Starting phenix.real_space_refine on Mon Sep 14 06:54:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qwp_14190/09_2026/7qwp_14190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qwp_14190/09_2026/7qwp_14190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qwp_14190/09_2026/7qwp_14190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qwp_14190/09_2026/7qwp_14190.map" model { file = "/net/cci-nas-00/data/ceres_data/7qwp_14190/09_2026/7qwp_14190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qwp_14190/09_2026/7qwp_14190.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 72 5.49 5 S 102 5.16 5 C 17968 2.51 5 N 5130 2.21 5 O 5734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29006 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2316 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1673 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 10135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10135 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 4, 'ASP:plan': 13, 'GLU:plan': 23, 'ASN:plan1': 4, 'ARG:plan': 13, 'HIS:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 284 Chain: "D" Number of atoms: 9638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 9638 Classifications: {'peptide': 1333} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 53, 'TRANS': 1279} Chain breaks: 6 Unresolved non-hydrogen bonds: 768 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 24, 'ASP:plan': 22, 'ASN:plan1': 7, 'PHE:plan': 9, 'HIS:plan': 2, 'GLN:plan1': 10, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 552 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3216 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 5.86, per 1000 atoms: 0.20 Number of scatterers: 29006 At special positions: 0 Unit cell: (148.5, 180.4, 168.3, 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 102 16.00 P 72 15.00 O 5734 8.00 N 5130 7.00 C 17968 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6846 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 37 sheets defined 38.7% alpha, 10.4% beta 33 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.003A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.796A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.680A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.561A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.639A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.516A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.588A 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 212 through 227 removed outlier: 3.592A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.562A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.539A pdb=" N LYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 9' Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.192A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.606A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.522A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.241A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.898A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 removed outlier: 3.994A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.921A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 removed outlier: 4.558A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.525A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.817A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.866A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.655A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.778A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.925A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.548A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.443A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.798A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 4.083A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.805A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.890A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.411A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.805A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.545A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1174 removed outlier: 3.841A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.908A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C1243 " --> pdb=" O VAL C1239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1238 through 1243' Processing helix chain 'C' and resid 1271 through 1280 removed outlier: 3.726A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.546A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 4.246A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.749A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.710A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.892A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 removed outlier: 4.634A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.713A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.560A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.775A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.633A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.527A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.926A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.626A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.972A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' 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 473 through 483 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.594A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 538 removed outlier: 4.269A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.642A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 removed outlier: 3.903A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.760A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.563A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.589A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 702 removed outlier: 4.534A pdb=" N VAL D 682 " --> pdb=" O ARG D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.712A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 876 Processing helix chain 'D' and resid 914 through 919 removed outlier: 3.547A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.516A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.874A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.061A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1291 removed outlier: 4.588A pdb=" N ILE D1287 " --> pdb=" O SER D1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.614A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1310 through 1316 Processing helix chain 'D' and resid 1318 through 1322 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.898A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.347A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.981A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'M' and resid 16 through 28 removed outlier: 3.604A pdb=" N ARG M 24 " --> pdb=" O GLN M 20 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 121 through 131 removed outlier: 3.722A pdb=" N GLN M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL M 128 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU M 129 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.819A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 165 removed outlier: 3.720A pdb=" N VAL M 162 " --> pdb=" O ILE M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.908A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG M 181 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 206 removed outlier: 3.944A pdb=" N LEU M 200 " --> pdb=" O ARG M 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.769A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 228 removed outlier: 3.822A pdb=" N LEU M 227 " --> pdb=" O HIS M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 240 removed outlier: 4.529A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 255 removed outlier: 3.816A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU M 252 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 removed outlier: 3.626A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 306 removed outlier: 3.897A pdb=" N ALA M 305 " --> pdb=" O GLN M 301 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET M 306 " --> pdb=" O GLN M 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 301 through 306' Processing helix chain 'M' and resid 313 through 351 removed outlier: 3.901A pdb=" N ILE M 347 " --> pdb=" O VAL M 343 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL M 348 " --> pdb=" O SER M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 357 removed outlier: 3.577A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 362 Processing helix chain 'M' and resid 366 through 372 Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.661A pdb=" N ARG M 383 " --> pdb=" O SER M 379 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 403 removed outlier: 4.135A pdb=" N PHE M 403 " --> pdb=" O LEU M 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 399 through 403' Processing helix chain 'M' and resid 410 through 412 No H-bonds generated for 'chain 'M' and resid 410 through 412' Processing helix chain 'M' and resid 417 through 431 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 465 removed outlier: 3.578A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.134A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.620A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.973A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 28 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.655A pdb=" N GLY B 149 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.269A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 3.842A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 114 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 3.842A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.143A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.246A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.613A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 7.076A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 755 through 758 removed outlier: 6.452A pdb=" N ILE C 765 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.868A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.928A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1210 " --> pdb=" O VAL C1225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 839 removed outlier: 4.086A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1335 through 1336 Processing sheet with id=AC9, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.582A pdb=" N PHE D 35 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 244 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 145 through 148 removed outlier: 3.518A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AD3, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.594A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.015A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 825 through 826 removed outlier: 3.731A pdb=" N VAL D 825 " --> pdb=" O GLU D 833 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AD7, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AD8, first strand: chain 'D' and resid 1265 through 1266 Processing sheet with id=AD9, first strand: chain 'M' and resid 286 through 289 removed outlier: 3.628A pdb=" N THR M 286 " --> pdb=" O ARG M 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 279 " --> pdb=" O THR M 286 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 406 through 408 975 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 7.76 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4907 1.28 - 1.41: 6680 1.41 - 1.55: 17487 1.55 - 1.68: 316 1.68 - 1.81: 181 Bond restraints: 29571 Sorted by residual: bond pdb=" C4' DC N -11 " pdb=" O4' DC N -11 " ideal model delta sigma weight residual 1.446 1.312 0.134 1.00e-02 1.00e+04 1.79e+02 bond pdb=" C4' DT T 23 " pdb=" O4' DT T 23 " ideal model delta sigma weight residual 1.446 1.578 -0.132 1.00e-02 1.00e+04 1.73e+02 bond pdb=" C4' DA T 17 " pdb=" O4' DA T 17 " ideal model delta sigma weight residual 1.446 1.565 -0.119 1.00e-02 1.00e+04 1.42e+02 bond pdb=" O3' DG T 13 " pdb=" P DC T 14 " ideal model delta sigma weight residual 1.607 1.474 0.133 1.20e-02 6.94e+03 1.23e+02 bond pdb=" O3' DT T 9 " pdb=" P DC T 10 " ideal model delta sigma weight residual 1.607 1.489 0.118 1.20e-02 6.94e+03 9.60e+01 ... (remaining 29566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 40084 4.20 - 8.41: 306 8.41 - 12.61: 41 12.61 - 16.82: 4 16.82 - 21.02: 1 Bond angle restraints: 40436 Sorted by residual: angle pdb=" C5' DG T 13 " pdb=" C4' DG T 13 " pdb=" O4' DG T 13 " ideal model delta sigma weight residual 109.30 130.32 -21.02 1.90e+00 2.77e-01 1.22e+02 angle pdb=" C3' DG T 7 " pdb=" O3' DG T 7 " pdb=" P DA T 8 " ideal model delta sigma weight residual 119.70 132.77 -13.07 1.20e+00 6.94e-01 1.19e+02 angle pdb=" C4' DT T 23 " pdb=" O4' DT T 23 " pdb=" C1' DT T 23 " ideal model delta sigma weight residual 110.10 101.14 8.96 1.00e+00 1.00e+00 8.02e+01 angle pdb=" CA ILE M 264 " pdb=" C ILE M 264 " pdb=" N GLN M 265 " ideal model delta sigma weight residual 115.28 105.57 9.71 1.14e+00 7.69e-01 7.25e+01 angle pdb=" O3' DG T 13 " pdb=" P DC T 14 " pdb=" O5' DC T 14 " ideal model delta sigma weight residual 104.00 120.05 -16.05 1.90e+00 2.77e-01 7.13e+01 ... (remaining 40431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 17257 32.42 - 64.83: 610 64.83 - 97.25: 8 97.25 - 129.67: 0 129.67 - 162.08: 1 Dihedral angle restraints: 17876 sinusoidal: 7272 harmonic: 10604 Sorted by residual: dihedral pdb=" C LEU M 31 " pdb=" N LEU M 31 " pdb=" CA LEU M 31 " pdb=" CB LEU M 31 " ideal model delta harmonic sigma weight residual -122.60 -139.61 17.01 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C GLN M 183 " pdb=" N GLN M 183 " pdb=" CA GLN M 183 " pdb=" CB GLN M 183 " ideal model delta harmonic sigma weight residual -122.60 -106.43 -16.17 0 2.50e+00 1.60e-01 4.18e+01 dihedral pdb=" N ASP M 275 " pdb=" C ASP M 275 " pdb=" CA ASP M 275 " pdb=" CB ASP M 275 " ideal model delta harmonic sigma weight residual 122.80 137.95 -15.15 0 2.50e+00 1.60e-01 3.67e+01 ... (remaining 17873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 4697 0.201 - 0.403: 65 0.403 - 0.604: 3 0.604 - 0.806: 1 0.806 - 1.007: 1 Chirality restraints: 4767 Sorted by residual: chirality pdb=" C4' DG T 13 " pdb=" C5' DG T 13 " pdb=" O4' DG T 13 " pdb=" C3' DG T 13 " both_signs ideal model delta sigma weight residual False -2.53 -1.52 -1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA LEU M 31 " pdb=" N LEU M 31 " pdb=" C LEU M 31 " pdb=" CB LEU M 31 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ARG M 311 " pdb=" N ARG M 311 " pdb=" C ARG M 311 " pdb=" CB ARG M 311 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.32e+00 ... (remaining 4764 not shown) Planarity restraints: 5059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 285 " 0.090 2.00e-02 2.50e+03 5.47e-02 7.48e+01 pdb=" CG TRP M 285 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP M 285 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP M 285 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP M 285 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TRP M 285 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP M 285 " -0.079 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 285 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 285 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP M 285 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 206 " -0.085 2.00e-02 2.50e+03 5.46e-02 5.22e+01 pdb=" CG PHE M 206 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE M 206 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE M 206 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE M 206 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE M 206 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE M 206 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N -11 " 0.066 2.00e-02 2.50e+03 3.96e-02 3.53e+01 pdb=" N1 DC N -11 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DC N -11 " -0.041 2.00e-02 2.50e+03 pdb=" O2 DC N -11 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DC N -11 " 0.041 2.00e-02 2.50e+03 pdb=" C4 DC N -11 " 0.015 2.00e-02 2.50e+03 pdb=" N4 DC N -11 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC N -11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC N -11 " -0.000 2.00e-02 2.50e+03 ... (remaining 5056 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1231 2.71 - 3.26: 28842 3.26 - 3.81: 44487 3.81 - 4.35: 54253 4.35 - 4.90: 90300 Nonbonded interactions: 219113 Sorted by model distance: nonbonded pdb=" N GLN A 194 " pdb=" OE1 GLN A 194 " model vdw 2.165 3.120 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.197 3.040 nonbonded pdb=" O SER C 166 " pdb=" OG SER C 166 " model vdw 2.201 3.040 nonbonded pdb=" O THR D1310 " pdb=" OG SER D1313 " model vdw 2.212 3.040 nonbonded pdb=" CB GLU A 29 " pdb=" CD PRO A 30 " model vdw 2.228 3.840 ... (remaining 219108 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 28.940 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.007 0.134 29571 Z= 0.478 Angle : 0.984 21.021 40436 Z= 0.631 Chirality : 0.062 1.007 4767 Planarity : 0.004 0.056 5059 Dihedral : 13.757 162.083 11030 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.51 % Favored : 93.16 % Rotamer: Outliers : 7.21 % Allowed : 7.63 % Favored : 85.16 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.12), residues: 3655 helix: -1.28 (0.14), residues: 1227 sheet: -1.89 (0.28), residues: 285 loop : -2.83 (0.11), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG M 24 TYR 0.050 0.001 TYR M 153 PHE 0.103 0.003 PHE M 206 TRP 0.090 0.004 TRP M 285 HIS 0.021 0.001 HIS M 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.48 (29571) covalent geometry : angle 0.98435 / 0.63 (40436) hydrogen bonds : bond 0.18746 / 12.90 ( 1053) hydrogen bonds : angle 6.88377 / 4.83 ( 2899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 865 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7296 (mmm160) REVERT: A 79 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 166 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8103 (ptt-90) REVERT: B 17 GLU cc_start: 0.7480 (pt0) cc_final: 0.7273 (mp0) REVERT: C 160 ASP cc_start: 0.7744 (m-30) cc_final: 0.7295 (t70) REVERT: C 169 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5776 (mtmt) REVERT: C 187 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7472 (tt0) REVERT: C 396 ASP cc_start: 0.6406 (t70) cc_final: 0.6201 (t70) REVERT: C 488 MET cc_start: 0.8743 (mmm) cc_final: 0.8446 (mmp) REVERT: C 565 GLU cc_start: 0.6150 (tp30) cc_final: 0.5918 (mt-10) REVERT: C 639 LYS cc_start: 0.7412 (mttp) cc_final: 0.6499 (mtmm) REVERT: C 905 ILE cc_start: 0.8230 (mt) cc_final: 0.7921 (mm) REVERT: C 1230 MET cc_start: 0.8031 (ttt) cc_final: 0.7821 (ttm) REVERT: D 20 ILE cc_start: 0.6843 (tp) cc_final: 0.6217 (mt) REVERT: D 44 ILE cc_start: 0.7798 (tt) cc_final: 0.7095 (pt) REVERT: D 123 ARG cc_start: 0.7234 (mmt90) cc_final: 0.6447 (mmt180) REVERT: D 142 GLU cc_start: 0.8478 (pt0) cc_final: 0.8205 (pm20) REVERT: D 264 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6586 (t0) REVERT: D 326 SER cc_start: 0.8561 (p) cc_final: 0.7922 (p) REVERT: D 340 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5817 (mm-40) REVERT: D 695 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8150 (tppt) REVERT: D 1040 MET cc_start: 0.3071 (mtp) cc_final: 0.2443 (mmt) REVERT: D 1260 MET cc_start: 0.9099 (ptt) cc_final: 0.8834 (ptp) REVERT: D 1266 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8215 (pt) REVERT: D 1278 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7077 (mt-10) REVERT: M 21 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8880 (mt0) REVERT: M 27 GLN cc_start: 0.8897 (pt0) cc_final: 0.8382 (tp40) REVERT: M 28 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8464 (pt) REVERT: M 115 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8809 (mm-30) REVERT: M 157 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7930 (tm-30) REVERT: M 185 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: M 212 TRP cc_start: 0.8639 (m-90) cc_final: 0.8404 (m-90) REVERT: M 223 HIS cc_start: 0.8806 (m-70) cc_final: 0.8039 (m90) REVERT: M 306 MET cc_start: 0.7977 (mtp) cc_final: 0.7325 (mtm) REVERT: M 337 ASN cc_start: 0.8566 (m-40) cc_final: 0.8246 (m110) REVERT: M 401 TYR cc_start: 0.8725 (t80) cc_final: 0.8483 (t80) REVERT: M 403 PHE cc_start: 0.9263 (m-80) cc_final: 0.8993 (m-80) REVERT: M 441 LYS cc_start: 0.9472 (tptt) cc_final: 0.8173 (mtpt) outliers start: 202 outliers final: 65 residues processed: 1011 average time/residue: 0.2021 time to fit residues: 313.3312 Evaluate side-chains 546 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 469 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 237 ARG Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 336 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN B 132 HIS C 343 HIS C 462 ASN C 618 GLN C 628 HIS C 684 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 560 ASN D 651 HIS D 667 GLN D 680 ASN D 700 ASN D 702 GLN E 29 GLN E 31 GLN M 113 GLN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN M 352 GLN M 406 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.182637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140713 restraints weight = 49905.139| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.60 r_work: 0.3488 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29571 Z= 0.155 Angle : 0.680 12.676 40436 Z= 0.344 Chirality : 0.046 0.394 4767 Planarity : 0.005 0.064 5059 Dihedral : 15.211 179.024 4925 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.76 % Favored : 93.19 % Rotamer: Outliers : 5.35 % Allowed : 15.77 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.13), residues: 3655 helix: -0.10 (0.15), residues: 1259 sheet: -1.32 (0.30), residues: 285 loop : -2.53 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 371 TYR 0.027 0.002 TYR M 361 PHE 0.024 0.002 PHE C 38 TRP 0.010 0.001 TRP M 285 HIS 0.012 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (29571) covalent geometry : angle 0.67966 / 0.34 (40436) hydrogen bonds : bond 0.04268 / 2.92 ( 1053) hydrogen bonds : angle 4.66010 / 3.25 ( 2899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 471 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6974 (ptp90) REVERT: B 80 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8631 (mt-10) REVERT: B 132 HIS cc_start: 0.6595 (t70) cc_final: 0.6122 (t-170) REVERT: C 169 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6084 (mtmt) REVERT: C 187 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7338 (tt0) REVERT: C 201 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.8045 (mtp180) REVERT: C 378 ARG cc_start: 0.8334 (tpt90) cc_final: 0.7988 (tpt90) REVERT: C 396 ASP cc_start: 0.6705 (t70) cc_final: 0.6307 (t70) REVERT: C 488 MET cc_start: 0.8892 (mmm) cc_final: 0.8587 (mmp) REVERT: C 696 ASP cc_start: 0.8081 (t70) cc_final: 0.7538 (t0) REVERT: C 870 ILE cc_start: 0.8026 (pt) cc_final: 0.7612 (pt) REVERT: C 905 ILE cc_start: 0.8451 (mt) cc_final: 0.8132 (mm) REVERT: D 142 GLU cc_start: 0.8602 (pt0) cc_final: 0.8062 (pm20) REVERT: D 227 PHE cc_start: 0.7619 (t80) cc_final: 0.7340 (t80) REVERT: D 326 SER cc_start: 0.8860 (p) cc_final: 0.8553 (p) REVERT: D 339 ARG cc_start: 0.7090 (mmp80) cc_final: 0.6565 (tmm-80) REVERT: D 626 TYR cc_start: 0.8453 (m-10) cc_final: 0.7904 (m-10) REVERT: D 695 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8126 (tppt) REVERT: D 817 HIS cc_start: 0.8154 (m-70) cc_final: 0.7737 (m-70) REVERT: D 818 GLU cc_start: 0.7651 (tp30) cc_final: 0.7226 (tm-30) REVERT: D 821 MET cc_start: 0.8712 (tpp) cc_final: 0.8480 (tpt) REVERT: D 1040 MET cc_start: 0.4317 (mtp) cc_final: 0.3301 (mmt) REVERT: D 1247 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7088 (ptmt) REVERT: D 1266 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8342 (pt) REVERT: D 1278 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7526 (mt-10) REVERT: E 3 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.7084 (tpp-160) REVERT: M 27 GLN cc_start: 0.8402 (pt0) cc_final: 0.7565 (tp40) REVERT: M 108 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.4520 (mp0) REVERT: M 157 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: M 180 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8333 (mtpp) REVERT: M 185 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7440 (m-10) REVERT: M 376 MET cc_start: 0.8878 (mmm) cc_final: 0.8607 (mmm) REVERT: M 389 TYR cc_start: 0.7124 (m-80) cc_final: 0.6868 (m-10) REVERT: M 403 PHE cc_start: 0.8895 (m-80) cc_final: 0.8549 (m-80) outliers start: 150 outliers final: 77 residues processed: 584 average time/residue: 0.1886 time to fit residues: 174.5698 Evaluate side-chains 461 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 375 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 237 ARG Chi-restraints excluded: chain M residue 239 THR Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 359 GLU Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 281 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 341 optimal weight: 7.9990 chunk 318 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN C 219 GLN C 343 HIS C 613 ASN C 618 GLN C 799 ASN C 832 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 560 ASN D 651 HIS E 62 GLN M 21 GLN M 406 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.180535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.138521 restraints weight = 49631.110| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.54 r_work: 0.3439 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29571 Z= 0.127 Angle : 0.626 15.818 40436 Z= 0.314 Chirality : 0.044 0.389 4767 Planarity : 0.005 0.093 5059 Dihedral : 14.599 172.807 4841 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 4.64 % Allowed : 17.16 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 3655 helix: 0.32 (0.15), residues: 1259 sheet: -0.86 (0.32), residues: 268 loop : -2.33 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 211 TYR 0.020 0.001 TYR D 995 PHE 0.017 0.001 PHE C 38 TRP 0.007 0.001 TRP M 126 HIS 0.015 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (29571) covalent geometry : angle 0.62628 / 0.31 (40436) hydrogen bonds : bond 0.03655 / 2.48 ( 1053) hydrogen bonds : angle 4.30060 / 3.00 ( 2899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 393 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8396 (m-80) cc_final: 0.8192 (m-80) REVERT: A 148 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.6811 (ptp90) REVERT: B 80 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 160 ASP cc_start: 0.8124 (t70) cc_final: 0.7908 (t70) REVERT: C 169 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6053 (mtmt) REVERT: C 187 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7336 (tt0) REVERT: C 378 ARG cc_start: 0.8347 (tpt90) cc_final: 0.7987 (tpt90) REVERT: C 396 ASP cc_start: 0.6499 (t70) cc_final: 0.6237 (t70) REVERT: C 488 MET cc_start: 0.8915 (mmm) cc_final: 0.8595 (mmp) REVERT: C 696 ASP cc_start: 0.8161 (t70) cc_final: 0.7881 (t0) REVERT: C 905 ILE cc_start: 0.8439 (mt) cc_final: 0.8075 (mm) REVERT: C 960 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8548 (tm) REVERT: C 1038 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 122 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7976 (t) REVERT: D 227 PHE cc_start: 0.7752 (t80) cc_final: 0.7406 (t80) REVERT: D 229 GLN cc_start: 0.9003 (pp30) cc_final: 0.8802 (tm-30) REVERT: D 326 SER cc_start: 0.8971 (p) cc_final: 0.8670 (p) REVERT: D 695 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8147 (tppt) REVERT: D 702 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 811 GLU cc_start: 0.7784 (tp30) cc_final: 0.7335 (tp30) REVERT: D 818 GLU cc_start: 0.7770 (tp30) cc_final: 0.7343 (tm-30) REVERT: D 1040 MET cc_start: 0.4193 (mtp) cc_final: 0.3169 (mmt) REVERT: D 1247 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7191 (ptmt) REVERT: D 1266 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8394 (pt) REVERT: D 1278 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7490 (mt-10) REVERT: E 3 ARG cc_start: 0.7338 (tpp-160) cc_final: 0.7072 (tpp-160) REVERT: M 27 GLN cc_start: 0.8364 (pt0) cc_final: 0.7664 (tp40) REVERT: M 180 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8385 (mtpp) REVERT: M 181 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8516 (tpt170) REVERT: M 185 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: M 203 LEU cc_start: 0.9253 (mt) cc_final: 0.9004 (tt) REVERT: M 237 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.9045 (ttp80) REVERT: M 362 MET cc_start: 0.8026 (ttt) cc_final: 0.7624 (ttt) REVERT: M 376 MET cc_start: 0.8938 (mmm) cc_final: 0.8610 (mmm) REVERT: M 403 PHE cc_start: 0.8882 (m-80) cc_final: 0.8550 (m-80) outliers start: 130 outliers final: 74 residues processed: 490 average time/residue: 0.1755 time to fit residues: 137.9119 Evaluate side-chains 439 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 354 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 237 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 220 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 162 optimal weight: 0.6980 chunk 368 optimal weight: 50.0000 chunk 78 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 360 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 282 optimal weight: 40.0000 chunk 169 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS A 283 GLN B 132 HIS C1244 HIS C1288 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D1238 GLN E 62 GLN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 406 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.173818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115228 restraints weight = 48877.606| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.96 r_work: 0.3318 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29571 Z= 0.193 Angle : 0.672 13.997 40436 Z= 0.340 Chirality : 0.046 0.390 4767 Planarity : 0.005 0.093 5059 Dihedral : 14.589 170.351 4821 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 4.85 % Allowed : 18.02 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3655 helix: 0.47 (0.15), residues: 1254 sheet: -0.74 (0.33), residues: 277 loop : -2.25 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 478 TYR 0.017 0.002 TYR C 92 PHE 0.027 0.002 PHE C 15 TRP 0.015 0.001 TRP C1276 HIS 0.024 0.002 HIS M 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (29571) covalent geometry : angle 0.67223 / 0.34 (40436) hydrogen bonds : bond 0.03948 / 2.67 ( 1053) hydrogen bonds : angle 4.24467 / 2.95 ( 2899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 394 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8334 (mtmm) REVERT: A 54 CYS cc_start: 0.8774 (m) cc_final: 0.8537 (m) REVERT: A 148 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7120 (ptp90) REVERT: A 283 GLN cc_start: 0.8742 (mt0) cc_final: 0.8427 (mt0) REVERT: B 80 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 99 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9083 (mt) REVERT: C 69 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: C 70 TYR cc_start: 0.6398 (p90) cc_final: 0.6104 (p90) REVERT: C 160 ASP cc_start: 0.8216 (t70) cc_final: 0.7925 (t70) REVERT: C 169 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6120 (mtmt) REVERT: C 187 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 396 ASP cc_start: 0.6596 (t70) cc_final: 0.6308 (t70) REVERT: C 488 MET cc_start: 0.8970 (mmm) cc_final: 0.8716 (mmp) REVERT: C 696 ASP cc_start: 0.8481 (t70) cc_final: 0.8257 (t0) REVERT: C 959 ASP cc_start: 0.7730 (t0) cc_final: 0.7406 (t0) REVERT: C 960 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8721 (tm) REVERT: D 102 MET cc_start: 0.9154 (mtp) cc_final: 0.8892 (mtm) REVERT: D 142 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: D 229 GLN cc_start: 0.9189 (pp30) cc_final: 0.8971 (tm-30) REVERT: D 326 SER cc_start: 0.9322 (p) cc_final: 0.9030 (p) REVERT: D 339 ARG cc_start: 0.7312 (mmp80) cc_final: 0.6617 (tmm160) REVERT: D 361 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9130 (mt) REVERT: D 695 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8206 (tmmm) REVERT: D 702 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 811 GLU cc_start: 0.7989 (tp30) cc_final: 0.7486 (tp30) REVERT: D 817 HIS cc_start: 0.8241 (m-70) cc_final: 0.7771 (m-70) REVERT: D 818 GLU cc_start: 0.7942 (tp30) cc_final: 0.7337 (tm-30) REVERT: D 821 MET cc_start: 0.8771 (tpp) cc_final: 0.8502 (tpt) REVERT: D 1040 MET cc_start: 0.4472 (mtp) cc_final: 0.3234 (mmt) REVERT: D 1247 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7583 (ptmt) REVERT: D 1266 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8495 (pt) REVERT: D 1278 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7596 (mt-10) REVERT: M 27 GLN cc_start: 0.8516 (pt0) cc_final: 0.7991 (tp40) REVERT: M 176 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: M 185 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7238 (m-10) REVERT: M 203 LEU cc_start: 0.9240 (mt) cc_final: 0.9016 (tt) REVERT: M 362 MET cc_start: 0.8388 (ttt) cc_final: 0.7981 (ttt) REVERT: M 365 MET cc_start: 0.6185 (ptt) cc_final: 0.5944 (ptt) REVERT: M 376 MET cc_start: 0.8998 (mmm) cc_final: 0.8606 (mmm) REVERT: M 389 TYR cc_start: 0.7098 (m-80) cc_final: 0.6785 (m-10) REVERT: M 446 LEU cc_start: 0.9649 (tp) cc_final: 0.9349 (tt) REVERT: M 461 TYR cc_start: 0.8969 (m-80) cc_final: 0.8758 (m-80) outliers start: 136 outliers final: 80 residues processed: 499 average time/residue: 0.1822 time to fit residues: 146.2010 Evaluate side-chains 439 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 347 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1013 GLN Chi-restraints excluded: chain C residue 1210 ILE Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 290 optimal weight: 9.9990 chunk 320 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.0770 chunk 222 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 651 HIS D 720 ASN E 62 GLN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.175692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117947 restraints weight = 48855.029| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.98 r_work: 0.3356 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29571 Z= 0.113 Angle : 0.604 14.362 40436 Z= 0.301 Chirality : 0.043 0.386 4767 Planarity : 0.004 0.060 5059 Dihedral : 14.451 170.273 4803 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 4.17 % Allowed : 18.87 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3655 helix: 0.71 (0.15), residues: 1253 sheet: -0.54 (0.33), residues: 274 loop : -2.11 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 166 TYR 0.025 0.001 TYR D 995 PHE 0.021 0.001 PHE M 354 TRP 0.039 0.002 TRP M 285 HIS 0.004 0.001 HIS M 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (29571) covalent geometry : angle 0.60368 / 0.30 (40436) hydrogen bonds : bond 0.03321 / 2.25 ( 1053) hydrogen bonds : angle 4.08843 / 2.83 ( 2899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 378 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8367 (t0) cc_final: 0.8161 (t0) REVERT: A 148 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.6935 (ptp90) REVERT: A 283 GLN cc_start: 0.8511 (mt0) cc_final: 0.8128 (mt0) REVERT: B 80 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8062 (mt-10) REVERT: B 99 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9065 (mt) REVERT: C 59 ILE cc_start: 0.5874 (tt) cc_final: 0.5583 (tt) REVERT: C 160 ASP cc_start: 0.8116 (t70) cc_final: 0.7749 (t70) REVERT: C 169 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6114 (mtmt) REVERT: C 187 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7425 (mt-10) REVERT: C 396 ASP cc_start: 0.6334 (t70) cc_final: 0.6060 (t70) REVERT: C 476 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7932 (tppt) REVERT: C 488 MET cc_start: 0.8921 (mmm) cc_final: 0.8674 (mmp) REVERT: C 766 ASN cc_start: 0.8530 (t0) cc_final: 0.8183 (t0) REVERT: C 903 ARG cc_start: 0.8544 (tpt170) cc_final: 0.7757 (tpm170) REVERT: C 959 ASP cc_start: 0.7535 (t0) cc_final: 0.7283 (t0) REVERT: D 17 PHE cc_start: 0.7655 (t80) cc_final: 0.7445 (t80) REVERT: D 102 MET cc_start: 0.9092 (mtp) cc_final: 0.8875 (mtm) REVERT: D 142 GLU cc_start: 0.8575 (pt0) cc_final: 0.8242 (pm20) REVERT: D 229 GLN cc_start: 0.9081 (pp30) cc_final: 0.8856 (tm-30) REVERT: D 326 SER cc_start: 0.9074 (p) cc_final: 0.8850 (p) REVERT: D 339 ARG cc_start: 0.7125 (mmp80) cc_final: 0.6549 (tmm-80) REVERT: D 466 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8628 (mmm) REVERT: D 695 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8147 (tmmm) REVERT: D 702 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7703 (tm-30) REVERT: D 811 GLU cc_start: 0.7672 (tp30) cc_final: 0.7225 (tp30) REVERT: D 817 HIS cc_start: 0.8127 (m-70) cc_final: 0.7698 (m-70) REVERT: D 818 GLU cc_start: 0.7749 (tp30) cc_final: 0.7488 (tp30) REVERT: D 821 MET cc_start: 0.8710 (tpp) cc_final: 0.8509 (tpt) REVERT: D 1040 MET cc_start: 0.4312 (mtp) cc_final: 0.3535 (mmt) REVERT: D 1247 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7465 (ptmt) REVERT: D 1266 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8460 (pt) REVERT: D 1278 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7471 (mt-10) REVERT: D 1292 LEU cc_start: 0.8459 (mm) cc_final: 0.8233 (tt) REVERT: E 62 GLN cc_start: 0.8480 (tp40) cc_final: 0.8262 (tp-100) REVERT: M 27 GLN cc_start: 0.8486 (pt0) cc_final: 0.7998 (tp40) REVERT: M 32 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: M 176 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: M 185 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: M 203 LEU cc_start: 0.9181 (mt) cc_final: 0.8938 (tt) REVERT: M 288 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: M 318 PHE cc_start: 0.8727 (t80) cc_final: 0.8401 (t80) REVERT: M 361 TYR cc_start: 0.9085 (m-80) cc_final: 0.8704 (m-10) REVERT: M 376 MET cc_start: 0.8926 (mmm) cc_final: 0.8538 (mmm) REVERT: M 446 LEU cc_start: 0.9632 (tp) cc_final: 0.9339 (tt) REVERT: M 461 TYR cc_start: 0.8996 (m-80) cc_final: 0.8643 (m-80) outliers start: 117 outliers final: 70 residues processed: 473 average time/residue: 0.1913 time to fit residues: 145.6971 Evaluate side-chains 433 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1013 GLN Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 250 optimal weight: 0.7980 chunk 177 optimal weight: 0.0980 chunk 310 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 123 optimal weight: 0.0010 chunk 317 optimal weight: 3.9990 chunk 244 optimal weight: 0.0270 chunk 205 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 overall best weight: 0.7846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 651 HIS ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.175115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118381 restraints weight = 48704.750| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.37 r_work: 0.3356 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29571 Z= 0.112 Angle : 0.595 14.285 40436 Z= 0.296 Chirality : 0.043 0.386 4767 Planarity : 0.004 0.060 5059 Dihedral : 14.378 169.602 4797 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 4.07 % Allowed : 19.09 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3655 helix: 0.88 (0.15), residues: 1251 sheet: -0.33 (0.33), residues: 275 loop : -2.07 (0.12), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.012 0.001 TYR D 995 PHE 0.015 0.001 PHE C 38 TRP 0.022 0.001 TRP M 285 HIS 0.007 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (29571) covalent geometry : angle 0.59506 / 0.30 (40436) hydrogen bonds : bond 0.03205 / 2.17 ( 1053) hydrogen bonds : angle 4.00599 / 2.78 ( 2899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 372 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8570 (t0) cc_final: 0.8345 (t0) REVERT: A 148 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7001 (ptp90) REVERT: A 283 GLN cc_start: 0.8380 (mt0) cc_final: 0.8020 (mt0) REVERT: B 80 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 99 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9060 (mt) REVERT: C 39 ILE cc_start: 0.8164 (tp) cc_final: 0.7939 (tp) REVERT: C 160 ASP cc_start: 0.8237 (t70) cc_final: 0.7860 (t70) REVERT: C 169 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6024 (mtmt) REVERT: C 187 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 396 ASP cc_start: 0.6494 (t70) cc_final: 0.6216 (t70) REVERT: C 476 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7840 (tppt) REVERT: C 488 MET cc_start: 0.8957 (mmm) cc_final: 0.8708 (mmp) REVERT: C 766 ASN cc_start: 0.8783 (t0) cc_final: 0.8464 (t0) REVERT: C 903 ARG cc_start: 0.8567 (tpt170) cc_final: 0.7897 (tpm170) REVERT: C 959 ASP cc_start: 0.7763 (t0) cc_final: 0.7399 (t0) REVERT: D 102 MET cc_start: 0.9116 (mtp) cc_final: 0.8849 (mtm) REVERT: D 142 GLU cc_start: 0.8662 (pt0) cc_final: 0.8264 (pm20) REVERT: D 229 GLN cc_start: 0.9227 (pp30) cc_final: 0.9008 (tm-30) REVERT: D 326 SER cc_start: 0.9189 (p) cc_final: 0.8982 (p) REVERT: D 339 ARG cc_start: 0.7264 (mmp80) cc_final: 0.6555 (tmm-80) REVERT: D 695 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7833 (tmmm) REVERT: D 702 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7777 (tm-30) REVERT: D 747 MET cc_start: 0.7219 (tpp) cc_final: 0.6937 (tpp) REVERT: D 811 GLU cc_start: 0.8000 (tp30) cc_final: 0.7505 (tp30) REVERT: D 817 HIS cc_start: 0.8223 (m-70) cc_final: 0.7746 (m-70) REVERT: D 818 GLU cc_start: 0.7995 (tp30) cc_final: 0.7705 (tp30) REVERT: D 897 HIS cc_start: 0.8239 (m90) cc_final: 0.7832 (m170) REVERT: D 1040 MET cc_start: 0.4593 (mtp) cc_final: 0.3704 (mmt) REVERT: D 1247 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7553 (ptmt) REVERT: D 1278 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7597 (mt-10) REVERT: D 1292 LEU cc_start: 0.8559 (mm) cc_final: 0.8257 (tt) REVERT: E 3 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7254 (tpt170) REVERT: M 27 GLN cc_start: 0.8508 (pt0) cc_final: 0.8039 (tp40) REVERT: M 32 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: M 176 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: M 185 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: M 202 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8803 (mt0) REVERT: M 203 LEU cc_start: 0.9154 (mt) cc_final: 0.8903 (tt) REVERT: M 362 MET cc_start: 0.8273 (ttt) cc_final: 0.7985 (ttt) REVERT: M 376 MET cc_start: 0.8930 (mmm) cc_final: 0.8507 (mmm) REVERT: M 402 PHE cc_start: 0.8992 (m-10) cc_final: 0.8710 (m-10) REVERT: M 446 LEU cc_start: 0.9631 (tp) cc_final: 0.9324 (tt) REVERT: M 461 TYR cc_start: 0.9008 (m-80) cc_final: 0.8700 (m-80) outliers start: 114 outliers final: 75 residues processed: 459 average time/residue: 0.1908 time to fit residues: 140.7022 Evaluate side-chains 428 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 344 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1210 ILE Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 194 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 151 optimal weight: 0.0370 chunk 112 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 360 optimal weight: 30.0000 chunk 319 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 322 optimal weight: 0.3980 chunk 253 optimal weight: 1.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 651 HIS E 62 GLN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.173901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116416 restraints weight = 48564.333| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.15 r_work: 0.3323 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29571 Z= 0.138 Angle : 0.620 14.272 40436 Z= 0.309 Chirality : 0.044 0.383 4767 Planarity : 0.004 0.063 5059 Dihedral : 14.359 169.170 4791 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.83 % Rotamer: Outliers : 3.92 % Allowed : 19.62 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3655 helix: 0.92 (0.15), residues: 1251 sheet: -0.35 (0.33), residues: 277 loop : -2.03 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1372 TYR 0.016 0.001 TYR C 172 PHE 0.014 0.001 PHE C 38 TRP 0.017 0.001 TRP M 285 HIS 0.005 0.001 HIS D1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (29571) covalent geometry : angle 0.62029 / 0.31 (40436) hydrogen bonds : bond 0.03360 / 2.27 ( 1053) hydrogen bonds : angle 4.02847 / 2.80 ( 2899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 358 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8541 (t0) cc_final: 0.8296 (t0) REVERT: A 54 CYS cc_start: 0.8794 (m) cc_final: 0.8465 (m) REVERT: A 148 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7183 (ptp90) REVERT: A 283 GLN cc_start: 0.8274 (mt0) cc_final: 0.7968 (mt0) REVERT: B 80 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8560 (mm-30) REVERT: B 99 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9078 (mt) REVERT: C 39 ILE cc_start: 0.8252 (tp) cc_final: 0.7963 (tp) REVERT: C 59 ILE cc_start: 0.5690 (tt) cc_final: 0.5267 (tt) REVERT: C 160 ASP cc_start: 0.8269 (t70) cc_final: 0.7883 (t70) REVERT: C 187 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 396 ASP cc_start: 0.6539 (t70) cc_final: 0.6246 (t70) REVERT: C 476 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7852 (tppt) REVERT: C 488 MET cc_start: 0.8955 (mmm) cc_final: 0.8694 (mmp) REVERT: C 959 ASP cc_start: 0.7736 (t0) cc_final: 0.7413 (t0) REVERT: C 960 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8740 (tm) REVERT: D 102 MET cc_start: 0.9140 (mtp) cc_final: 0.8876 (mtm) REVERT: D 142 GLU cc_start: 0.8677 (pt0) cc_final: 0.8269 (pm20) REVERT: D 196 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8978 (tm-30) REVERT: D 217 LEU cc_start: 0.5882 (pp) cc_final: 0.5591 (pp) REVERT: D 229 GLN cc_start: 0.9191 (pp30) cc_final: 0.8971 (tm-30) REVERT: D 339 ARG cc_start: 0.7480 (mmp80) cc_final: 0.6647 (tmm160) REVERT: D 422 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8956 (pp) REVERT: D 695 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8170 (tmmm) REVERT: D 702 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 707 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5150 (mm) REVERT: D 712 GLN cc_start: 0.7807 (mp10) cc_final: 0.7450 (tp-100) REVERT: D 811 GLU cc_start: 0.8028 (tp30) cc_final: 0.7528 (tp30) REVERT: D 817 HIS cc_start: 0.8228 (m-70) cc_final: 0.7741 (m-70) REVERT: D 818 GLU cc_start: 0.8006 (tp30) cc_final: 0.7670 (tp30) REVERT: D 821 MET cc_start: 0.8715 (tpp) cc_final: 0.8356 (tpt) REVERT: D 897 HIS cc_start: 0.8374 (m90) cc_final: 0.8061 (m170) REVERT: D 1040 MET cc_start: 0.4561 (mtp) cc_final: 0.3689 (mmt) REVERT: D 1278 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7594 (mt-10) REVERT: D 1292 LEU cc_start: 0.8581 (mm) cc_final: 0.8265 (tt) REVERT: E 3 ARG cc_start: 0.7878 (tpp-160) cc_final: 0.7337 (tpt170) REVERT: M 27 GLN cc_start: 0.8521 (pt0) cc_final: 0.8054 (tp40) REVERT: M 32 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: M 176 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8251 (tp30) REVERT: M 185 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: M 202 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8780 (mt0) REVERT: M 203 LEU cc_start: 0.9150 (mt) cc_final: 0.8882 (tt) REVERT: M 288 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: M 361 TYR cc_start: 0.9129 (m-80) cc_final: 0.8788 (m-10) REVERT: M 362 MET cc_start: 0.8124 (ttt) cc_final: 0.7922 (ttt) REVERT: M 376 MET cc_start: 0.8981 (mmm) cc_final: 0.8635 (mmm) REVERT: M 446 LEU cc_start: 0.9626 (tp) cc_final: 0.9324 (tt) REVERT: M 461 TYR cc_start: 0.9019 (m-80) cc_final: 0.8683 (m-80) outliers start: 110 outliers final: 88 residues processed: 445 average time/residue: 0.1887 time to fit residues: 135.8816 Evaluate side-chains 445 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 346 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1210 ILE Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 156 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 182 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 437 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 720 ASN E 62 GLN M 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.168617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111163 restraints weight = 48476.127| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.07 r_work: 0.3235 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29571 Z= 0.179 Angle : 0.665 13.758 40436 Z= 0.334 Chirality : 0.045 0.381 4767 Planarity : 0.005 0.060 5059 Dihedral : 14.408 168.505 4784 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.18 % Rotamer: Outliers : 4.53 % Allowed : 19.27 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3655 helix: 0.86 (0.15), residues: 1257 sheet: -0.39 (0.32), residues: 287 loop : -2.05 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 166 TYR 0.025 0.002 TYR D 995 PHE 0.022 0.002 PHE M 318 TRP 0.016 0.001 TRP M 285 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (29571) covalent geometry : angle 0.66471 / 0.33 (40436) hydrogen bonds : bond 0.03790 / 2.53 ( 1053) hydrogen bonds : angle 4.10459 / 2.85 ( 2899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 361 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8611 (t0) cc_final: 0.8374 (t0) REVERT: A 54 CYS cc_start: 0.8782 (m) cc_final: 0.8420 (m) REVERT: A 148 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7259 (ptp90) REVERT: A 283 GLN cc_start: 0.8243 (mt0) cc_final: 0.7883 (mt0) REVERT: B 80 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8545 (mm-30) REVERT: B 99 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9110 (mt) REVERT: C 39 ILE cc_start: 0.8372 (tp) cc_final: 0.7967 (tp) REVERT: C 59 ILE cc_start: 0.5913 (tt) cc_final: 0.5511 (tt) REVERT: C 160 ASP cc_start: 0.8282 (t70) cc_final: 0.7882 (t70) REVERT: C 187 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7581 (mt-10) REVERT: C 396 ASP cc_start: 0.6688 (t70) cc_final: 0.6397 (t70) REVERT: C 476 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7869 (tppt) REVERT: C 488 MET cc_start: 0.8962 (mmm) cc_final: 0.8630 (mmp) REVERT: C 903 ARG cc_start: 0.8580 (tpt170) cc_final: 0.7535 (tpm170) REVERT: C 959 ASP cc_start: 0.7826 (t0) cc_final: 0.7445 (t0) REVERT: C 960 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8581 (tm) REVERT: D 196 GLN cc_start: 0.9270 (tm-30) cc_final: 0.9010 (tm-30) REVERT: D 314 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7064 (ptt90) REVERT: D 339 ARG cc_start: 0.7593 (mmp80) cc_final: 0.6615 (tmm160) REVERT: D 422 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8880 (pp) REVERT: D 626 TYR cc_start: 0.8553 (m-10) cc_final: 0.8298 (m-80) REVERT: D 695 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8252 (tmmm) REVERT: D 702 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 707 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.5509 (mm) REVERT: D 811 GLU cc_start: 0.8146 (tp30) cc_final: 0.7633 (tp30) REVERT: D 817 HIS cc_start: 0.8225 (m-70) cc_final: 0.7755 (m-70) REVERT: D 818 GLU cc_start: 0.8044 (tp30) cc_final: 0.7825 (tp30) REVERT: D 821 MET cc_start: 0.8656 (tpp) cc_final: 0.8343 (tpt) REVERT: D 1263 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6226 (tmtt) REVERT: D 1278 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7618 (mt-10) REVERT: D 1292 LEU cc_start: 0.8678 (mm) cc_final: 0.8329 (tt) REVERT: E 3 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7383 (tpt170) REVERT: M 27 GLN cc_start: 0.8601 (pt0) cc_final: 0.8189 (tp40) REVERT: M 32 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: M 176 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: M 185 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: M 203 LEU cc_start: 0.9147 (mt) cc_final: 0.8901 (tt) REVERT: M 361 TYR cc_start: 0.9167 (m-80) cc_final: 0.8807 (m-10) REVERT: M 376 MET cc_start: 0.8989 (mmm) cc_final: 0.8652 (mmm) REVERT: M 461 TYR cc_start: 0.9021 (m-80) cc_final: 0.8669 (m-80) outliers start: 127 outliers final: 90 residues processed: 458 average time/residue: 0.1876 time to fit residues: 137.5110 Evaluate side-chains 447 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 347 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1210 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 50 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 54 optimal weight: 2.9990 chunk 298 optimal weight: 50.0000 chunk 213 optimal weight: 7.9990 chunk 353 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 50.0000 chunk 303 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 651 HIS D 897 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.167811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110401 restraints weight = 48124.133| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.10 r_work: 0.3213 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29571 Z= 0.173 Angle : 0.659 14.120 40436 Z= 0.330 Chirality : 0.045 0.381 4767 Planarity : 0.005 0.059 5059 Dihedral : 14.380 168.116 4782 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.34 % Rotamer: Outliers : 3.92 % Allowed : 19.98 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3655 helix: 0.84 (0.15), residues: 1258 sheet: -0.53 (0.31), residues: 298 loop : -2.03 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1269 TYR 0.014 0.001 TYR D 723 PHE 0.020 0.001 PHE M 318 TRP 0.017 0.001 TRP M 285 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (29571) covalent geometry : angle 0.65880 / 0.33 (40436) hydrogen bonds : bond 0.03755 / 2.53 ( 1053) hydrogen bonds : angle 4.13883 / 2.88 ( 2899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 351 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8614 (mtmm) cc_final: 0.7996 (mtpt) REVERT: A 51 MET cc_start: 0.8354 (tpp) cc_final: 0.8151 (mmm) REVERT: A 54 CYS cc_start: 0.8533 (m) cc_final: 0.8206 (m) REVERT: A 148 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7199 (ptp90) REVERT: A 283 GLN cc_start: 0.8244 (mt0) cc_final: 0.7908 (mt0) REVERT: B 80 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8451 (mm-30) REVERT: B 99 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9120 (mt) REVERT: C 39 ILE cc_start: 0.8360 (tp) cc_final: 0.7929 (tp) REVERT: C 59 ILE cc_start: 0.5908 (tt) cc_final: 0.5525 (tt) REVERT: C 160 ASP cc_start: 0.8178 (t70) cc_final: 0.7785 (t70) REVERT: C 187 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 396 ASP cc_start: 0.6790 (t70) cc_final: 0.6559 (t70) REVERT: C 476 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7944 (tppt) REVERT: C 488 MET cc_start: 0.8935 (mmm) cc_final: 0.8672 (mmp) REVERT: C 694 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6733 (mtt180) REVERT: C 959 ASP cc_start: 0.7645 (t0) cc_final: 0.7323 (t0) REVERT: C 960 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8575 (tm) REVERT: D 196 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8936 (tm-30) REVERT: D 314 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7006 (ptt90) REVERT: D 339 ARG cc_start: 0.7096 (mmp80) cc_final: 0.6542 (tmm160) REVERT: D 422 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8807 (pp) REVERT: D 626 TYR cc_start: 0.8477 (m-10) cc_final: 0.8264 (m-80) REVERT: D 695 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8301 (tmmm) REVERT: D 702 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 707 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.5582 (mm) REVERT: D 811 GLU cc_start: 0.7898 (tp30) cc_final: 0.7461 (tp30) REVERT: D 817 HIS cc_start: 0.8149 (m-70) cc_final: 0.7697 (m-70) REVERT: D 818 GLU cc_start: 0.8074 (tp30) cc_final: 0.7735 (tp30) REVERT: D 1040 MET cc_start: 0.4880 (mmm) cc_final: 0.3662 (mmt) REVERT: D 1263 LYS cc_start: 0.7258 (mmmt) cc_final: 0.6299 (tmtt) REVERT: D 1278 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7529 (mt-10) REVERT: D 1292 LEU cc_start: 0.8561 (mm) cc_final: 0.8272 (tt) REVERT: M 27 GLN cc_start: 0.8590 (pt0) cc_final: 0.8176 (tp40) REVERT: M 32 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: M 176 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8239 (tp30) REVERT: M 185 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6461 (m-80) REVERT: M 202 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8720 (mt0) REVERT: M 203 LEU cc_start: 0.9134 (mt) cc_final: 0.8890 (tt) REVERT: M 362 MET cc_start: 0.8177 (ttt) cc_final: 0.7867 (ttt) REVERT: M 376 MET cc_start: 0.8988 (mmm) cc_final: 0.8523 (mmm) REVERT: M 461 TYR cc_start: 0.9001 (m-80) cc_final: 0.8683 (m-80) outliers start: 110 outliers final: 89 residues processed: 436 average time/residue: 0.1889 time to fit residues: 130.7794 Evaluate side-chains 439 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 339 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 204 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 85 optimal weight: 40.0000 chunk 360 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.168244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110938 restraints weight = 47994.830| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.12 r_work: 0.3223 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29571 Z= 0.145 Angle : 0.663 14.593 40436 Z= 0.330 Chirality : 0.044 0.380 4767 Planarity : 0.005 0.059 5059 Dihedral : 14.338 167.651 4781 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.48 % Rotamer: Outliers : 3.53 % Allowed : 20.76 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3655 helix: 0.93 (0.15), residues: 1256 sheet: -0.55 (0.32), residues: 286 loop : -1.98 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1269 TYR 0.012 0.001 TYR D 723 PHE 0.028 0.001 PHE M 397 TRP 0.017 0.001 TRP M 285 HIS 0.004 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (29571) covalent geometry : angle 0.66331 / 0.33 (40436) hydrogen bonds : bond 0.03618 / 2.43 ( 1053) hydrogen bonds : angle 4.11875 / 2.88 ( 2899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 347 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8010 (mtpt) REVERT: A 54 CYS cc_start: 0.8535 (m) cc_final: 0.8165 (m) REVERT: A 148 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7216 (ptp90) REVERT: A 283 GLN cc_start: 0.8182 (mt0) cc_final: 0.7845 (mt0) REVERT: B 80 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8432 (mm-30) REVERT: B 99 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9119 (mt) REVERT: C 39 ILE cc_start: 0.8336 (tp) cc_final: 0.7889 (tp) REVERT: C 59 ILE cc_start: 0.5853 (tt) cc_final: 0.5457 (tt) REVERT: C 160 ASP cc_start: 0.8231 (t70) cc_final: 0.7824 (t70) REVERT: C 187 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 396 ASP cc_start: 0.6769 (t70) cc_final: 0.6539 (t70) REVERT: C 476 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7949 (tppt) REVERT: C 488 MET cc_start: 0.8939 (mmm) cc_final: 0.8668 (mmp) REVERT: C 545 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6950 (t80) REVERT: C 694 ARG cc_start: 0.7451 (mtp180) cc_final: 0.6753 (mtt180) REVERT: C 903 ARG cc_start: 0.8548 (tpt170) cc_final: 0.7517 (tpm170) REVERT: C 959 ASP cc_start: 0.7632 (t0) cc_final: 0.7295 (t0) REVERT: C 960 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8567 (tm) REVERT: C 1170 MET cc_start: 0.8823 (mmm) cc_final: 0.8445 (tpp) REVERT: D 196 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8949 (tm-30) REVERT: D 314 ARG cc_start: 0.7293 (ptt90) cc_final: 0.7059 (ptt90) REVERT: D 339 ARG cc_start: 0.7141 (mmp80) cc_final: 0.6571 (tmm160) REVERT: D 626 TYR cc_start: 0.8464 (m-10) cc_final: 0.8053 (m-10) REVERT: D 695 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8294 (tmmm) REVERT: D 702 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 707 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.5473 (mm) REVERT: D 712 GLN cc_start: 0.7516 (mp10) cc_final: 0.7129 (tp-100) REVERT: D 811 GLU cc_start: 0.7957 (tp30) cc_final: 0.7503 (tp30) REVERT: D 817 HIS cc_start: 0.8133 (m-70) cc_final: 0.7677 (m-70) REVERT: D 818 GLU cc_start: 0.8000 (tp30) cc_final: 0.7677 (tp30) REVERT: D 1040 MET cc_start: 0.4748 (mmm) cc_final: 0.3638 (mmt) REVERT: D 1263 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6289 (tmtt) REVERT: D 1278 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7539 (mt-10) REVERT: D 1292 LEU cc_start: 0.8545 (mm) cc_final: 0.8257 (tt) REVERT: M 27 GLN cc_start: 0.8573 (pt0) cc_final: 0.8172 (tp40) REVERT: M 32 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: M 176 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: M 185 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: M 202 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8720 (mt0) REVERT: M 203 LEU cc_start: 0.9170 (mt) cc_final: 0.8907 (tt) REVERT: M 362 MET cc_start: 0.8016 (ttt) cc_final: 0.7778 (ttt) REVERT: M 376 MET cc_start: 0.8976 (mmm) cc_final: 0.8466 (mmm) REVERT: M 461 TYR cc_start: 0.8997 (m-80) cc_final: 0.8630 (m-80) outliers start: 99 outliers final: 82 residues processed: 426 average time/residue: 0.1889 time to fit residues: 127.7670 Evaluate side-chains 435 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 343 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 311 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 308 optimal weight: 0.0570 chunk 242 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 371 optimal weight: 50.0000 chunk 221 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 720 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.168817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111144 restraints weight = 48413.982| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.04 r_work: 0.3237 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29571 Z= 0.128 Angle : 0.644 14.302 40436 Z= 0.321 Chirality : 0.044 0.378 4767 Planarity : 0.005 0.063 5059 Dihedral : 14.299 167.106 4781 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.59 % Rotamer: Outliers : 3.39 % Allowed : 21.01 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.14), residues: 3655 helix: 0.96 (0.15), residues: 1272 sheet: -0.59 (0.33), residues: 278 loop : -1.98 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 371 TYR 0.020 0.001 TYR D 995 PHE 0.023 0.001 PHE M 318 TRP 0.016 0.001 TRP M 285 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (29571) covalent geometry : angle 0.64418 / 0.32 (40436) hydrogen bonds : bond 0.03398 / 2.28 ( 1053) hydrogen bonds : angle 4.08551 / 2.85 ( 2899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9173.95 seconds wall clock time: 156 minutes 41.75 seconds (9401.75 seconds total)