Starting phenix.real_space_refine on Mon Mar 18 13:19:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we7_37473/03_2024/8we7_37473_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we7_37473/03_2024/8we7_37473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we7_37473/03_2024/8we7_37473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we7_37473/03_2024/8we7_37473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we7_37473/03_2024/8we7_37473_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we7_37473/03_2024/8we7_37473_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.098 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 Ca 2 9.91 5 S 114 5.16 5 C 13548 2.51 5 N 3488 2.21 5 O 3862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 160": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "A PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A TYR 1243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1553": "OD1" <-> "OD2" Residue "A GLU 1631": "OE1" <-> "OE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 984": "OD1" <-> "OD2" Residue "D ASP 995": "OD1" <-> "OD2" Residue "D ASP 1070": "OD1" <-> "OD2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21014 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1251, 10101 Classifications: {'peptide': 1251} Link IDs: {'PTRANS': 39, 'TRANS': 1211} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "B" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 56} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.84, per 1000 atoms: 0.52 Number of scatterers: 21014 At special positions: 0 Unit cell: (168.214, 177.126, 188.266, 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) Ca 2 19.99 S 114 16.00 O 3862 8.00 N 3488 7.00 C 13548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG G 3 " - " NAG G 4 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2304 " - " ASN A1436 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 184 " " NAG F 1 " - " ASN D 348 " " NAG G 1 " - " ASN D 468 " " NAG H 1 " - " ASN D 613 " " NAG I 1 " - " ASN D 895 " Time building additional restraints: 7.96 Conformation dependent library (CDL) restraints added in 4.1 seconds 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 17 sheets defined 44.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 181 removed outlier: 3.558A pdb=" N GLU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 216 Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 239 through 250 Proline residue: A 244 - end of helix removed outlier: 4.105A pdb=" N GLY A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 removed outlier: 5.104A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.350A pdb=" N VAL A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.808A pdb=" N ALA A 375 " --> pdb=" O TRP A 371 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 397 through 416 removed outlier: 3.572A pdb=" N LEU A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 3.851A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 521 removed outlier: 3.630A pdb=" N ALA A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 542 removed outlier: 3.627A pdb=" N PHE A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 578 removed outlier: 4.154A pdb=" N ASN A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 587 through 601 Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 625 through 630 removed outlier: 4.081A pdb=" N ILE A 630 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 removed outlier: 5.041A pdb=" N ASN A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 672 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 708 through 718 removed outlier: 3.582A pdb=" N MET A 712 " --> pdb=" O TRP A 708 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 748 removed outlier: 3.740A pdb=" N VAL A 729 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS A 730 " --> pdb=" O MET A 727 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 739 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 748 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 766 Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.848A pdb=" N GLU A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 776 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 removed outlier: 4.138A pdb=" N PHE A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 No H-bonds generated for 'chain 'A' and resid 929 through 952' Processing helix chain 'A' and resid 959 through 974 removed outlier: 3.934A pdb=" N ILE A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 973 " --> pdb=" O ILE A 969 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1003 removed outlier: 3.521A pdb=" N LEU A 992 " --> pdb=" O TYR A 988 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A1000 " --> pdb=" O VAL A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1017 No H-bonds generated for 'chain 'A' and resid 1014 through 1017' Processing helix chain 'A' and resid 1019 through 1029 removed outlier: 3.774A pdb=" N LEU A1023 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1024 " --> pdb=" O ARG A1021 " (cutoff:3.500A) Proline residue: A1025 - end of helix Processing helix chain 'A' and resid 1035 through 1068 removed outlier: 5.277A pdb=" N ASN A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE A1052 " --> pdb=" O THR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1121 through 1132 Processing helix chain 'A' and resid 1137 through 1144 Processing helix chain 'A' and resid 1161 through 1172 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.666A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1196 No H-bonds generated for 'chain 'A' and resid 1194 through 1196' Processing helix chain 'A' and resid 1206 through 1214 Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1241 through 1258 removed outlier: 3.547A pdb=" N ILE A1249 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1292 removed outlier: 3.699A pdb=" N ILE A1269 " --> pdb=" O CYS A1265 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A1291 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1292 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1299 removed outlier: 4.617A pdb=" N PHE A1299 " --> pdb=" O PRO A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1321 removed outlier: 4.066A pdb=" N ILE A1316 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP A1317 " --> pdb=" O GLY A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1389 removed outlier: 4.210A pdb=" N LEU A1378 " --> pdb=" O THR A1374 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A1379 " --> pdb=" O PHE A1375 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A1382 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1407 Processing helix chain 'A' and resid 1412 through 1429 removed outlier: 4.784A pdb=" N MET A1417 " --> pdb=" O LEU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1462 Processing helix chain 'A' and resid 1466 through 1472 Processing helix chain 'A' and resid 1498 through 1525 removed outlier: 3.994A pdb=" N VAL A1501 " --> pdb=" O SER A1498 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1507 " --> pdb=" O PHE A1504 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A1525 " --> pdb=" O VAL A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1530 No H-bonds generated for 'chain 'A' and resid 1527 through 1530' Processing helix chain 'A' and resid 1539 through 1552 removed outlier: 4.328A pdb=" N GLU A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR A1552 " --> pdb=" O ILE A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1571 removed outlier: 3.825A pdb=" N LEU A1569 " --> pdb=" O VAL A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1593 Processing helix chain 'A' and resid 1606 through 1617 Processing helix chain 'A' and resid 1626 through 1632 Processing helix chain 'A' and resid 1646 through 1648 No H-bonds generated for 'chain 'A' and resid 1646 through 1648' Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.886A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 63 removed outlier: 4.105A pdb=" N ASP D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.781A pdb=" N LEU D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.665A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.768A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 4.134A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.577A pdb=" N SER D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 321 removed outlier: 3.636A pdb=" N LEU D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 4.165A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.507A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.729A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 580 Processing helix chain 'D' and resid 640 through 643 No H-bonds generated for 'chain 'D' and resid 640 through 643' Processing helix chain 'D' and resid 676 through 687 Processing helix chain 'D' and resid 700 through 716 removed outlier: 4.247A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 722 No H-bonds generated for 'chain 'D' and resid 719 through 722' Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.717A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 826 removed outlier: 3.777A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.675A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 4.072A pdb=" N GLU C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 133 removed outlier: 4.300A pdb=" N GLN C 133 " --> pdb=" O LYS C 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 192 through 199 removed outlier: 4.261A pdb=" N LYS C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.570A pdb=" N GLU C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 282 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.940A pdb=" N TYR C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 323 " --> pdb=" O MET C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 360 removed outlier: 4.147A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id= B, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id= C, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= D, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.744A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 409 through 413 removed outlier: 3.862A pdb=" N TYR D 409 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN D 290 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL D 258 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 292 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= G, first strand: chain 'D' and resid 512 through 515 removed outlier: 3.550A pdb=" N ILE D 515 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 588 through 593 removed outlier: 3.506A pdb=" N ARG D 605 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 601 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 732 through 735 removed outlier: 3.528A pdb=" N PHE D 733 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 774 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 848 through 854 Processing sheet with id= K, first strand: chain 'D' and resid 892 through 894 Processing sheet with id= L, first strand: chain 'D' and resid 897 through 899 Processing sheet with id= M, first strand: chain 'D' and resid 902 through 904 removed outlier: 3.727A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 993 through 995 Processing sheet with id= O, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= P, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.650A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.859A pdb=" N GLY B 38 " --> pdb=" O TYR B 23 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3418 1.31 - 1.44: 5742 1.44 - 1.57: 12133 1.57 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 21465 Sorted by residual: bond pdb=" CA TYR A 527 " pdb=" C TYR A 527 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.24e-02 6.50e+03 4.28e+01 bond pdb=" CA GLU D 182 " pdb=" C GLU D 182 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.29e-02 6.01e+03 2.08e+01 bond pdb=" C1 NAG G 3 " pdb=" O5 NAG G 3 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C THR D 212 " pdb=" O THR D 212 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.33e-02 5.65e+03 1.38e+01 bond pdb=" CA ARG C 178 " pdb=" C ARG C 178 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.18e+01 ... (remaining 21460 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.64: 535 106.64 - 113.85: 12120 113.85 - 121.07: 10503 121.07 - 128.29: 5787 128.29 - 135.51: 139 Bond angle restraints: 29084 Sorted by residual: angle pdb=" C ARG C 178 " pdb=" N PRO C 179 " pdb=" CA PRO C 179 " ideal model delta sigma weight residual 119.78 112.22 7.56 1.03e+00 9.43e-01 5.38e+01 angle pdb=" N ASN A 904 " pdb=" CA ASN A 904 " pdb=" C ASN A 904 " ideal model delta sigma weight residual 111.40 103.31 8.09 1.22e+00 6.72e-01 4.40e+01 angle pdb=" N SER A 636 " pdb=" CA SER A 636 " pdb=" C SER A 636 " ideal model delta sigma weight residual 114.62 107.19 7.43 1.14e+00 7.69e-01 4.25e+01 angle pdb=" C TYR A 527 " pdb=" CA TYR A 527 " pdb=" CB TYR A 527 " ideal model delta sigma weight residual 110.96 100.92 10.04 1.54e+00 4.22e-01 4.25e+01 angle pdb=" N ARG A 626 " pdb=" CA ARG A 626 " pdb=" C ARG A 626 " ideal model delta sigma weight residual 111.36 104.88 6.48 1.09e+00 8.42e-01 3.53e+01 ... (remaining 29079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 11829 24.48 - 48.97: 1158 48.97 - 73.45: 165 73.45 - 97.93: 43 97.93 - 122.42: 10 Dihedral angle restraints: 13205 sinusoidal: 5644 harmonic: 7561 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 -177.66 -89.34 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 17 " pdb=" SG CYS B 17 " pdb=" SG CYS B 39 " pdb=" CB CYS B 39 " ideal model delta sinusoidal sigma weight residual -86.00 -19.15 -66.85 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS D 404 " pdb=" SG CYS D 404 " pdb=" SG CYS D1071 " pdb=" CB CYS D1071 " ideal model delta sinusoidal sigma weight residual 93.00 153.88 -60.88 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 13202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2780 0.056 - 0.112: 488 0.112 - 0.168: 52 0.168 - 0.224: 2 0.224 - 0.280: 6 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 613 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3325 not shown) Planarity restraints: 3674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 78 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 79 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 921 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 922 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 922 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 922 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 744 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO D 745 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 745 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 745 " 0.047 5.00e-02 4.00e+02 ... (remaining 3671 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1767 2.74 - 3.28: 21834 3.28 - 3.82: 33879 3.82 - 4.36: 40785 4.36 - 4.90: 68231 Nonbonded interactions: 166496 Sorted by model distance: nonbonded pdb=" O ASN A1012 " pdb=" N VAL A1014 " model vdw 2.198 2.520 nonbonded pdb=" OG SER D 388 " pdb=" NH1 ARG D 396 " model vdw 2.215 2.520 nonbonded pdb=" O LEU D 506 " pdb=" OH TYR D 759 " model vdw 2.216 2.440 nonbonded pdb=" O ALA C 55 " pdb=" N HIS C 57 " model vdw 2.217 2.520 nonbonded pdb=" NH1 ARG D 884 " pdb=" O ARG D1029 " model vdw 2.218 2.520 ... (remaining 166491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 5.870 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 55.470 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.004 0.083 21465 Z= 0.237 Angle : 0.747 10.510 29084 Z= 0.423 Chirality : 0.044 0.280 3328 Planarity : 0.006 0.113 3666 Dihedral : 18.919 122.416 8269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 1.02 % Allowed : 9.92 % Favored : 89.06 % Rotamer: Outliers : 0.74 % Allowed : 29.47 % Favored : 69.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2551 helix: -0.53 (0.16), residues: 1109 sheet: -1.91 (0.33), residues: 231 loop : -2.63 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 336 HIS 0.004 0.001 HIS C 94 PHE 0.036 0.001 PHE D 780 TYR 0.039 0.001 TYR A1503 ARG 0.006 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 300 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TRP cc_start: 0.7469 (m100) cc_final: 0.7182 (m100) REVERT: A 1119 ASP cc_start: 0.8285 (m-30) cc_final: 0.7859 (m-30) REVERT: A 1191 GLU cc_start: 0.6456 (pp20) cc_final: 0.6206 (tp30) REVERT: A 1382 MET cc_start: 0.7137 (mmt) cc_final: 0.6889 (mmp) REVERT: A 1499 PHE cc_start: 0.8273 (t80) cc_final: 0.8000 (t80) REVERT: D 182 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: D 259 ASP cc_start: 0.8938 (t0) cc_final: 0.8629 (t0) REVERT: C 230 ASN cc_start: 0.5102 (OUTLIER) cc_final: 0.4666 (m110) REVERT: C 320 MET cc_start: 0.7554 (mpp) cc_final: 0.7329 (mpp) outliers start: 17 outliers final: 5 residues processed: 311 average time/residue: 0.3141 time to fit residues: 152.6473 Evaluate side-chains 282 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 304 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 4.9990 chunk 194 optimal weight: 0.0050 chunk 108 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 201 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 755 ASN A 931 HIS D 311 ASN D 374 ASN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21465 Z= 0.186 Angle : 0.639 8.871 29084 Z= 0.325 Chirality : 0.042 0.267 3328 Planarity : 0.005 0.111 3666 Dihedral : 9.706 106.363 3276 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.00 % Favored : 89.14 % Rotamer: Outliers : 3.41 % Allowed : 27.28 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2551 helix: -0.51 (0.15), residues: 1136 sheet: -1.75 (0.34), residues: 221 loop : -2.58 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 634 HIS 0.004 0.001 HIS C 348 PHE 0.031 0.001 PHE D 780 TYR 0.023 0.001 TYR C 356 ARG 0.003 0.000 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.6355 (mtm-85) cc_final: 0.6079 (mtm-85) REVERT: A 746 ASN cc_start: 0.8392 (m-40) cc_final: 0.8107 (m110) REVERT: A 958 TYR cc_start: 0.7309 (m-80) cc_final: 0.6978 (m-80) REVERT: A 963 ILE cc_start: 0.6493 (tp) cc_final: 0.6238 (mm) REVERT: A 1119 ASP cc_start: 0.8302 (m-30) cc_final: 0.7929 (m-30) REVERT: A 1379 PHE cc_start: 0.4874 (m-80) cc_final: 0.4582 (m-80) REVERT: A 1382 MET cc_start: 0.7241 (mmt) cc_final: 0.6952 (mmp) REVERT: D 182 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: D 259 ASP cc_start: 0.9021 (t0) cc_final: 0.8724 (t0) REVERT: D 396 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8052 (mtt-85) REVERT: D 782 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7248 (mtpp) REVERT: C 177 MET cc_start: 0.3965 (mmm) cc_final: 0.3131 (tpp) REVERT: C 320 MET cc_start: 0.7712 (mpp) cc_final: 0.7225 (mpp) REVERT: B 5 ILE cc_start: 0.0217 (OUTLIER) cc_final: -0.0124 (pt) outliers start: 78 outliers final: 39 residues processed: 363 average time/residue: 0.2982 time to fit residues: 171.6704 Evaluate side-chains 325 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 282 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 374 ASN Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 694 ASN Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 64 optimal weight: 9.9990 chunk 233 optimal weight: 0.7980 chunk 252 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A1628 GLN D 246 GLN D 311 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21465 Z= 0.189 Angle : 0.611 9.802 29084 Z= 0.309 Chirality : 0.042 0.244 3328 Planarity : 0.005 0.110 3666 Dihedral : 8.481 102.070 3271 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.49 % Favored : 89.77 % Rotamer: Outliers : 4.02 % Allowed : 27.55 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.16), residues: 2551 helix: -0.39 (0.16), residues: 1130 sheet: -1.65 (0.34), residues: 214 loop : -2.43 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 634 HIS 0.004 0.001 HIS C 348 PHE 0.021 0.001 PHE D 780 TYR 0.018 0.001 TYR C 356 ARG 0.002 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 296 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TRP cc_start: 0.7649 (m100) cc_final: 0.7029 (m100) REVERT: A 528 TRP cc_start: 0.6536 (OUTLIER) cc_final: 0.6260 (m-10) REVERT: A 590 ARG cc_start: 0.6410 (mtm-85) cc_final: 0.6148 (mtm-85) REVERT: A 746 ASN cc_start: 0.8365 (m-40) cc_final: 0.7906 (m110) REVERT: A 963 ILE cc_start: 0.6445 (tp) cc_final: 0.6199 (mm) REVERT: A 1119 ASP cc_start: 0.8316 (m-30) cc_final: 0.8085 (m-30) REVERT: A 1125 MET cc_start: 0.7775 (mmm) cc_final: 0.7544 (mtp) REVERT: A 1286 MET cc_start: 0.7547 (mmm) cc_final: 0.7215 (mmt) REVERT: A 1379 PHE cc_start: 0.5082 (m-80) cc_final: 0.4741 (m-80) REVERT: A 1382 MET cc_start: 0.7300 (mmt) cc_final: 0.7036 (mmp) REVERT: D 182 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: D 259 ASP cc_start: 0.9027 (t0) cc_final: 0.8730 (t0) REVERT: D 396 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8025 (mtt-85) REVERT: D 592 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8971 (m) REVERT: D 671 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7922 (mmmt) REVERT: D 690 LYS cc_start: 0.6954 (tptt) cc_final: 0.6636 (tptt) REVERT: D 757 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: D 760 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: D 1017 MET cc_start: 0.7056 (mtp) cc_final: 0.6625 (mtp) REVERT: C 177 MET cc_start: 0.4146 (mmm) cc_final: 0.3069 (tpt) REVERT: C 200 LEU cc_start: 0.6702 (mt) cc_final: 0.6106 (tp) REVERT: C 209 ASP cc_start: 0.3689 (t0) cc_final: 0.2844 (m-30) REVERT: C 320 MET cc_start: 0.7835 (mpp) cc_final: 0.7287 (mpp) REVERT: C 347 GLU cc_start: 0.8006 (tp30) cc_final: 0.7672 (mt-10) REVERT: B 5 ILE cc_start: 0.0223 (OUTLIER) cc_final: -0.0105 (pt) outliers start: 92 outliers final: 52 residues processed: 364 average time/residue: 0.2990 time to fit residues: 173.2561 Evaluate side-chains 330 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1628 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 694 ASN Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 814 ILE Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 0.9980 chunk 175 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21465 Z= 0.170 Angle : 0.601 12.554 29084 Z= 0.302 Chirality : 0.041 0.239 3328 Planarity : 0.004 0.076 3666 Dihedral : 7.927 98.551 3271 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.41 % Favored : 89.96 % Rotamer: Outliers : 4.02 % Allowed : 27.90 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2551 helix: -0.30 (0.16), residues: 1133 sheet: -1.57 (0.34), residues: 214 loop : -2.38 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.005 0.001 HIS C 314 PHE 0.021 0.001 PHE A 208 TYR 0.015 0.001 TYR C 356 ARG 0.005 0.000 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 301 time to evaluate : 2.248 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: A 325 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.5402 (mm-40) REVERT: A 590 ARG cc_start: 0.6458 (mtm-85) cc_final: 0.6198 (mtm-85) REVERT: A 746 ASN cc_start: 0.8330 (m-40) cc_final: 0.7887 (m110) REVERT: A 963 ILE cc_start: 0.6473 (tp) cc_final: 0.6237 (mm) REVERT: A 1084 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6337 (pt0) REVERT: A 1102 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8567 (t70) REVERT: A 1119 ASP cc_start: 0.8334 (m-30) cc_final: 0.8096 (m-30) REVERT: A 1206 GLN cc_start: 0.6519 (mp10) cc_final: 0.6135 (mp10) REVERT: A 1309 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 1382 MET cc_start: 0.7284 (mmt) cc_final: 0.7023 (mmp) REVERT: A 1525 ASP cc_start: 0.8311 (t70) cc_final: 0.8061 (t70) REVERT: D 259 ASP cc_start: 0.9007 (t0) cc_final: 0.8685 (t0) REVERT: D 396 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7767 (mtt-85) REVERT: D 592 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8921 (m) REVERT: D 671 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8019 (mmmt) REVERT: D 678 GLU cc_start: 0.6006 (mp0) cc_final: 0.5535 (mp0) REVERT: D 690 LYS cc_start: 0.6941 (tptt) cc_final: 0.6629 (tptt) REVERT: D 714 GLU cc_start: 0.8780 (tp30) cc_final: 0.8567 (tm-30) REVERT: D 753 GLN cc_start: 0.8128 (pm20) cc_final: 0.7892 (pm20) REVERT: D 760 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8603 (mp0) REVERT: C 177 MET cc_start: 0.4350 (mmm) cc_final: 0.3731 (mmm) REVERT: C 200 LEU cc_start: 0.6473 (mt) cc_final: 0.5922 (tp) REVERT: C 309 LYS cc_start: 0.1950 (mmtm) cc_final: 0.1138 (ptmm) REVERT: C 347 GLU cc_start: 0.7988 (tp30) cc_final: 0.7669 (mt-10) REVERT: B 5 ILE cc_start: 0.0203 (OUTLIER) cc_final: -0.0126 (pt) outliers start: 92 outliers final: 58 residues processed: 366 average time/residue: 0.2997 time to fit residues: 174.4981 Evaluate side-chains 345 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 279 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1102 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 814 ILE Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN A1630 ASN D 295 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21465 Z= 0.212 Angle : 0.606 10.744 29084 Z= 0.305 Chirality : 0.042 0.251 3328 Planarity : 0.004 0.076 3666 Dihedral : 7.519 92.270 3268 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.04 % Favored : 89.38 % Rotamer: Outliers : 4.85 % Allowed : 26.76 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2551 helix: -0.25 (0.16), residues: 1135 sheet: -1.65 (0.34), residues: 221 loop : -2.36 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1137 HIS 0.006 0.001 HIS C 57 PHE 0.022 0.001 PHE A 208 TYR 0.018 0.001 TYR D 629 ARG 0.003 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 290 time to evaluate : 2.307 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 325 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.5364 (mm-40) REVERT: A 590 ARG cc_start: 0.6462 (mtm-85) cc_final: 0.6210 (mtm-85) REVERT: A 746 ASN cc_start: 0.8520 (m-40) cc_final: 0.8003 (m110) REVERT: A 963 ILE cc_start: 0.6484 (tp) cc_final: 0.6244 (mm) REVERT: A 1084 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6452 (pt0) REVERT: A 1119 ASP cc_start: 0.8346 (m-30) cc_final: 0.8096 (m-30) REVERT: A 1125 MET cc_start: 0.7325 (mtp) cc_final: 0.7061 (mtp) REVERT: A 1206 GLN cc_start: 0.6395 (mp10) cc_final: 0.5990 (mp10) REVERT: A 1286 MET cc_start: 0.7621 (mmm) cc_final: 0.7255 (mmt) REVERT: D 396 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7816 (mtt-85) REVERT: D 629 TYR cc_start: 0.8810 (m-10) cc_final: 0.8597 (m-10) REVERT: D 690 LYS cc_start: 0.7032 (tptt) cc_final: 0.6704 (tptt) REVERT: D 714 GLU cc_start: 0.8786 (tp30) cc_final: 0.8344 (tp30) REVERT: D 757 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: D 760 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: D 875 PHE cc_start: 0.8849 (t80) cc_final: 0.8575 (t80) REVERT: C 200 LEU cc_start: 0.6511 (mt) cc_final: 0.5972 (tp) REVERT: C 209 ASP cc_start: 0.3579 (t0) cc_final: 0.2906 (m-30) REVERT: C 309 LYS cc_start: 0.1895 (mmtm) cc_final: 0.1293 (ptmm) REVERT: B 5 ILE cc_start: 0.0273 (OUTLIER) cc_final: -0.0074 (pt) outliers start: 111 outliers final: 79 residues processed: 374 average time/residue: 0.3013 time to fit residues: 181.0127 Evaluate side-chains 359 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 274 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 694 ASN Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 888 ASN Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 318 GLN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 145 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN C 47 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 21465 Z= 0.161 Angle : 0.596 10.788 29084 Z= 0.296 Chirality : 0.041 0.246 3328 Planarity : 0.004 0.077 3666 Dihedral : 7.107 86.986 3266 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.13 % Favored : 90.28 % Rotamer: Outliers : 4.15 % Allowed : 28.07 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 2551 helix: -0.13 (0.16), residues: 1142 sheet: -1.52 (0.34), residues: 217 loop : -2.33 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.003 0.000 HIS C 348 PHE 0.023 0.001 PHE A 208 TYR 0.014 0.001 TYR D 629 ARG 0.008 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 299 time to evaluate : 2.393 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 325 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.5357 (mm-40) REVERT: A 548 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: A 590 ARG cc_start: 0.6391 (mtm-85) cc_final: 0.6153 (mtm-85) REVERT: A 746 ASN cc_start: 0.8426 (m-40) cc_final: 0.7941 (m-40) REVERT: A 958 TYR cc_start: 0.7028 (m-80) cc_final: 0.6717 (m-80) REVERT: A 963 ILE cc_start: 0.6570 (tp) cc_final: 0.6348 (mm) REVERT: A 1119 ASP cc_start: 0.8341 (m-30) cc_final: 0.8097 (m-30) REVERT: A 1206 GLN cc_start: 0.6529 (mp10) cc_final: 0.6180 (mp10) REVERT: A 1382 MET cc_start: 0.7402 (mmt) cc_final: 0.7142 (mmp) REVERT: A 1516 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7265 (mp) REVERT: D 259 ASP cc_start: 0.9035 (t0) cc_final: 0.8758 (t0) REVERT: D 396 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7845 (mtt-85) REVERT: D 690 LYS cc_start: 0.7024 (tptt) cc_final: 0.6688 (tptt) REVERT: D 714 GLU cc_start: 0.8762 (tp30) cc_final: 0.8317 (tp30) REVERT: D 1010 ASN cc_start: 0.8518 (m-40) cc_final: 0.8176 (t0) REVERT: C 47 GLN cc_start: 0.3957 (tp40) cc_final: 0.3412 (tt0) REVERT: C 200 LEU cc_start: 0.6391 (mt) cc_final: 0.5937 (tp) REVERT: C 209 ASP cc_start: 0.3550 (t0) cc_final: 0.2856 (m-30) REVERT: C 347 GLU cc_start: 0.7863 (tp30) cc_final: 0.7574 (mt-10) REVERT: B 5 ILE cc_start: 0.0308 (OUTLIER) cc_final: -0.0057 (pt) outliers start: 95 outliers final: 67 residues processed: 369 average time/residue: 0.2966 time to fit residues: 175.6771 Evaluate side-chains 348 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 276 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LYS Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1524 MET Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 694 ASN Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 141 optimal weight: 0.3980 chunk 181 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN C 49 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21465 Z= 0.170 Angle : 0.597 11.303 29084 Z= 0.296 Chirality : 0.041 0.249 3328 Planarity : 0.004 0.076 3666 Dihedral : 6.811 79.296 3266 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.25 % Favored : 90.16 % Rotamer: Outliers : 4.24 % Allowed : 28.33 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 2551 helix: -0.06 (0.16), residues: 1138 sheet: -1.54 (0.34), residues: 219 loop : -2.32 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 509 HIS 0.011 0.001 HIS C 314 PHE 0.020 0.001 PHE A1545 TYR 0.015 0.001 TYR D 629 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 295 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TRP cc_start: 0.7684 (m100) cc_final: 0.6822 (m100) REVERT: A 325 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.5335 (mm-40) REVERT: A 548 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: A 561 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.7010 (mmtm) REVERT: A 590 ARG cc_start: 0.6411 (mtm-85) cc_final: 0.6181 (mtm-85) REVERT: A 746 ASN cc_start: 0.8449 (m-40) cc_final: 0.7975 (m-40) REVERT: A 963 ILE cc_start: 0.6571 (tp) cc_final: 0.6349 (mm) REVERT: A 1119 ASP cc_start: 0.8356 (m-30) cc_final: 0.8112 (m-30) REVERT: A 1125 MET cc_start: 0.7394 (mtp) cc_final: 0.7053 (mtp) REVERT: A 1206 GLN cc_start: 0.6494 (mp10) cc_final: 0.6156 (mp10) REVERT: A 1382 MET cc_start: 0.7290 (mmt) cc_final: 0.7035 (mmp) REVERT: D 158 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: D 197 ARG cc_start: 0.8146 (tmm160) cc_final: 0.7944 (ttp80) REVERT: D 396 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7807 (mtt-85) REVERT: D 690 LYS cc_start: 0.7020 (tptt) cc_final: 0.6680 (tptt) REVERT: D 714 GLU cc_start: 0.8761 (tp30) cc_final: 0.8298 (tp30) REVERT: D 757 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: D 760 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: D 1010 ASN cc_start: 0.8515 (m-40) cc_final: 0.8146 (t0) REVERT: D 1042 ASN cc_start: 0.8511 (t0) cc_final: 0.8257 (t0) REVERT: C 47 GLN cc_start: 0.3975 (tp40) cc_final: 0.3375 (tt0) REVERT: C 200 LEU cc_start: 0.6606 (mt) cc_final: 0.6120 (tp) REVERT: C 320 MET cc_start: 0.8086 (mpp) cc_final: 0.7608 (mpp) REVERT: C 347 GLU cc_start: 0.8020 (tp30) cc_final: 0.7674 (mt-10) REVERT: B 5 ILE cc_start: 0.0292 (OUTLIER) cc_final: -0.0069 (pt) outliers start: 97 outliers final: 73 residues processed: 373 average time/residue: 0.2957 time to fit residues: 176.9049 Evaluate side-chains 354 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 273 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LYS Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1524 MET Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 694 ASN Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 814 ILE Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 168 optimal weight: 0.0570 chunk 122 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 0.0980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 21465 Z= 0.159 Angle : 0.600 11.446 29084 Z= 0.295 Chirality : 0.041 0.247 3328 Planarity : 0.004 0.076 3666 Dihedral : 6.474 70.538 3266 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.98 % Favored : 90.44 % Rotamer: Outliers : 4.07 % Allowed : 28.47 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2551 helix: 0.07 (0.16), residues: 1136 sheet: -1.40 (0.35), residues: 215 loop : -2.28 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.004 0.000 HIS C 314 PHE 0.024 0.001 PHE A 175 TYR 0.013 0.001 TYR D 629 ARG 0.005 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 288 time to evaluate : 2.033 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 325 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5330 (mm-40) REVERT: A 548 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: A 590 ARG cc_start: 0.6405 (mtm-85) cc_final: 0.6182 (mtm-85) REVERT: A 648 VAL cc_start: 0.6708 (p) cc_final: 0.6243 (t) REVERT: A 746 ASN cc_start: 0.8362 (m-40) cc_final: 0.7922 (m-40) REVERT: A 958 TYR cc_start: 0.7048 (m-80) cc_final: 0.6824 (m-80) REVERT: A 963 ILE cc_start: 0.6563 (tp) cc_final: 0.6344 (mm) REVERT: A 1119 ASP cc_start: 0.8369 (m-30) cc_final: 0.8128 (m-30) REVERT: A 1206 GLN cc_start: 0.6481 (mp10) cc_final: 0.6156 (mp10) REVERT: A 1382 MET cc_start: 0.7436 (mmt) cc_final: 0.7191 (mmp) REVERT: D 396 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7952 (mtt-85) REVERT: D 506 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7258 (mt) REVERT: D 690 LYS cc_start: 0.7013 (tptt) cc_final: 0.6653 (tptt) REVERT: D 714 GLU cc_start: 0.8694 (tp30) cc_final: 0.8236 (tp30) REVERT: D 760 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: D 1010 ASN cc_start: 0.8482 (m-40) cc_final: 0.8122 (t0) REVERT: D 1042 ASN cc_start: 0.8453 (t0) cc_final: 0.8203 (t0) REVERT: C 47 GLN cc_start: 0.3942 (tp40) cc_final: 0.3338 (tt0) REVERT: C 200 LEU cc_start: 0.6465 (mt) cc_final: 0.5969 (tp) REVERT: C 208 PHE cc_start: 0.5438 (OUTLIER) cc_final: 0.4604 (t80) REVERT: C 320 MET cc_start: 0.8178 (mpp) cc_final: 0.7572 (mpp) REVERT: C 343 GLU cc_start: 0.8242 (pt0) cc_final: 0.7015 (mm-30) REVERT: C 347 GLU cc_start: 0.7968 (tp30) cc_final: 0.7648 (mt-10) REVERT: B 5 ILE cc_start: 0.0256 (OUTLIER) cc_final: -0.0095 (pt) outliers start: 93 outliers final: 74 residues processed: 359 average time/residue: 0.3001 time to fit residues: 171.2846 Evaluate side-chains 349 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 268 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LYS Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1524 MET Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 814 ILE Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 4.9990 chunk 237 optimal weight: 30.0000 chunk 216 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 208 optimal weight: 0.4980 chunk 218 optimal weight: 1.9990 chunk 151 optimal weight: 0.0070 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21465 Z= 0.175 Angle : 0.598 12.121 29084 Z= 0.296 Chirality : 0.041 0.254 3328 Planarity : 0.004 0.075 3666 Dihedral : 6.259 61.045 3266 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.21 % Favored : 90.24 % Rotamer: Outliers : 3.98 % Allowed : 28.60 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2551 helix: 0.11 (0.16), residues: 1135 sheet: -1.36 (0.36), residues: 208 loop : -2.29 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 509 HIS 0.004 0.001 HIS C 314 PHE 0.026 0.001 PHE A 175 TYR 0.016 0.001 TYR D 629 ARG 0.004 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 286 time to evaluate : 2.232 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 325 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5378 (mm-40) REVERT: A 548 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: A 561 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6912 (mmtm) REVERT: A 590 ARG cc_start: 0.6411 (mtm-85) cc_final: 0.6196 (mtm-85) REVERT: A 648 VAL cc_start: 0.6702 (p) cc_final: 0.6244 (t) REVERT: A 746 ASN cc_start: 0.8427 (m-40) cc_final: 0.8008 (m-40) REVERT: A 958 TYR cc_start: 0.6981 (m-80) cc_final: 0.6776 (m-80) REVERT: A 1119 ASP cc_start: 0.8381 (m-30) cc_final: 0.8132 (m-30) REVERT: A 1125 MET cc_start: 0.7425 (mtp) cc_final: 0.7051 (mtp) REVERT: A 1151 ASP cc_start: 0.8064 (m-30) cc_final: 0.7278 (t0) REVERT: A 1206 GLN cc_start: 0.6471 (mp10) cc_final: 0.6153 (mp10) REVERT: A 1382 MET cc_start: 0.7486 (mmt) cc_final: 0.7229 (mmp) REVERT: D 158 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: D 396 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: D 499 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7984 (mtm-85) REVERT: D 670 LEU cc_start: 0.7221 (tt) cc_final: 0.6945 (tp) REVERT: D 690 LYS cc_start: 0.6994 (tptt) cc_final: 0.6593 (tptt) REVERT: D 714 GLU cc_start: 0.8696 (tp30) cc_final: 0.8273 (tm-30) REVERT: D 757 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: D 760 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: D 1010 ASN cc_start: 0.8465 (m-40) cc_final: 0.8103 (t0) REVERT: D 1042 ASN cc_start: 0.8457 (t0) cc_final: 0.8208 (t0) REVERT: C 47 GLN cc_start: 0.3936 (tp40) cc_final: 0.3340 (tt0) REVERT: C 200 LEU cc_start: 0.6492 (mt) cc_final: 0.5948 (tp) REVERT: C 208 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.4578 (t80) REVERT: C 320 MET cc_start: 0.8161 (mpp) cc_final: 0.7486 (mpp) REVERT: C 343 GLU cc_start: 0.8273 (pt0) cc_final: 0.7157 (mm-30) REVERT: C 347 GLU cc_start: 0.7971 (tp30) cc_final: 0.7637 (mt-10) REVERT: B 5 ILE cc_start: 0.0244 (OUTLIER) cc_final: -0.0095 (pt) outliers start: 91 outliers final: 72 residues processed: 355 average time/residue: 0.2889 time to fit residues: 165.1422 Evaluate side-chains 357 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 276 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LYS Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1524 MET Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 235 optimal weight: 0.0070 chunk 203 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 161 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN D1062 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 21465 Z= 0.164 Angle : 0.604 11.227 29084 Z= 0.298 Chirality : 0.041 0.250 3328 Planarity : 0.004 0.075 3666 Dihedral : 6.049 58.421 3266 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.98 % Favored : 90.47 % Rotamer: Outliers : 3.54 % Allowed : 28.99 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2551 helix: 0.19 (0.16), residues: 1137 sheet: -1.31 (0.36), residues: 208 loop : -2.28 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.003 0.000 HIS C 314 PHE 0.028 0.001 PHE A 175 TYR 0.015 0.001 TYR D 629 ARG 0.003 0.000 ARG A1383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 291 time to evaluate : 1.877 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 325 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.5380 (mm-40) REVERT: A 548 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: A 590 ARG cc_start: 0.6409 (mtm-85) cc_final: 0.6200 (mtm-85) REVERT: A 648 VAL cc_start: 0.6811 (p) cc_final: 0.6376 (t) REVERT: A 746 ASN cc_start: 0.8464 (m-40) cc_final: 0.8038 (m-40) REVERT: A 1119 ASP cc_start: 0.8382 (m-30) cc_final: 0.8136 (m-30) REVERT: A 1151 ASP cc_start: 0.8122 (m-30) cc_final: 0.7491 (t0) REVERT: A 1206 GLN cc_start: 0.6467 (mp10) cc_final: 0.6159 (mp10) REVERT: A 1379 PHE cc_start: 0.5562 (m-80) cc_final: 0.5325 (m-80) REVERT: A 1382 MET cc_start: 0.7496 (mmt) cc_final: 0.7266 (mmp) REVERT: A 1403 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6650 (mmtt) REVERT: A 1464 GLU cc_start: 0.7262 (tp30) cc_final: 0.6980 (mm-30) REVERT: D 158 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: D 396 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8012 (mtt-85) REVERT: D 499 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7961 (mtm-85) REVERT: D 506 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7319 (mt) REVERT: D 690 LYS cc_start: 0.7010 (tptt) cc_final: 0.6604 (tptt) REVERT: D 714 GLU cc_start: 0.8688 (tp30) cc_final: 0.8250 (tp30) REVERT: D 760 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: D 1010 ASN cc_start: 0.8443 (m-40) cc_final: 0.8075 (t0) REVERT: D 1042 ASN cc_start: 0.8431 (t0) cc_final: 0.8193 (t0) REVERT: C 47 GLN cc_start: 0.3965 (tp40) cc_final: 0.3367 (tt0) REVERT: C 200 LEU cc_start: 0.6512 (mt) cc_final: 0.5963 (tp) REVERT: C 208 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.4599 (t80) REVERT: C 320 MET cc_start: 0.8131 (mpp) cc_final: 0.7483 (mpp) REVERT: C 343 GLU cc_start: 0.8244 (pt0) cc_final: 0.7097 (mm-30) REVERT: C 347 GLU cc_start: 0.7950 (tp30) cc_final: 0.7646 (mt-10) REVERT: B 5 ILE cc_start: 0.0225 (OUTLIER) cc_final: -0.0118 (pt) outliers start: 81 outliers final: 68 residues processed: 350 average time/residue: 0.2927 time to fit residues: 163.3996 Evaluate side-chains 353 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 276 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LYS Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 760 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.195464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141243 restraints weight = 31192.901| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.21 r_work: 0.3467 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21465 Z= 0.213 Angle : 0.614 11.698 29084 Z= 0.304 Chirality : 0.042 0.266 3328 Planarity : 0.004 0.075 3666 Dihedral : 6.071 59.436 3266 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.76 % Favored : 89.73 % Rotamer: Outliers : 3.59 % Allowed : 28.90 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2551 helix: 0.15 (0.16), residues: 1135 sheet: -1.36 (0.35), residues: 210 loop : -2.31 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS D 864 PHE 0.027 0.001 PHE A 175 TYR 0.014 0.001 TYR D 629 ARG 0.003 0.000 ARG D 732 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5244.00 seconds wall clock time: 94 minutes 36.81 seconds (5676.81 seconds total)