Starting phenix.real_space_refine on Thu Oct 29 02:18:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igs_52854/10_2026/9igs_52854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igs_52854/10_2026/9igs_52854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9igs_52854/10_2026/9igs_52854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igs_52854/10_2026/9igs_52854.map" model { file = "/net/cci-nas-00/data/ceres_data/9igs_52854/10_2026/9igs_52854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igs_52854/10_2026/9igs_52854.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 18712 2.51 5 N 5040 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29504 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 14527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1888, 14527 Classifications: {'peptide': 1888} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 73, 'TRANS': 1814} Chain breaks: 14 Unresolved non-hydrogen bonds: 487 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 17, 'ASP:plan': 29, 'ASN:plan1': 9, 'PHE:plan': 2, 'ARG:plan': 9, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 328 Chain: "B" Number of atoms: 14527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1888, 14527 Classifications: {'peptide': 1888} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 73, 'TRANS': 1814} Chain breaks: 14 Unresolved non-hydrogen bonds: 487 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 17, 'ASP:plan': 29, 'ASN:plan1': 9, 'PHE:plan': 2, 'ARG:plan': 9, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 328 Chain: "C" 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: "D" 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: "E" 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: "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: 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: "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: "J" 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: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 113 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 113 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.87, per 1000 atoms: 0.23 Number of scatterers: 29504 At special positions: 0 Unit cell: (174.724, 173.052, 98.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 5642 8.00 N 5040 7.00 C 18712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 773 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS A 804 " - pdb=" SG CYS A 815 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 821 " distance=2.03 Simple disulfide: pdb=" SG CYS A 963 " - pdb=" SG CYS A1097 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1172 " distance=2.03 Simple disulfide: pdb=" SG CYS A1464 " - pdb=" SG CYS A1472 " distance=2.03 Simple disulfide: pdb=" SG CYS A1466 " - pdb=" SG CYS A1474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 804 " - pdb=" SG CYS B 815 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 821 " distance=2.03 Simple disulfide: pdb=" SG CYS B 963 " - pdb=" SG CYS B1097 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1172 " distance=2.03 Simple disulfide: pdb=" SG CYS B1464 " - pdb=" SG CYS B1472 " distance=2.03 Simple disulfide: pdb=" SG CYS B1466 " - pdb=" SG CYS B1474 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A2801 " - " ASN A1543 " " NAG A2802 " - " ASN A1693 " " NAG A2803 " - " ASN A1836 " " NAG A2804 " - " ASN A1937 " " NAG A2805 " - " ASN A2140 " " NAG A2806 " - " ASN A2592 " " NAG A2808 " - " ASN A 869 " " NAG B2801 " - " ASN B1543 " " NAG B2802 " - " ASN B1693 " " NAG B2803 " - " ASN B1836 " " NAG B2804 " - " ASN B1937 " " NAG B2805 " - " ASN B2140 " " NAG B2806 " - " ASN B2592 " " NAG B2808 " - " ASN B 869 " " NAG C 1 " - " ASN A1560 " " NAG D 1 " - " ASN A1656 " " NAG E 1 " - " ASN A1751 " " NAG F 1 " - " ASN A2280 " " NAG G 1 " - " ASN B1560 " " NAG H 1 " - " ASN B1656 " " NAG I 1 " - " ASN B1751 " " NAG J 1 " - " ASN B2280 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 46 sheets defined 9.1% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 818 through 822 removed outlier: 4.130A pdb=" N ARG A 822 " --> pdb=" O PRO A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1149 through 1151 No H-bonds generated for 'chain 'A' and resid 1149 through 1151' Processing helix chain 'A' and resid 1481 through 1485 Processing helix chain 'A' and resid 2353 through 2357 Processing helix chain 'A' and resid 2386 through 2394 Processing helix chain 'A' and resid 2403 through 2407 Processing helix chain 'A' and resid 2416 through 2421 removed outlier: 3.509A pdb=" N THR A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A2421 " --> pdb=" O ASP A2417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2416 through 2421' Processing helix chain 'A' and resid 2422 through 2427 removed outlier: 3.569A pdb=" N LEU A2426 " --> pdb=" O VAL A2422 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2437 removed outlier: 3.927A pdb=" N ALA A2436 " --> pdb=" O HIS A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2458 Processing helix chain 'A' and resid 2467 through 2481 removed outlier: 3.718A pdb=" N LEU A2481 " --> pdb=" O ALA A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2522 No H-bonds generated for 'chain 'A' and resid 2520 through 2522' Processing helix chain 'A' and resid 2535 through 2544 removed outlier: 4.019A pdb=" N LYS A2539 " --> pdb=" O GLU A2535 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A2540 " --> pdb=" O ASP A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2578 removed outlier: 3.722A pdb=" N THR A2577 " --> pdb=" O SER A2573 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2659 Processing helix chain 'A' and resid 2667 through 2678 Processing helix chain 'A' and resid 2694 through 2699 removed outlier: 3.985A pdb=" N ASP A2699 " --> pdb=" O GLU A2696 " (cutoff:3.500A) Processing helix chain 'A' and resid 2700 through 2702 No H-bonds generated for 'chain 'A' and resid 2700 through 2702' Processing helix chain 'B' and resid 754 through 759 Processing helix chain 'B' and resid 818 through 822 removed outlier: 4.131A pdb=" N ARG B 822 " --> pdb=" O PRO B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 845 through 851 Processing helix chain 'B' and resid 852 through 854 No H-bonds generated for 'chain 'B' and resid 852 through 854' Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1149 through 1151 No H-bonds generated for 'chain 'B' and resid 1149 through 1151' Processing helix chain 'B' and resid 1481 through 1485 Processing helix chain 'B' and resid 2353 through 2357 Processing helix chain 'B' and resid 2386 through 2394 Processing helix chain 'B' and resid 2403 through 2407 Processing helix chain 'B' and resid 2416 through 2421 removed outlier: 3.509A pdb=" N THR B2420 " --> pdb=" O LYS B2416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B2421 " --> pdb=" O ASP B2417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2416 through 2421' Processing helix chain 'B' and resid 2422 through 2427 removed outlier: 3.569A pdb=" N LEU B2426 " --> pdb=" O VAL B2422 " (cutoff:3.500A) Processing helix chain 'B' and resid 2432 through 2437 removed outlier: 3.927A pdb=" N ALA B2436 " --> pdb=" O HIS B2432 " (cutoff:3.500A) Processing helix chain 'B' and resid 2451 through 2458 Processing helix chain 'B' and resid 2467 through 2481 removed outlier: 3.718A pdb=" N LEU B2481 " --> pdb=" O ALA B2477 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2522 No H-bonds generated for 'chain 'B' and resid 2520 through 2522' Processing helix chain 'B' and resid 2535 through 2544 removed outlier: 4.020A pdb=" N LYS B2539 " --> pdb=" O GLU B2535 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B2540 " --> pdb=" O ASP B2536 " (cutoff:3.500A) Processing helix chain 'B' and resid 2571 through 2578 removed outlier: 3.723A pdb=" N THR B2577 " --> pdb=" O SER B2573 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2659 Processing helix chain 'B' and resid 2667 through 2678 Processing helix chain 'B' and resid 2694 through 2699 removed outlier: 3.984A pdb=" N ASP B2699 " --> pdb=" O GLU B2696 " (cutoff:3.500A) Processing helix chain 'B' and resid 2700 through 2702 No H-bonds generated for 'chain 'B' and resid 2700 through 2702' Processing sheet with id=AA1, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.532A pdb=" N GLY A 768 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS A 762 " --> pdb=" O GLN B2597 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B2597 " --> pdb=" O CYS A 762 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B2595 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B2619 " --> pdb=" O PHE B2616 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B2547 " --> pdb=" O VAL B2525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.532A pdb=" N GLY A 768 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS A 762 " --> pdb=" O GLN B2597 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B2597 " --> pdb=" O CYS A 762 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B2595 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B2619 " --> pdb=" O PHE B2616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AA4, first strand: chain 'A' and resid 873 through 875 Processing sheet with id=AA5, first strand: chain 'A' and resid 911 through 912 Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AA7, first strand: chain 'A' and resid 974 through 977 Processing sheet with id=AA8, first strand: chain 'A' and resid 993 through 994 Processing sheet with id=AA9, first strand: chain 'A' and resid 1054 through 1059 removed outlier: 3.553A pdb=" N TYR A1092 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A1102 " --> pdb=" O TYR A1092 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1130 through 1132 Processing sheet with id=AB2, first strand: chain 'A' and resid 1154 through 1159 removed outlier: 6.953A pdb=" N ILE A1511 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A1502 " --> pdb=" O LEU A1493 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A1493 " --> pdb=" O TYR A1502 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA A1504 " --> pdb=" O SER A1491 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1174 through 1175 removed outlier: 6.534A pdb=" N VAL A1203 " --> pdb=" O VAL A1215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1234 through 1237 removed outlier: 5.614A pdb=" N LEU A1244 " --> pdb=" O PRO A1257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A1248 " --> pdb=" O ARG A1253 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A1253 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A1254 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1294 through 1295 removed outlier: 4.252A pdb=" N ALA A1294 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1315 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A1314 " --> pdb=" O ALA A1306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1361 through 1366 removed outlier: 4.044A pdb=" N ASP A1363 " --> pdb=" O LEU A1376 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1381 " --> pdb=" O ALA A1393 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1424 through 1426 removed outlier: 6.710A pdb=" N ILE A1445 " --> pdb=" O VAL A1457 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1527 through 1531 removed outlier: 8.594A pdb=" N GLN A1547 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN A1560 " --> pdb=" O GLN A1547 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A1549 " --> pdb=" O LEU A1558 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A1571 " --> pdb=" O SER A1562 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR A1570 " --> pdb=" O ILE A1582 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A1574 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASN A1578 " --> pdb=" O ASP A1574 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A1592 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP A1602 " --> pdb=" O MET A1614 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET A1614 " --> pdb=" O TRP A1602 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A1604 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LYS A1612 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A1623 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET A1614 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A1621 " --> pdb=" O ASP A1638 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP A1638 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1623 " --> pdb=" O LYS A1636 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A1636 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR A1625 " --> pdb=" O ALA A1634 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA A1634 " --> pdb=" O PHE A1646 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A1638 " --> pdb=" O TRP A1642 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TRP A1642 " --> pdb=" O ASP A1638 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A1656 " --> pdb=" O ASP A1647 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR A1655 " --> pdb=" O LEU A1667 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1688 " --> pdb=" O ILE A1679 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1698 through 1703 removed outlier: 3.921A pdb=" N LYS A1749 " --> pdb=" O GLN A1733 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A1735 " --> pdb=" O VAL A1747 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL A1747 " --> pdb=" O GLU A1735 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS A1737 " --> pdb=" O PRO A1745 " (cutoff:3.500A) removed outlier: 16.247A pdb=" N THR A1742 " --> pdb=" O GLN A1771 " (cutoff:3.500A) removed outlier: 18.659A pdb=" N GLN A1771 " --> pdb=" O THR A1742 " (cutoff:3.500A) removed outlier: 17.519A pdb=" N ASN A1744 " --> pdb=" O LYS A1769 " (cutoff:3.500A) removed outlier: 14.050A pdb=" N LYS A1769 " --> pdb=" O ASN A1744 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N THR A1746 " --> pdb=" O PHE A1767 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N PHE A1767 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A1748 " --> pdb=" O TRP A1765 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A1778 " --> pdb=" O GLU A1770 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA A1772 " --> pdb=" O VAL A1776 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL A1776 " --> pdb=" O ALA A1772 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A1785 " --> pdb=" O ASN A1789 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A1812 " --> pdb=" O PRO A1828 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A1814 " --> pdb=" O TRP A1826 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP A1826 " --> pdb=" O ARG A1814 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A1816 " --> pdb=" O THR A1824 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A1824 " --> pdb=" O VAL A1837 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN A1836 " --> pdb=" O ILE A1848 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A1848 " --> pdb=" O ASN A1836 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A1838 " --> pdb=" O ALA A1846 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA A1846 " --> pdb=" O VAL A1857 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A1856 " --> pdb=" O ARG A1868 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A1868 " --> pdb=" O LYS A1856 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP A1858 " --> pdb=" O VAL A1866 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL A1866 " --> pdb=" O TYR A1878 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU A1898 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER A1906 " --> pdb=" O MET A1918 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A1952 " --> pdb=" O ASP A1943 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A1951 " --> pdb=" O PHE A1964 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A1963 " --> pdb=" O ILE A1975 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A1975 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A1965 " --> pdb=" O SER A1973 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A1997 " --> pdb=" O SER A1983 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A2005 " --> pdb=" O LEU A1998 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE A2012 " --> pdb=" O ILE A2016 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE A2016 " --> pdb=" O ILE A2012 " (cutoff:3.500A) removed outlier: 12.576A pdb=" N LEU A2015 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR A2037 " --> pdb=" O LEU A2015 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A2017 " --> pdb=" O TYR A2035 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A2045 " --> pdb=" O SER A2036 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1698 through 1703 removed outlier: 3.921A pdb=" N LYS A1749 " --> pdb=" O GLN A1733 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A1735 " --> pdb=" O VAL A1747 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL A1747 " --> pdb=" O GLU A1735 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS A1737 " --> pdb=" O PRO A1745 " (cutoff:3.500A) removed outlier: 16.247A pdb=" N THR A1742 " --> pdb=" O GLN A1771 " (cutoff:3.500A) removed outlier: 18.659A pdb=" N GLN A1771 " --> pdb=" O THR A1742 " (cutoff:3.500A) removed outlier: 17.519A pdb=" N ASN A1744 " --> pdb=" O LYS A1769 " (cutoff:3.500A) removed outlier: 14.050A pdb=" N LYS A1769 " --> pdb=" O ASN A1744 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N THR A1746 " --> pdb=" O PHE A1767 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N PHE A1767 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A1748 " --> pdb=" O TRP A1765 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A1778 " --> pdb=" O GLU A1770 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA A1772 " --> pdb=" O VAL A1776 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL A1776 " --> pdb=" O ALA A1772 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A1785 " --> pdb=" O ASN A1789 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A1812 " --> pdb=" O PRO A1828 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A1814 " --> pdb=" O TRP A1826 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP A1826 " --> pdb=" O ARG A1814 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A1816 " --> pdb=" O THR A1824 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A1824 " --> pdb=" O VAL A1837 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN A1836 " --> pdb=" O ILE A1848 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A1848 " --> pdb=" O ASN A1836 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A1838 " --> pdb=" O ALA A1846 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA A1846 " --> pdb=" O VAL A1857 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A1856 " --> pdb=" O ARG A1868 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A1868 " --> pdb=" O LYS A1856 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP A1858 " --> pdb=" O VAL A1866 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL A1866 " --> pdb=" O TYR A1878 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU A1898 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER A1906 " --> pdb=" O MET A1918 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A1952 " --> pdb=" O ASP A1943 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A1951 " --> pdb=" O PHE A1964 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A1963 " --> pdb=" O ILE A1975 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A1975 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A1965 " --> pdb=" O SER A1973 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A1997 " --> pdb=" O SER A1983 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A2005 " --> pdb=" O LEU A1998 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE A2012 " --> pdb=" O ILE A2016 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE A2016 " --> pdb=" O ILE A2012 " (cutoff:3.500A) removed outlier: 12.576A pdb=" N LEU A2015 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR A2037 " --> pdb=" O LEU A2015 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A2017 " --> pdb=" O TYR A2035 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A2045 " --> pdb=" O SER A2036 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR A2044 " --> pdb=" O TYR A2060 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU A2070 " --> pdb=" O VAL A2077 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A2076 " --> pdb=" O SER A2087 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A2109 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A2104 " --> pdb=" O ILE A2120 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A2106 " --> pdb=" O ILE A2118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A2118 " --> pdb=" O ILE A2106 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A2110 " --> pdb=" O LEU A2114 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A2114 " --> pdb=" O ILE A2110 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET A2115 " --> pdb=" O ILE A2135 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE A2135 " --> pdb=" O MET A2115 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TRP A2117 " --> pdb=" O ILE A2133 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE A2133 " --> pdb=" O TRP A2117 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR A2119 " --> pdb=" O ARG A2131 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A2131 " --> pdb=" O THR A2119 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN A2121 " --> pdb=" O THR A2129 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A2140 " --> pdb=" O ILE A2135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2144 through 2148 removed outlier: 3.966A pdb=" N TRP A2165 " --> pdb=" O VAL A2157 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A2159 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A2163 " --> pdb=" O LEU A2159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2168 through 2169 removed outlier: 6.394A pdb=" N ASN A2168 " --> pdb=" O HIS A2176 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N HIS A2176 " --> pdb=" O LEU A2189 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A2178 " --> pdb=" O THR A2187 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU A2200 " --> pdb=" O PRO A2188 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A2190 " --> pdb=" O THR A2198 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR A2198 " --> pdb=" O TYR A2205 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG A2214 " --> pdb=" O PHE A2221 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A2231 " --> pdb=" O GLU A2222 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR A2230 " --> pdb=" O TYR A2243 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL A2252 " --> pdb=" O PHE A2264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A2299 " --> pdb=" O TYR A2290 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A2298 " --> pdb=" O ILE A2310 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A2306 " --> pdb=" O ILE A2302 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A2309 " --> pdb=" O VAL A2321 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A2321 " --> pdb=" O TYR A2309 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA A2311 " --> pdb=" O LEU A2319 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU A2319 " --> pdb=" O GLN A2331 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN A2331 " --> pdb=" O LEU A2319 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A2321 " --> pdb=" O LEU A2329 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN A2331 " --> pdb=" O ASP A2343 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A2343 " --> pdb=" O GLN A2331 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN A2333 " --> pdb=" O TYR A2341 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2358 through 2360 removed outlier: 3.538A pdb=" N ASP A2360 " --> pdb=" O LEU A2365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A2365 " --> pdb=" O ASP A2360 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2524 through 2525 removed outlier: 3.772A pdb=" N ALA A2547 " --> pdb=" O VAL A2525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2524 through 2525 removed outlier: 3.772A pdb=" N ALA A2547 " --> pdb=" O VAL A2525 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A2619 " --> pdb=" O PHE A2616 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A2595 " --> pdb=" O LEU B 764 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A2597 " --> pdb=" O CYS B 762 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS B 762 " --> pdb=" O GLN A2597 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 768 " --> pdb=" O ASP B 765 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2684 through 2687 Processing sheet with id=AC8, first strand: chain 'B' and resid 777 through 778 Processing sheet with id=AC9, first strand: chain 'B' and resid 873 through 875 Processing sheet with id=AD1, first strand: chain 'B' and resid 911 through 912 Processing sheet with id=AD2, first strand: chain 'B' and resid 904 through 905 Processing sheet with id=AD3, first strand: chain 'B' and resid 974 through 977 Processing sheet with id=AD4, first strand: chain 'B' and resid 993 through 994 Processing sheet with id=AD5, first strand: chain 'B' and resid 1054 through 1059 removed outlier: 3.552A pdb=" N TYR B1092 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B1102 " --> pdb=" O TYR B1092 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1130 through 1132 Processing sheet with id=AD7, first strand: chain 'B' and resid 1154 through 1159 removed outlier: 6.954A pdb=" N ILE B1511 " --> pdb=" O ILE B1158 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR B1502 " --> pdb=" O LEU B1493 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B1493 " --> pdb=" O TYR B1502 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B1504 " --> pdb=" O SER B1491 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1174 through 1175 removed outlier: 6.535A pdb=" N VAL B1203 " --> pdb=" O VAL B1215 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1234 through 1237 removed outlier: 5.614A pdb=" N LEU B1244 " --> pdb=" O PRO B1257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B1248 " --> pdb=" O ARG B1253 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B1253 " --> pdb=" O ASP B1248 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B1254 " --> pdb=" O VAL B1273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1294 through 1295 removed outlier: 4.253A pdb=" N ALA B1294 " --> pdb=" O ILE B1330 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B1315 " --> pdb=" O ARG B1322 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B1314 " --> pdb=" O ALA B1306 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1361 through 1366 removed outlier: 4.043A pdb=" N ASP B1363 " --> pdb=" O LEU B1376 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1381 " --> pdb=" O ALA B1393 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 6.710A pdb=" N ILE B1445 " --> pdb=" O VAL B1457 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1527 through 1531 removed outlier: 8.594A pdb=" N GLN B1547 " --> pdb=" O ASN B1560 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASN B1560 " --> pdb=" O GLN B1547 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR B1549 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B1571 " --> pdb=" O SER B1562 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR B1570 " --> pdb=" O ILE B1582 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B1574 " --> pdb=" O ASN B1578 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASN B1578 " --> pdb=" O ASP B1574 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B1592 " --> pdb=" O ARG B1583 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP B1602 " --> pdb=" O MET B1614 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET B1614 " --> pdb=" O TRP B1602 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1604 " --> pdb=" O LYS B1612 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LYS B1612 " --> pdb=" O LEU B1623 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B1623 " --> pdb=" O LYS B1612 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET B1614 " --> pdb=" O LEU B1621 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B1621 " --> pdb=" O ASP B1638 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP B1638 " --> pdb=" O LEU B1621 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B1623 " --> pdb=" O LYS B1636 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B1636 " --> pdb=" O LEU B1623 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR B1625 " --> pdb=" O ALA B1634 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B1634 " --> pdb=" O PHE B1646 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP B1638 " --> pdb=" O TRP B1642 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TRP B1642 " --> pdb=" O ASP B1638 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B1656 " --> pdb=" O ASP B1647 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR B1655 " --> pdb=" O LEU B1667 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B1688 " --> pdb=" O ILE B1679 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1698 through 1703 removed outlier: 3.921A pdb=" N LYS B1749 " --> pdb=" O GLN B1733 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B1735 " --> pdb=" O VAL B1747 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL B1747 " --> pdb=" O GLU B1735 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS B1737 " --> pdb=" O PRO B1745 " (cutoff:3.500A) removed outlier: 16.247A pdb=" N THR B1742 " --> pdb=" O GLN B1771 " (cutoff:3.500A) removed outlier: 18.659A pdb=" N GLN B1771 " --> pdb=" O THR B1742 " (cutoff:3.500A) removed outlier: 17.519A pdb=" N ASN B1744 " --> pdb=" O LYS B1769 " (cutoff:3.500A) removed outlier: 14.049A pdb=" N LYS B1769 " --> pdb=" O ASN B1744 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N THR B1746 " --> pdb=" O PHE B1767 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N PHE B1767 " --> pdb=" O THR B1746 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA B1748 " --> pdb=" O TRP B1765 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B1778 " --> pdb=" O GLU B1770 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B1772 " --> pdb=" O VAL B1776 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL B1776 " --> pdb=" O ALA B1772 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B1785 " --> pdb=" O ASN B1789 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN B1789 " --> pdb=" O VAL B1785 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B1812 " --> pdb=" O PRO B1828 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B1814 " --> pdb=" O TRP B1826 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP B1826 " --> pdb=" O ARG B1814 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B1816 " --> pdb=" O THR B1824 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR B1824 " --> pdb=" O VAL B1837 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN B1836 " --> pdb=" O ILE B1848 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B1848 " --> pdb=" O ASN B1836 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B1838 " --> pdb=" O ALA B1846 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA B1846 " --> pdb=" O VAL B1857 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS B1856 " --> pdb=" O ARG B1868 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG B1868 " --> pdb=" O LYS B1856 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B1858 " --> pdb=" O VAL B1866 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL B1866 " --> pdb=" O TYR B1878 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU B1898 " --> pdb=" O SER B1906 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER B1906 " --> pdb=" O MET B1918 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B1952 " --> pdb=" O ASP B1943 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU B1951 " --> pdb=" O PHE B1964 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B1963 " --> pdb=" O ILE B1975 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B1975 " --> pdb=" O LEU B1963 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B1965 " --> pdb=" O SER B1973 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B1997 " --> pdb=" O SER B1983 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS B2005 " --> pdb=" O LEU B1998 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B2012 " --> pdb=" O ILE B2016 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE B2016 " --> pdb=" O ILE B2012 " (cutoff:3.500A) removed outlier: 12.576A pdb=" N LEU B2015 " --> pdb=" O TYR B2037 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR B2037 " --> pdb=" O LEU B2015 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B2017 " --> pdb=" O TYR B2035 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B2045 " --> pdb=" O SER B2036 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1698 through 1703 removed outlier: 3.921A pdb=" N LYS B1749 " --> pdb=" O GLN B1733 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B1735 " --> pdb=" O VAL B1747 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL B1747 " --> pdb=" O GLU B1735 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS B1737 " --> pdb=" O PRO B1745 " (cutoff:3.500A) removed outlier: 16.247A pdb=" N THR B1742 " --> pdb=" O GLN B1771 " (cutoff:3.500A) removed outlier: 18.659A pdb=" N GLN B1771 " --> pdb=" O THR B1742 " (cutoff:3.500A) removed outlier: 17.519A pdb=" N ASN B1744 " --> pdb=" O LYS B1769 " (cutoff:3.500A) removed outlier: 14.049A pdb=" N LYS B1769 " --> pdb=" O ASN B1744 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N THR B1746 " --> pdb=" O PHE B1767 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N PHE B1767 " --> pdb=" O THR B1746 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA B1748 " --> pdb=" O TRP B1765 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B1778 " --> pdb=" O GLU B1770 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B1772 " --> pdb=" O VAL B1776 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL B1776 " --> pdb=" O ALA B1772 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B1785 " --> pdb=" O ASN B1789 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN B1789 " --> pdb=" O VAL B1785 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B1812 " --> pdb=" O PRO B1828 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B1814 " --> pdb=" O TRP B1826 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP B1826 " --> pdb=" O ARG B1814 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B1816 " --> pdb=" O THR B1824 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR B1824 " --> pdb=" O VAL B1837 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN B1836 " --> pdb=" O ILE B1848 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B1848 " --> pdb=" O ASN B1836 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B1838 " --> pdb=" O ALA B1846 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA B1846 " --> pdb=" O VAL B1857 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS B1856 " --> pdb=" O ARG B1868 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG B1868 " --> pdb=" O LYS B1856 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B1858 " --> pdb=" O VAL B1866 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL B1866 " --> pdb=" O TYR B1878 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU B1898 " --> pdb=" O SER B1906 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER B1906 " --> pdb=" O MET B1918 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B1952 " --> pdb=" O ASP B1943 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU B1951 " --> pdb=" O PHE B1964 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B1963 " --> pdb=" O ILE B1975 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B1975 " --> pdb=" O LEU B1963 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B1965 " --> pdb=" O SER B1973 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B1997 " --> pdb=" O SER B1983 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS B2005 " --> pdb=" O LEU B1998 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B2012 " --> pdb=" O ILE B2016 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE B2016 " --> pdb=" O ILE B2012 " (cutoff:3.500A) removed outlier: 12.576A pdb=" N LEU B2015 " --> pdb=" O TYR B2037 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR B2037 " --> pdb=" O LEU B2015 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B2017 " --> pdb=" O TYR B2035 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B2045 " --> pdb=" O SER B2036 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR B2044 " --> pdb=" O TYR B2060 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU B2070 " --> pdb=" O VAL B2077 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B2076 " --> pdb=" O SER B2087 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B2109 " --> pdb=" O THR B2092 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS B2104 " --> pdb=" O ILE B2120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B2106 " --> pdb=" O ILE B2118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B2118 " --> pdb=" O ILE B2106 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B2110 " --> pdb=" O LEU B2114 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B2114 " --> pdb=" O ILE B2110 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET B2115 " --> pdb=" O ILE B2135 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B2135 " --> pdb=" O MET B2115 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B2117 " --> pdb=" O ILE B2133 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE B2133 " --> pdb=" O TRP B2117 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR B2119 " --> pdb=" O ARG B2131 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG B2131 " --> pdb=" O THR B2119 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN B2121 " --> pdb=" O THR B2129 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B2140 " --> pdb=" O ILE B2135 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 2144 through 2148 removed outlier: 3.967A pdb=" N TRP B2165 " --> pdb=" O VAL B2157 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B2159 " --> pdb=" O ILE B2163 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE B2163 " --> pdb=" O LEU B2159 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 2168 through 2169 removed outlier: 6.394A pdb=" N ASN B2168 " --> pdb=" O HIS B2176 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N HIS B2176 " --> pdb=" O LEU B2189 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B2178 " --> pdb=" O THR B2187 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B2200 " --> pdb=" O PRO B2188 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B2190 " --> pdb=" O THR B2198 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR B2198 " --> pdb=" O TYR B2205 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG B2214 " --> pdb=" O PHE B2221 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B2231 " --> pdb=" O GLU B2222 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR B2230 " --> pdb=" O TYR B2243 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B2252 " --> pdb=" O PHE B2264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B2299 " --> pdb=" O TYR B2290 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B2298 " --> pdb=" O ILE B2310 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B2306 " --> pdb=" O ILE B2302 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR B2309 " --> pdb=" O VAL B2321 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B2321 " --> pdb=" O TYR B2309 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B2311 " --> pdb=" O LEU B2319 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU B2319 " --> pdb=" O GLN B2331 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN B2331 " --> pdb=" O LEU B2319 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B2321 " --> pdb=" O LEU B2329 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN B2331 " --> pdb=" O ASP B2343 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B2343 " --> pdb=" O GLN B2331 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN B2333 " --> pdb=" O TYR B2341 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 2358 through 2360 removed outlier: 3.539A pdb=" N ASP B2360 " --> pdb=" O LEU B2365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B2365 " --> pdb=" O ASP B2360 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 2684 through 2687 1218 hydrogen bonds defined for protein. 3177 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: 12.89 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9573 1.34 - 1.46: 7337 1.46 - 1.58: 13058 1.58 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 30142 Sorted by residual: bond pdb=" C1 NAG B2805 " pdb=" O5 NAG B2805 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C1 NAG A2805 " pdb=" O5 NAG A2805 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C LEU B1694 " pdb=" N SER B1695 " ideal model delta sigma weight residual 1.331 1.281 0.049 1.29e-02 6.01e+03 1.47e+01 bond pdb=" C LEU A1694 " pdb=" N SER A1695 " ideal model delta sigma weight residual 1.331 1.281 0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 30137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 40385 2.12 - 4.23: 525 4.23 - 6.35: 69 6.35 - 8.46: 14 8.46 - 10.58: 5 Bond angle restraints: 40998 Sorted by residual: angle pdb=" N HIS B1225 " pdb=" CA HIS B1225 " pdb=" C HIS B1225 " ideal model delta sigma weight residual 112.45 122.16 -9.71 1.39e+00 5.18e-01 4.88e+01 angle pdb=" N ALA B1938 " pdb=" CA ALA B1938 " pdb=" C ALA B1938 " ideal model delta sigma weight residual 108.63 98.05 10.58 1.60e+00 3.91e-01 4.37e+01 angle pdb=" N ALA A1938 " pdb=" CA ALA A1938 " pdb=" C ALA A1938 " ideal model delta sigma weight residual 108.63 98.06 10.57 1.60e+00 3.91e-01 4.37e+01 angle pdb=" N GLN A1707 " pdb=" CA GLN A1707 " pdb=" CB GLN A1707 " ideal model delta sigma weight residual 110.88 103.01 7.87 1.38e+00 5.25e-01 3.25e+01 angle pdb=" N GLN B1707 " pdb=" CA GLN B1707 " pdb=" CB GLN B1707 " ideal model delta sigma weight residual 110.88 103.04 7.84 1.38e+00 5.25e-01 3.23e+01 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 16716 23.81 - 47.63: 1249 47.63 - 71.44: 201 71.44 - 95.25: 40 95.25 - 119.07: 28 Dihedral angle restraints: 18234 sinusoidal: 7274 harmonic: 10960 Sorted by residual: dihedral pdb=" CB CYS B1464 " pdb=" SG CYS B1464 " pdb=" SG CYS B1472 " pdb=" CB CYS B1472 " ideal model delta sinusoidal sigma weight residual 93.00 -177.76 -89.24 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A1464 " pdb=" SG CYS A1464 " pdb=" SG CYS A1472 " pdb=" CB CYS A1472 " ideal model delta sinusoidal sigma weight residual 93.00 -177.78 -89.22 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A1169 " pdb=" SG CYS A1169 " pdb=" SG CYS A1172 " pdb=" CB CYS A1172 " ideal model delta sinusoidal sigma weight residual 93.00 4.00 89.00 1 1.00e+01 1.00e-02 9.43e+01 ... (remaining 18231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4277 0.086 - 0.172: 422 0.172 - 0.259: 6 0.259 - 0.345: 7 0.345 - 0.431: 6 Chirality restraints: 4718 Sorted by residual: chirality pdb=" C1 NAG B2802 " pdb=" ND2 ASN B1693 " pdb=" C2 NAG B2802 " pdb=" O5 NAG B2802 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG A2802 " pdb=" ND2 ASN A1693 " pdb=" C2 NAG A2802 " pdb=" O5 NAG A2802 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C1 NAG B2805 " pdb=" ND2 ASN B2140 " pdb=" C2 NAG B2805 " pdb=" O5 NAG B2805 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 4715 not shown) Planarity restraints: 5250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 907 " -0.891 9.50e-02 1.11e+02 3.99e-01 9.67e+01 pdb=" NE ARG A 907 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 907 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 907 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 907 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 869 " -0.002 2.00e-02 2.50e+03 5.48e-02 3.75e+01 pdb=" CG ASN A 869 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 869 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 869 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG A2808 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 869 " 0.002 2.00e-02 2.50e+03 5.47e-02 3.74e+01 pdb=" CG ASN B 869 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN B 869 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN B 869 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG B2808 " -0.059 2.00e-02 2.50e+03 ... (remaining 5247 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4031 2.76 - 3.30: 27531 3.30 - 3.83: 49235 3.83 - 4.37: 57531 4.37 - 4.90: 101929 Nonbonded interactions: 240257 Sorted by model distance: nonbonded pdb=" OG SER B1496 " pdb=" OD2 ASP B1498 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A1496 " pdb=" OD2 ASP A1498 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP B2313 " pdb=" OG1 THR B2315 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP A2313 " pdb=" OG1 THR A2315 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B1564 " pdb=" OG1 THR B1570 " model vdw 2.236 3.040 ... (remaining 240252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 35.400 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.003 0.080 30190 Z= 0.165 Angle : 0.648 21.794 41124 Z= 0.327 Chirality : 0.048 0.431 4718 Planarity : 0.007 0.399 5228 Dihedral : 16.946 119.067 11164 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.40 % Favored : 92.55 % Rotamer: Outliers : 1.19 % Allowed : 22.84 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3718 helix: -0.07 (0.34), residues: 246 sheet: -0.42 (0.15), residues: 1218 loop : -0.97 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2672 TYR 0.010 0.001 TYR B1233 PHE 0.021 0.001 PHE A1200 TRP 0.010 0.001 TRP A1902 HIS 0.007 0.001 HIS A1231 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (30142) covalent geometry : angle 0.57980 / 0.31 (40998) SS BOND : bond 0.00148 / 0.11 ( 18) SS BOND : angle 0.81027 / 0.52 ( 36) hydrogen bonds : bond 0.24976 / 16.83 ( 962) hydrogen bonds : angle 10.29471 / 7.22 ( 3177) link_BETA1-4 : bond 0.01092 / 0.42 ( 8) link_BETA1-4 : angle 3.06221 / 1.66 ( 24) link_NAG-ASN : bond 0.01406 / 0.80 ( 22) link_NAG-ASN : angle 6.99553 / 5.03 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1694 LEU cc_start: 0.9029 (tm) cc_final: 0.8823 (tp) REVERT: A 2115 MET cc_start: 0.7470 (mmm) cc_final: 0.6966 (mpm) REVERT: B 2115 MET cc_start: 0.7455 (mmm) cc_final: 0.6961 (mpm) outliers start: 36 outliers final: 24 residues processed: 185 average time/residue: 0.4900 time to fit residues: 113.2174 Evaluate side-chains 151 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1764 GLU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2391 ILE Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1375 VAL Chi-restraints excluded: chain B residue 1764 GLU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1898 GLU Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2391 ILE Chi-restraints excluded: chain B residue 2400 LEU Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2595 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0060 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 HIS A 892 ASN A1129 HIS A1146 GLN ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 ASN A1733 GLN A1744 ASN ** A2084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2534 ASN A2673 GLN B 860 HIS B 892 ASN B1129 HIS B1146 GLN B1173 ASN B1508 ASN B1733 GLN B1744 ASN ** B2084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2534 ASN B2673 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065096 restraints weight = 80025.732| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.33 r_work: 0.3073 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30190 Z= 0.143 Angle : 0.610 19.370 41124 Z= 0.306 Chirality : 0.047 0.396 4718 Planarity : 0.004 0.047 5228 Dihedral : 9.549 112.911 4858 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 3.22 % Allowed : 20.36 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3718 helix: 0.06 (0.33), residues: 262 sheet: -0.45 (0.15), residues: 1230 loop : -0.86 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 907 TYR 0.017 0.001 TYR B1716 PHE 0.011 0.001 PHE B2565 TRP 0.008 0.001 TRP B2460 HIS 0.006 0.001 HIS A1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (30142) covalent geometry : angle 0.57220 / 0.30 (40998) SS BOND : bond 0.00234 / 0.18 ( 18) SS BOND : angle 0.79690 / 0.51 ( 36) hydrogen bonds : bond 0.04730 / 3.20 ( 962) hydrogen bonds : angle 6.56380 / 4.57 ( 3177) link_BETA1-4 : bond 0.00599 / 0.22 ( 8) link_BETA1-4 : angle 2.45914 / 1.48 ( 24) link_NAG-ASN : bond 0.00987 / 0.54 ( 22) link_NAG-ASN : angle 5.06077 / 3.54 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 141 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1159 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8680 (tmt) REVERT: A 1377 ASP cc_start: 0.7349 (t0) cc_final: 0.7060 (t70) REVERT: A 1551 SER cc_start: 0.9093 (m) cc_final: 0.8877 (p) REVERT: A 1885 MET cc_start: 0.8186 (tmm) cc_final: 0.7889 (tmm) REVERT: A 2115 MET cc_start: 0.7844 (mmm) cc_final: 0.7025 (mpm) REVERT: B 1159 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8688 (tmt) REVERT: B 1377 ASP cc_start: 0.7280 (t0) cc_final: 0.7001 (t70) REVERT: B 1885 MET cc_start: 0.8219 (tmm) cc_final: 0.7924 (tmm) REVERT: B 1994 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8752 (ttpt) REVERT: B 2115 MET cc_start: 0.7851 (mmm) cc_final: 0.7032 (mpm) outliers start: 97 outliers final: 29 residues processed: 224 average time/residue: 0.4470 time to fit residues: 126.8657 Evaluate side-chains 160 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 1159 MET Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1898 GLU Chi-restraints excluded: chain B residue 1994 LYS Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2544 LEU Chi-restraints excluded: chain B residue 2614 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [96, 295, 129, 353, 133, 169, 191, 323, 334, 199, 160] chunk 96 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 169 optimal weight: 0.0970 chunk 191 optimal weight: 0.9980 chunk 323 optimal weight: 8.9990 chunk 334 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1326 GLN ** A2084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1326 GLN ** B2084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.085577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065660 restraints weight = 79670.888| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.32 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30190 Z= 0.107 Angle : 0.578 19.251 41124 Z= 0.282 Chirality : 0.046 0.419 4718 Planarity : 0.003 0.047 5228 Dihedral : 8.288 110.430 4834 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 2.88 % Allowed : 20.36 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3718 helix: 0.40 (0.34), residues: 250 sheet: -0.33 (0.15), residues: 1206 loop : -0.82 (0.14), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2672 TYR 0.021 0.001 TYR B 898 PHE 0.014 0.001 PHE B 895 TRP 0.009 0.001 TRP B1902 HIS 0.004 0.001 HIS A1231 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (30142) covalent geometry : angle 0.53881 / 0.27 (40998) SS BOND : bond 0.00115 / 0.10 ( 18) SS BOND : angle 0.55910 / 0.34 ( 36) hydrogen bonds : bond 0.03758 / 2.53 ( 962) hydrogen bonds : angle 5.77019 / 4.00 ( 3177) link_BETA1-4 : bond 0.00823 / 0.31 ( 8) link_BETA1-4 : angle 2.58427 / 1.46 ( 24) link_NAG-ASN : bond 0.00932 / 0.51 ( 22) link_NAG-ASN : angle 5.02786 / 3.58 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 146 time to evaluate : 1.179 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 1159 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8735 (tmt) REVERT: A 1244 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8615 (tm) REVERT: A 1253 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7816 (ttp-110) REVERT: A 1313 ILE cc_start: 0.7992 (mt) cc_final: 0.7790 (mp) REVERT: A 1377 ASP cc_start: 0.7536 (t0) cc_final: 0.7183 (t70) REVERT: A 1551 SER cc_start: 0.9086 (m) cc_final: 0.8856 (p) REVERT: A 1885 MET cc_start: 0.8121 (tmm) cc_final: 0.7895 (tmm) REVERT: A 1898 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 2115 MET cc_start: 0.7780 (mmm) cc_final: 0.7228 (mpt) REVERT: A 2449 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: A 2627 MET cc_start: 0.8338 (mtp) cc_final: 0.7991 (mtp) REVERT: B 847 TYR cc_start: 0.8447 (t80) cc_final: 0.8104 (t80) REVERT: B 1159 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8728 (tmt) REVERT: B 1244 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8617 (tm) REVERT: B 1253 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7862 (ttp-110) REVERT: B 1377 ASP cc_start: 0.7477 (t0) cc_final: 0.7132 (t70) REVERT: B 1647 ASP cc_start: 0.8574 (m-30) cc_final: 0.8275 (m-30) REVERT: B 1885 MET cc_start: 0.8174 (tmm) cc_final: 0.7831 (tmm) REVERT: B 2115 MET cc_start: 0.7767 (mmm) cc_final: 0.7197 (mpt) REVERT: B 2164 MET cc_start: 0.7087 (pmm) cc_final: 0.6571 (pmm) REVERT: B 2449 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7548 (pm20) outliers start: 87 outliers final: 29 residues processed: 222 average time/residue: 0.4848 time to fit residues: 133.4526 Evaluate side-chains 167 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1253 ARG Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 1159 MET Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1253 ARG Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2449 GLU Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2544 LEU Chi-restraints excluded: chain B residue 2595 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [311, 77, 180, 2, 372, 15, 63, 72, 17, 364, 6] chunk 311 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 372 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 364 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1627 HIS ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1932 ASN A2084 GLN ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2434 HIS ** B1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN B1627 HIS ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 ASN B2084 GLN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2434 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.081552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061248 restraints weight = 80315.986| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.31 r_work: 0.2981 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 30190 Z= 0.298 Angle : 0.706 18.346 41124 Z= 0.351 Chirality : 0.049 0.396 4718 Planarity : 0.005 0.051 5228 Dihedral : 8.165 110.388 4829 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer: Outliers : 3.75 % Allowed : 20.95 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3718 helix: 0.20 (0.33), residues: 262 sheet: -0.56 (0.14), residues: 1242 loop : -0.93 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1388 TYR 0.026 0.002 TYR B1716 PHE 0.014 0.002 PHE A 945 TRP 0.021 0.002 TRP A2460 HIS 0.005 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.30 (30142) covalent geometry : angle 0.67468 / 0.34 (40998) SS BOND : bond 0.00265 / 0.17 ( 18) SS BOND : angle 0.87626 / 0.64 ( 36) hydrogen bonds : bond 0.04172 / 2.81 ( 962) hydrogen bonds : angle 5.79929 / 4.00 ( 3177) link_BETA1-4 : bond 0.00663 / 0.35 ( 8) link_BETA1-4 : angle 2.49814 / 1.47 ( 24) link_NAG-ASN : bond 0.00943 / 0.51 ( 22) link_NAG-ASN : angle 5.04702 / 3.67 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 131 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1244 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8694 (tm) REVERT: A 1377 ASP cc_start: 0.7475 (t70) cc_final: 0.7096 (t70) REVERT: A 1548 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8025 (p90) REVERT: A 1647 ASP cc_start: 0.8694 (m-30) cc_final: 0.8429 (m-30) REVERT: A 1901 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8408 (ppp) REVERT: A 2115 MET cc_start: 0.7918 (mmm) cc_final: 0.7365 (mpt) REVERT: A 2449 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: B 1244 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8695 (tm) REVERT: B 1377 ASP cc_start: 0.7453 (t70) cc_final: 0.7086 (t70) REVERT: B 1548 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8049 (p90) REVERT: B 1647 ASP cc_start: 0.8691 (m-30) cc_final: 0.8460 (m-30) REVERT: B 2115 MET cc_start: 0.7951 (mmm) cc_final: 0.7380 (mpt) REVERT: B 2449 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (pm20) outliers start: 113 outliers final: 52 residues processed: 228 average time/residue: 0.4499 time to fit residues: 129.9162 Evaluate side-chains 179 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 120 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1126 ASP Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1322 ARG Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1790 LEU Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2449 GLU Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2544 LEU Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [64, 363, 49, 290, 149, 181, 344, 214, 283, 179, 187] chunk 64 optimal weight: 8.9990 chunk 363 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 344 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 770 HIS ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.082622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062447 restraints weight = 79945.969| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.31 r_work: 0.3010 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30190 Z= 0.162 Angle : 0.616 18.642 41124 Z= 0.301 Chirality : 0.046 0.426 4718 Planarity : 0.004 0.049 5228 Dihedral : 7.563 108.033 4822 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 3.61 % Allowed : 21.52 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3718 helix: 0.31 (0.33), residues: 262 sheet: -0.46 (0.15), residues: 1186 loop : -1.00 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2672 TYR 0.020 0.001 TYR B1716 PHE 0.012 0.001 PHE B2565 TRP 0.017 0.001 TRP B2460 HIS 0.003 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (30142) covalent geometry : angle 0.57883 / 0.29 (40998) SS BOND : bond 0.00148 / 0.11 ( 18) SS BOND : angle 0.62604 / 0.43 ( 36) hydrogen bonds : bond 0.03530 / 2.38 ( 962) hydrogen bonds : angle 5.54375 / 3.83 ( 3177) link_BETA1-4 : bond 0.00751 / 0.26 ( 8) link_BETA1-4 : angle 2.47648 / 1.41 ( 24) link_NAG-ASN : bond 0.00902 / 0.48 ( 22) link_NAG-ASN : angle 5.06647 / 3.67 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 129 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 770 HIS cc_start: 0.7896 (p90) cc_final: 0.7599 (p-80) REVERT: A 1126 ASP cc_start: 0.7752 (p0) cc_final: 0.7484 (p0) REVERT: A 1244 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8629 (tm) REVERT: A 1314 TYR cc_start: 0.7656 (m-80) cc_final: 0.7377 (m-80) REVERT: A 1320 MET cc_start: 0.7743 (mtt) cc_final: 0.7539 (mtp) REVERT: A 1377 ASP cc_start: 0.7439 (t70) cc_final: 0.7023 (t70) REVERT: A 1548 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7975 (p90) REVERT: A 1647 ASP cc_start: 0.8683 (m-30) cc_final: 0.8433 (m-30) REVERT: A 2115 MET cc_start: 0.7871 (mmm) cc_final: 0.7257 (mpt) REVERT: A 2449 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 770 HIS cc_start: 0.7994 (p90) cc_final: 0.7729 (p-80) REVERT: B 847 TYR cc_start: 0.8487 (t80) cc_final: 0.8145 (t80) REVERT: B 1126 ASP cc_start: 0.7735 (p0) cc_final: 0.7461 (p0) REVERT: B 1244 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8631 (tm) REVERT: B 1377 ASP cc_start: 0.7384 (t70) cc_final: 0.6978 (t70) REVERT: B 1548 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8017 (p90) REVERT: B 1647 ASP cc_start: 0.8697 (m-30) cc_final: 0.8440 (m-30) REVERT: B 2115 MET cc_start: 0.7897 (mmm) cc_final: 0.7287 (mpt) outliers start: 109 outliers final: 55 residues processed: 228 average time/residue: 0.4446 time to fit residues: 128.1783 Evaluate side-chains 178 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1551 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2278 VAL Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1375 VAL Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2544 LEU Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [244, 134, 361, 150, 267, 29, 239, 116, 125, 356, 340] chunk 244 optimal weight: 40.0000 chunk 134 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 267 optimal weight: 0.3980 chunk 29 optimal weight: 40.0000 chunk 239 optimal weight: 40.0000 chunk 116 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 chunk 340 optimal weight: 9.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2084 GLN ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2294 GLN ** B1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2084 GLN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.080769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060521 restraints weight = 80024.953| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.29 r_work: 0.2966 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30190 Z= 0.299 Angle : 0.702 17.988 41124 Z= 0.348 Chirality : 0.049 0.437 4718 Planarity : 0.005 0.051 5228 Dihedral : 7.736 107.081 4822 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.02 % Favored : 91.88 % Rotamer: Outliers : 4.28 % Allowed : 21.15 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3718 helix: 0.18 (0.32), residues: 262 sheet: -0.71 (0.14), residues: 1270 loop : -1.05 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B2672 TYR 0.027 0.002 TYR B1716 PHE 0.014 0.002 PHE B2565 TRP 0.025 0.002 TRP A2460 HIS 0.007 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.30 (30142) covalent geometry : angle 0.66989 / 0.34 (40998) SS BOND : bond 0.00275 / 0.18 ( 18) SS BOND : angle 0.89445 / 0.66 ( 36) hydrogen bonds : bond 0.03917 / 2.65 ( 962) hydrogen bonds : angle 5.67423 / 3.91 ( 3177) link_BETA1-4 : bond 0.00690 / 0.34 ( 8) link_BETA1-4 : angle 2.61962 / 1.51 ( 24) link_NAG-ASN : bond 0.00980 / 0.52 ( 22) link_NAG-ASN : angle 5.03970 / 3.69 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 116 time to evaluate : 1.059 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 1079 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8747 (mtmt) REVERT: A 1244 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8665 (tm) REVERT: A 1299 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7413 (mm) REVERT: A 1305 MET cc_start: 0.8656 (mtp) cc_final: 0.8228 (mtt) REVERT: A 1377 ASP cc_start: 0.7399 (t70) cc_final: 0.6996 (t70) REVERT: A 1548 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8032 (p90) REVERT: A 1647 ASP cc_start: 0.8711 (m-30) cc_final: 0.8463 (m-30) REVERT: A 2115 MET cc_start: 0.7935 (mmm) cc_final: 0.7365 (mpt) REVERT: A 2177 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 1079 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8746 (mtmt) REVERT: B 1244 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8648 (tm) REVERT: B 1305 MET cc_start: 0.8678 (mtp) cc_final: 0.8264 (mtt) REVERT: B 1377 ASP cc_start: 0.7390 (t70) cc_final: 0.7001 (t70) REVERT: B 1548 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8029 (p90) REVERT: B 1647 ASP cc_start: 0.8715 (m-30) cc_final: 0.8468 (m-30) REVERT: B 2115 MET cc_start: 0.7945 (mmm) cc_final: 0.7367 (mpt) outliers start: 129 outliers final: 69 residues processed: 234 average time/residue: 0.4031 time to fit residues: 121.4071 Evaluate side-chains 189 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 112 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1079 LYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1551 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2177 LEU Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2278 VAL Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1079 LYS Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1375 VAL Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1675 ILE Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1790 LEU Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2253 SER Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2544 LEU Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2614 MET Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [21, 83, 95, 226, 326, 44, 198, 307, 13, 266, 281] chunk 21 optimal weight: 40.0000 chunk 83 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061306 restraints weight = 79976.556| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.29 r_work: 0.2985 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30190 Z= 0.211 Angle : 0.641 17.889 41124 Z= 0.316 Chirality : 0.048 0.451 4718 Planarity : 0.004 0.049 5228 Dihedral : 7.417 102.706 4822 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 3.71 % Allowed : 22.02 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3718 helix: 0.32 (0.33), residues: 262 sheet: -0.64 (0.15), residues: 1256 loop : -1.06 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2672 TYR 0.022 0.001 TYR B1716 PHE 0.013 0.001 PHE A1200 TRP 0.022 0.001 TRP A2460 HIS 0.005 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (30142) covalent geometry : angle 0.60603 / 0.31 (40998) SS BOND : bond 0.00201 / 0.14 ( 18) SS BOND : angle 0.71676 / 0.50 ( 36) hydrogen bonds : bond 0.03548 / 2.40 ( 962) hydrogen bonds : angle 5.52296 / 3.81 ( 3177) link_BETA1-4 : bond 0.00750 / 0.29 ( 8) link_BETA1-4 : angle 2.56017 / 1.45 ( 24) link_NAG-ASN : bond 0.00924 / 0.48 ( 22) link_NAG-ASN : angle 5.04086 / 3.70 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 119 time to evaluate : 1.187 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 1244 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8613 (tm) REVERT: A 1305 MET cc_start: 0.8669 (mtp) cc_final: 0.8232 (mtt) REVERT: A 1377 ASP cc_start: 0.7362 (t70) cc_final: 0.6970 (t70) REVERT: A 1548 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7967 (p90) REVERT: A 1647 ASP cc_start: 0.8702 (m-30) cc_final: 0.8460 (m-30) REVERT: A 2115 MET cc_start: 0.7909 (mmm) cc_final: 0.7262 (mpt) REVERT: B 1244 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8622 (tm) REVERT: B 1305 MET cc_start: 0.8688 (mtp) cc_final: 0.8272 (mtt) REVERT: B 1377 ASP cc_start: 0.7395 (t70) cc_final: 0.7005 (t70) REVERT: B 1548 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7895 (p90) REVERT: B 1647 ASP cc_start: 0.8696 (m-30) cc_final: 0.8457 (m-30) REVERT: B 2115 MET cc_start: 0.7932 (mmm) cc_final: 0.7284 (mpt) REVERT: B 2177 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8528 (mp) outliers start: 112 outliers final: 67 residues processed: 220 average time/residue: 0.3982 time to fit residues: 114.1378 Evaluate side-chains 188 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 116 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1551 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2278 VAL Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 796 ASN Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1375 VAL Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1790 LEU Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2177 LEU Chi-restraints excluded: chain B residue 2253 SER Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2614 MET Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [241, 198, 57, 68, 226, 133, 244, 136, 173, 292, 63] chunk 241 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 244 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 292 optimal weight: 0.0370 chunk 63 optimal weight: 10.0000 overall best weight: 2.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 GLN ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1760 GLN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.082207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062045 restraints weight = 79663.545| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.30 r_work: 0.3002 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30190 Z= 0.157 Angle : 0.618 17.641 41124 Z= 0.301 Chirality : 0.047 0.456 4718 Planarity : 0.004 0.048 5228 Dihedral : 7.117 98.263 4822 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 3.65 % Allowed : 22.12 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3718 helix: 0.38 (0.33), residues: 262 sheet: -0.53 (0.15), residues: 1224 loop : -1.05 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2672 TYR 0.020 0.001 TYR B1716 PHE 0.012 0.001 PHE A1200 TRP 0.016 0.001 TRP B2460 HIS 0.004 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (30142) covalent geometry : angle 0.58222 / 0.29 (40998) SS BOND : bond 0.00163 / 0.12 ( 18) SS BOND : angle 0.59190 / 0.41 ( 36) hydrogen bonds : bond 0.03315 / 2.24 ( 962) hydrogen bonds : angle 5.34590 / 3.69 ( 3177) link_BETA1-4 : bond 0.00711 / 0.26 ( 8) link_BETA1-4 : angle 2.50428 / 1.41 ( 24) link_NAG-ASN : bond 0.00916 / 0.48 ( 22) link_NAG-ASN : angle 4.98630 / 3.65 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 120 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1244 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8591 (tm) REVERT: A 1305 MET cc_start: 0.8668 (mtp) cc_final: 0.8250 (mtt) REVERT: A 1377 ASP cc_start: 0.7395 (t70) cc_final: 0.6977 (t70) REVERT: A 1548 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7921 (p90) REVERT: A 1647 ASP cc_start: 0.8687 (m-30) cc_final: 0.8446 (m-30) REVERT: A 1994 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8794 (ttpt) REVERT: A 2115 MET cc_start: 0.7806 (mmm) cc_final: 0.7162 (mpt) REVERT: B 1031 MET cc_start: 0.8577 (mpt) cc_final: 0.6956 (mpt) REVERT: B 1244 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8596 (tm) REVERT: B 1305 MET cc_start: 0.8654 (mtp) cc_final: 0.8200 (mtm) REVERT: B 1377 ASP cc_start: 0.7383 (t70) cc_final: 0.6981 (t70) REVERT: B 1509 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 1548 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7843 (p90) REVERT: B 1647 ASP cc_start: 0.8694 (m-30) cc_final: 0.8452 (m-30) REVERT: B 1994 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8806 (ttpt) REVERT: B 2115 MET cc_start: 0.7816 (mmm) cc_final: 0.7177 (mpt) REVERT: B 2177 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8540 (mp) outliers start: 110 outliers final: 69 residues processed: 221 average time/residue: 0.4253 time to fit residues: 120.6810 Evaluate side-chains 192 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 115 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1551 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1656 ASN Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 1994 LYS Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2278 VAL Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2614 MET Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 796 ASN Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1509 ILE Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1656 ASN Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 1994 LYS Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2177 LEU Chi-restraints excluded: chain B residue 2253 SER Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2614 MET Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [85, 321, 153, 46, 272, 360, 59, 362, 2, 345, 88] chunk 85 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 360 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 770 HIS ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2597 GLN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.081943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061742 restraints weight = 79796.469| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.30 r_work: 0.2993 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30190 Z= 0.187 Angle : 0.632 17.320 41124 Z= 0.309 Chirality : 0.047 0.457 4718 Planarity : 0.004 0.048 5228 Dihedral : 7.072 95.102 4822 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 3.48 % Allowed : 22.75 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3718 helix: 0.41 (0.33), residues: 262 sheet: -0.54 (0.15), residues: 1236 loop : -1.06 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2672 TYR 0.027 0.001 TYR A 898 PHE 0.013 0.001 PHE A1200 TRP 0.016 0.001 TRP A2460 HIS 0.005 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (30142) covalent geometry : angle 0.59798 / 0.30 (40998) SS BOND : bond 0.00195 / 0.14 ( 18) SS BOND : angle 0.64262 / 0.45 ( 36) hydrogen bonds : bond 0.03384 / 2.29 ( 962) hydrogen bonds : angle 5.33706 / 3.68 ( 3177) link_BETA1-4 : bond 0.00759 / 0.28 ( 8) link_BETA1-4 : angle 2.55048 / 1.44 ( 24) link_NAG-ASN : bond 0.00900 / 0.47 ( 22) link_NAG-ASN : angle 4.93988 / 3.62 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 117 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1244 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8611 (tm) REVERT: A 1305 MET cc_start: 0.8673 (mtp) cc_final: 0.8268 (mtt) REVERT: A 1377 ASP cc_start: 0.7386 (t70) cc_final: 0.6981 (t70) REVERT: A 1509 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (mp) REVERT: A 1548 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7923 (p90) REVERT: A 1647 ASP cc_start: 0.8687 (m-30) cc_final: 0.8468 (m-30) REVERT: A 1994 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (ttpt) REVERT: A 2115 MET cc_start: 0.7772 (mmm) cc_final: 0.7130 (mpt) REVERT: B 854 ILE cc_start: 0.7687 (tp) cc_final: 0.7057 (mt) REVERT: B 1031 MET cc_start: 0.8547 (mpt) cc_final: 0.7016 (mpt) REVERT: B 1244 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8617 (tm) REVERT: B 1305 MET cc_start: 0.8659 (mtp) cc_final: 0.8214 (mtm) REVERT: B 1377 ASP cc_start: 0.7401 (t70) cc_final: 0.7001 (t70) REVERT: B 1548 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7928 (p90) REVERT: B 1647 ASP cc_start: 0.8694 (m-30) cc_final: 0.8474 (m-30) REVERT: B 2115 MET cc_start: 0.7776 (mmm) cc_final: 0.7144 (mpt) REVERT: B 2177 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8555 (mp) outliers start: 105 outliers final: 72 residues processed: 213 average time/residue: 0.4234 time to fit residues: 114.6895 Evaluate side-chains 196 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 117 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1551 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1656 ASN Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 1994 LYS Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2278 VAL Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 796 ASN Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1656 ASN Chi-restraints excluded: chain B residue 1675 ILE Chi-restraints excluded: chain B residue 1696 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 1995 THR Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2177 LEU Chi-restraints excluded: chain B residue 2253 SER Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2614 MET Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [22, 295, 16, 67, 8, 286, 54, 28, 120, 216, 142] chunk 22 optimal weight: 0.5980 chunk 295 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2084 GLN ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 GLN A2597 GLN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.082532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062380 restraints weight = 79391.972| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.30 r_work: 0.3010 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30190 Z= 0.147 Angle : 0.623 16.668 41124 Z= 0.300 Chirality : 0.047 0.437 4718 Planarity : 0.004 0.047 5228 Dihedral : 6.798 87.875 4822 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 2.82 % Allowed : 23.41 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3718 helix: 0.47 (0.33), residues: 262 sheet: -0.50 (0.15), residues: 1226 loop : -0.99 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2672 TYR 0.019 0.001 TYR B1716 PHE 0.011 0.001 PHE B2565 TRP 0.014 0.001 TRP A2460 HIS 0.004 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (30142) covalent geometry : angle 0.58886 / 0.29 (40998) SS BOND : bond 0.00160 / 0.12 ( 18) SS BOND : angle 0.55878 / 0.37 ( 36) hydrogen bonds : bond 0.03220 / 2.17 ( 962) hydrogen bonds : angle 5.21629 / 3.60 ( 3177) link_BETA1-4 : bond 0.00758 / 0.28 ( 8) link_BETA1-4 : angle 2.48095 / 1.38 ( 24) link_NAG-ASN : bond 0.00901 / 0.47 ( 22) link_NAG-ASN : angle 4.88050 / 3.57 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 121 time to evaluate : 0.824 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 854 ILE cc_start: 0.7642 (tp) cc_final: 0.7004 (mt) REVERT: A 1244 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8585 (tm) REVERT: A 1305 MET cc_start: 0.8614 (mtp) cc_final: 0.8179 (mtm) REVERT: A 1377 ASP cc_start: 0.7404 (t70) cc_final: 0.6998 (t70) REVERT: A 1509 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 1548 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7844 (p90) REVERT: A 1647 ASP cc_start: 0.8704 (m-30) cc_final: 0.8461 (m-30) REVERT: A 1994 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8784 (ttpt) REVERT: A 2115 MET cc_start: 0.7747 (mmm) cc_final: 0.7070 (mpt) REVERT: A 2125 MET cc_start: 0.8976 (mmm) cc_final: 0.8767 (mmm) REVERT: B 854 ILE cc_start: 0.7576 (tp) cc_final: 0.6920 (mt) REVERT: B 1031 MET cc_start: 0.8540 (mpt) cc_final: 0.6943 (mpt) REVERT: B 1244 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8590 (tm) REVERT: B 1305 MET cc_start: 0.8646 (mtp) cc_final: 0.8171 (mtm) REVERT: B 1377 ASP cc_start: 0.7381 (t70) cc_final: 0.6973 (t70) REVERT: B 1509 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 1548 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7859 (p90) REVERT: B 1647 ASP cc_start: 0.8704 (m-30) cc_final: 0.8462 (m-30) REVERT: B 2115 MET cc_start: 0.7728 (mmm) cc_final: 0.7047 (mpt) REVERT: B 2125 MET cc_start: 0.8975 (mmm) cc_final: 0.8724 (mmm) REVERT: B 2177 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8522 (mp) outliers start: 85 outliers final: 67 residues processed: 201 average time/residue: 0.4312 time to fit residues: 110.9400 Evaluate side-chains 194 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1322 ARG Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1551 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1656 ASN Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1937 ASN Chi-restraints excluded: chain A residue 1941 ILE Chi-restraints excluded: chain A residue 1994 LYS Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2135 ILE Chi-restraints excluded: chain A residue 2141 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2278 VAL Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2653 GLN Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1244 LEU Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1375 VAL Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1509 ILE Chi-restraints excluded: chain B residue 1548 TYR Chi-restraints excluded: chain B residue 1549 THR Chi-restraints excluded: chain B residue 1650 SER Chi-restraints excluded: chain B residue 1656 ASN Chi-restraints excluded: chain B residue 1675 ILE Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1836 ASN Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1937 ASN Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 1995 THR Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2135 ILE Chi-restraints excluded: chain B residue 2141 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2177 LEU Chi-restraints excluded: chain B residue 2278 VAL Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2481 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2614 MET Chi-restraints excluded: chain B residue 2653 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: [115, 124, 166, 21, 84, 239, 59, 158, 331, 313, 270] chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 239 optimal weight: 0.0050 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 770 HIS ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2084 GLN ** A2261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS ** B1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 HIS ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.081646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.061430 restraints weight = 80086.842| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.30 r_work: 0.2987 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30190 Z= 0.205 Angle : 0.652 15.772 41124 Z= 0.317 Chirality : 0.047 0.419 4718 Planarity : 0.004 0.048 5228 Dihedral : 6.806 80.357 4822 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.88 % Favored : 92.01 % Rotamer: Outliers : 3.08 % Allowed : 23.14 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3718 helix: 0.50 (0.34), residues: 250 sheet: -0.58 (0.15), residues: 1238 loop : -0.99 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B2672 TYR 0.022 0.002 TYR B1716 PHE 0.012 0.001 PHE B2565 TRP 0.017 0.001 TRP B2460 HIS 0.004 0.001 HIS B1731 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (30142) covalent geometry : angle 0.62089 / 0.31 (40998) SS BOND : bond 0.00206 / 0.14 ( 18) SS BOND : angle 0.66892 / 0.47 ( 36) hydrogen bonds : bond 0.03425 / 2.31 ( 962) hydrogen bonds : angle 5.30882 / 3.66 ( 3177) link_BETA1-4 : bond 0.00799 / 0.31 ( 8) link_BETA1-4 : angle 2.58184 / 1.44 ( 24) link_NAG-ASN : bond 0.00885 / 0.46 ( 22) link_NAG-ASN : angle 4.79182 / 3.51 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6201.12 seconds wall clock time: 107 minutes 18.55 seconds (6438.55 seconds total)