm) REVERT: A 80 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7893 (mt-10) REVERT: B 80 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: B 188 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7404 (mt-10) outliers start: 54 outliers final: 41 residues processed: 322 average time/residue: 0.2116 time to fit residues: 112.0325 Evaluate side-chains 306 residues out of total 3403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 817 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1305 ASP Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 299 optimal weight: 0.0470 chunk 172 optimal weight: 0.2980 chunk 38 optimal weight: 0.0030 chunk 368 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 334 optimal weight: 0.0000 chunk 223 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1135 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.182125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151365 restraints weight = 48278.919| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.93 r_work: 0.3204 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35095 Z= 0.087 Angle : 0.451 9.191 48039 Z= 0.244 Chirality : 0.039 0.141 5479 Planarity : 0.003 0.043 5736 Dihedral : 16.715 177.335 6001 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 1.42 % Allowed : 18.25 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3929 helix: 0.10 (0.14), residues: 1504 sheet: -0.02 (0.27), residues: 398 loop : -1.05 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 542 TYR 0.011 0.001 TYR F 137 PHE 0.016 0.001 PHE F 256 TRP 0.011 0.001 TRP D1020 HIS 0.002 0.000 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00189 (35095) covalent geometry : angle 0.45142 (48039) hydrogen bonds : bond 0.02522 ( 1032) hydrogen bonds : angle 3.98390 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7071.79 seconds wall clock time: 121 minutes 56.84 seconds (7316.84 seconds total)