Starting phenix.real_space_refine on Wed May 28 02:09:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r50_18889/05_2025/8r50_18889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r50_18889/05_2025/8r50_18889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r50_18889/05_2025/8r50_18889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r50_18889/05_2025/8r50_18889.map" model { file = "/net/cci-nas-00/data/ceres_data/8r50_18889/05_2025/8r50_18889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r50_18889/05_2025/8r50_18889.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 126 5.16 5 C 18840 2.51 5 N 5078 2.21 5 O 5708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29752 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 14651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1889, 14651 Classifications: {'peptide': 1889} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 73, 'TRANS': 1815} Chain breaks: 15 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 247 Chain: "A" Number of atoms: 14651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1889, 14651 Classifications: {'peptide': 1889} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 73, 'TRANS': 1815} Chain breaks: 15 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 247 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: "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 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 Time building chain proxies: 16.41, per 1000 atoms: 0.55 Number of scatterers: 29752 At special positions: 0 Unit cell: (176.396, 176.396, 96.976, 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 126 16.00 O 5708 8.00 N 5078 7.00 C 18840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 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 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 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 B1560 " " NAG D 1 " - " ASN B1656 " " NAG E 1 " - " ASN B1751 " " NAG F 1 " - " ASN B2280 " " NAG G 1 " - " ASN A1560 " " NAG H 1 " - " ASN A1656 " " NAG I 1 " - " ASN A1751 " " NAG J 1 " - " ASN A2280 " Time building additional restraints: 7.26 Conformation dependent library (CDL) restraints added in 3.6 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 52 sheets defined 9.5% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'B' and resid 754 through 758 removed outlier: 3.552A pdb=" N SER B 758 " --> pdb=" O LEU B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.942A pdb=" N ARG B 822 " --> pdb=" O PRO B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 removed outlier: 3.767A pdb=" N ILE B 830 " --> pdb=" O ASP B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 841 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 1352 through 1356 removed outlier: 3.697A pdb=" N VAL B1356 " --> pdb=" O ILE B1353 " (cutoff:3.500A) 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: 3.650A pdb=" N THR B2420 " --> pdb=" O LYS B2416 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.531A pdb=" N LEU B2426 " --> pdb=" O VAL B2422 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B2427 " --> pdb=" O ASN B2423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2422 through 2427' Processing helix chain 'B' and resid 2432 through 2437 removed outlier: 3.946A 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 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 2545 removed outlier: 3.763A pdb=" N LYS B2539 " --> pdb=" O GLU B2535 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B2540 " --> pdb=" O ASP B2536 " (cutoff:3.500A) Processing helix chain 'B' and resid 2571 through 2576 removed outlier: 3.838A pdb=" N GLY B2576 " --> pdb=" O GLU B2572 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2659 Processing helix chain 'B' and resid 2667 through 2677 Processing helix chain 'B' and resid 2694 through 2702 removed outlier: 4.129A pdb=" N ASP B2699 " --> pdb=" O GLU B2696 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA B2701 " --> pdb=" O ALA B2698 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN B2702 " --> pdb=" O ASP B2699 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.551A pdb=" N SER A 758 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 removed outlier: 3.942A pdb=" N ARG A 822 " --> pdb=" O PRO A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 3.767A pdb=" N ILE A 830 " --> pdb=" O ASP A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 841 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 1352 through 1356 removed outlier: 3.697A pdb=" N VAL A1356 " --> pdb=" O ILE A1353 " (cutoff:3.500A) 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: 3.650A pdb=" N THR A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.530A pdb=" N LEU A2426 " --> pdb=" O VAL A2422 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A2427 " --> pdb=" O ASN A2423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2422 through 2427' Processing helix chain 'A' and resid 2432 through 2437 removed outlier: 3.945A 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 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 2545 removed outlier: 3.763A pdb=" N LYS A2539 " --> pdb=" O GLU A2535 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A2540 " --> pdb=" O ASP A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2576 removed outlier: 3.838A pdb=" N GLY A2576 " --> pdb=" O GLU A2572 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2659 Processing helix chain 'A' and resid 2667 through 2677 Processing helix chain 'A' and resid 2694 through 2702 removed outlier: 4.130A pdb=" N ASP A2699 " --> pdb=" O GLU A2696 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA A2701 " --> pdb=" O ALA A2698 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN A2702 " --> pdb=" O ASP A2699 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 768 through 773 removed outlier: 5.524A pdb=" N GLY B 760 " --> pdb=" O THR A2599 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR A2599 " --> pdb=" O GLY B 760 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A2597 " --> pdb=" O CYS B 762 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 764 " --> pdb=" O VAL A2595 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL A2595 " --> pdb=" O LEU B 764 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A2610 " --> pdb=" O TYR A2625 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A2619 " --> pdb=" O PHE A2616 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP A2561 " --> pdb=" O ALA A2620 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N HIS A2622 " --> pdb=" O ASP A2561 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A2563 " --> pdb=" O HIS A2622 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ARG A2624 " --> pdb=" O HIS A2563 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A2565 " --> pdb=" O ARG A2624 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A2547 " --> pdb=" O VAL A2525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 768 through 773 removed outlier: 5.524A pdb=" N GLY B 760 " --> pdb=" O THR A2599 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR A2599 " --> pdb=" O GLY B 760 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A2597 " --> pdb=" O CYS B 762 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 764 " --> pdb=" O VAL A2595 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL A2595 " --> pdb=" O LEU B 764 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A2610 " --> pdb=" O TYR A2625 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A2619 " --> pdb=" O PHE A2616 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP A2561 " --> pdb=" O ALA A2620 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N HIS A2622 " --> pdb=" O ASP A2561 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A2563 " --> pdb=" O HIS A2622 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ARG A2624 " --> pdb=" O HIS A2563 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A2565 " --> pdb=" O ARG A2624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 777 through 778 Processing sheet with id=AA4, first strand: chain 'B' and resid 911 through 912 removed outlier: 3.716A pdb=" N PHE B 912 " --> pdb=" O GLY B 878 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 878 " --> pdb=" O PHE B 912 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 915 through 917 Processing sheet with id=AA6, first strand: chain 'B' and resid 904 through 905 Processing sheet with id=AA7, first strand: chain 'B' and resid 974 through 977 Processing sheet with id=AA8, first strand: chain 'B' and resid 1001 through 1003 Processing sheet with id=AA9, first strand: chain 'B' and resid 1054 through 1059 removed outlier: 3.509A pdb=" N LYS B1042 " --> pdb=" O GLU B1093 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B1102 " --> pdb=" O TYR B1092 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1130 through 1132 Processing sheet with id=AB2, first strand: chain 'B' and resid 1154 through 1159 removed outlier: 5.768A pdb=" N VAL B1155 " --> pdb=" O SER B1515 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER B1515 " --> pdb=" O VAL B1155 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER B1157 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA B1513 " --> pdb=" O SER B1157 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B1502 " --> pdb=" O LEU B1493 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B1493 " --> pdb=" O TYR B1502 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B1504 " --> pdb=" O SER B1491 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1174 through 1175 Processing sheet with id=AB4, first strand: chain 'B' and resid 1195 through 1197 removed outlier: 6.532A pdb=" N VAL B1203 " --> pdb=" O VAL B1215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1235 through 1237 removed outlier: 5.582A pdb=" N LEU B1244 " --> pdb=" O PRO B1257 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B1253 " --> pdb=" O ASP B1248 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE B1254 " --> pdb=" O VAL B1273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1302 through 1307 removed outlier: 5.075A pdb=" N GLY B1304 " --> pdb=" O VAL B1316 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B1315 " --> pdb=" O ARG B1322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1361 through 1366 removed outlier: 3.762A pdb=" N ASP B1363 " --> pdb=" O LEU B1376 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1381 " --> pdb=" O ALA B1393 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1421 through 1426 removed outlier: 5.097A pdb=" N ALA B1421 " --> pdb=" O THR B1437 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR B1437 " --> pdb=" O ALA B1421 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B1423 " --> pdb=" O THR B1435 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B1445 " --> pdb=" O VAL B1457 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1527 through 1531 removed outlier: 3.568A pdb=" N TYR B1548 " --> pdb=" O ILE B1539 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN B1547 " --> pdb=" O ASN B1560 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN B1560 " --> pdb=" O GLN B1547 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR B1549 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B1571 " --> pdb=" O SER B1562 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR B1570 " --> pdb=" O ILE B1582 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B1574 " --> pdb=" O ASN B1578 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASN B1578 " --> pdb=" O ASP B1574 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG B1592 " --> pdb=" O ARG B1583 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP B1602 " --> pdb=" O MET B1614 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET B1614 " --> pdb=" O TRP B1602 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B1604 " --> pdb=" O LYS B1612 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS B1612 " --> pdb=" O PHE B1624 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B1622 " --> pdb=" O MET B1614 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B1621 " --> pdb=" O ASP B1638 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP B1638 " --> pdb=" O LEU B1621 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1623 " --> pdb=" O LYS B1636 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS B1636 " --> pdb=" O LEU B1623 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR B1625 " --> pdb=" O ALA B1634 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA B1634 " --> pdb=" O PHE B1646 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B1638 " --> pdb=" O TRP B1642 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TRP B1642 " --> pdb=" O ASP B1638 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR B1655 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1698 through 1704 removed outlier: 3.820A pdb=" N LYS B1749 " --> pdb=" O GLN B1733 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU B1735 " --> pdb=" O VAL B1747 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL B1747 " --> pdb=" O GLU B1735 " (cutoff:3.500A) removed outlier: 11.990A pdb=" N THR B1746 " --> pdb=" O PHE B1767 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N PHE B1767 " --> pdb=" O THR B1746 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA B1748 " --> pdb=" O TRP B1765 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B1764 " --> pdb=" O LEU B1783 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU B1783 " --> pdb=" O GLU B1764 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG B1766 " --> pdb=" O ARG B1781 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG B1781 " --> pdb=" O ARG B1766 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B1768 " --> pdb=" O PHE B1779 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B1779 " --> pdb=" O ARG B1768 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU B1770 " --> pdb=" O ASN B1777 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B1785 " --> pdb=" O ASN B1789 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASN B1789 " --> pdb=" O VAL B1785 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B1812 " --> pdb=" O PRO B1828 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG B1814 " --> pdb=" O TRP B1826 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP B1826 " --> pdb=" O ARG B1814 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B1816 " --> pdb=" O THR B1824 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR B1824 " --> pdb=" O VAL B1837 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA B1846 " --> pdb=" O VAL B1857 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1877 through 1879 removed outlier: 3.575A pdb=" N MET B1885 " --> pdb=" O PHE B1897 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B1907 " --> pdb=" O GLU B1898 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER B1906 " --> pdb=" O MET B1918 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B1952 " --> pdb=" O ASP B1943 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU B1951 " --> pdb=" O PHE B1964 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B1963 " --> pdb=" O ILE B1975 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B1975 " --> pdb=" O LEU B1963 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS B1965 " --> pdb=" O SER B1973 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B2005 " --> pdb=" O LEU B1998 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE B2012 " --> pdb=" O ILE B2016 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE B2016 " --> pdb=" O ILE B2012 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N LEU B2015 " --> pdb=" O TYR B2037 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N TYR B2037 " --> pdb=" O LEU B2015 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B2017 " --> pdb=" O TYR B2035 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B2045 " --> pdb=" O SER B2036 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1877 through 1879 removed outlier: 3.575A pdb=" N MET B1885 " --> pdb=" O PHE B1897 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B1907 " --> pdb=" O GLU B1898 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER B1906 " --> pdb=" O MET B1918 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B1952 " --> pdb=" O ASP B1943 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU B1951 " --> pdb=" O PHE B1964 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B1963 " --> pdb=" O ILE B1975 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B1975 " --> pdb=" O LEU B1963 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS B1965 " --> pdb=" O SER B1973 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B2005 " --> pdb=" O LEU B1998 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE B2012 " --> pdb=" O ILE B2016 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE B2016 " --> pdb=" O ILE B2012 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N LEU B2015 " --> pdb=" O TYR B2037 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N TYR B2037 " --> pdb=" O LEU B2015 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B2017 " --> pdb=" O TYR B2035 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B2045 " --> pdb=" O SER B2036 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 2061 through 2062 removed outlier: 5.101A pdb=" N GLU B2070 " --> pdb=" O VAL B2077 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B2076 " --> pdb=" O SER B2087 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B2109 " --> pdb=" O THR B2092 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS B2104 " --> pdb=" O THR B2119 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B2119 " --> pdb=" O LYS B2104 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B2106 " --> pdb=" O TRP B2117 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP B2117 " --> pdb=" O ILE B2106 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR B2108 " --> pdb=" O MET B2115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 2145 through 2148 removed outlier: 3.967A pdb=" N TRP B2165 " --> pdb=" O VAL B2157 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B2159 " --> pdb=" O ILE B2163 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE B2163 " --> pdb=" O LEU B2159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 2168 through 2169 removed outlier: 6.397A pdb=" N ASN B2168 " --> pdb=" O HIS B2176 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HIS B2176 " --> pdb=" O LEU B2189 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B2178 " --> pdb=" O THR B2187 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU B2200 " --> pdb=" O PRO B2188 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG B2190 " --> pdb=" O THR B2198 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B2198 " --> pdb=" O TYR B2205 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG B2214 " --> pdb=" O PHE B2221 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B2231 " --> pdb=" O GLU B2222 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR B2230 " --> pdb=" O TYR B2243 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL B2252 " --> pdb=" O PHE B2264 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B2299 " --> pdb=" O TYR B2290 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B2298 " --> pdb=" O ILE B2310 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B2306 " --> pdb=" O ILE B2302 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B2342 " --> pdb=" O GLN B2333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 2358 through 2360 removed outlier: 3.723A pdb=" N LEU B2365 " --> pdb=" O ASP B2360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 2524 through 2525 removed outlier: 3.670A pdb=" N ALA B2547 " --> pdb=" O VAL B2525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 2524 through 2525 removed outlier: 3.670A pdb=" N ALA B2547 " --> pdb=" O VAL B2525 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP B2561 " --> pdb=" O ALA B2620 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N HIS B2622 " --> pdb=" O ASP B2561 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N HIS B2563 " --> pdb=" O HIS B2622 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG B2624 " --> pdb=" O HIS B2563 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE B2565 " --> pdb=" O ARG B2624 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B2619 " --> pdb=" O PHE B2616 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B2610 " --> pdb=" O TYR B2625 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL B2595 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 764 " --> pdb=" O VAL B2595 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B2597 " --> pdb=" O CYS A 762 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR B2599 " --> pdb=" O GLY A 760 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 760 " --> pdb=" O THR B2599 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 2684 through 2687 Processing sheet with id=AD2, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AD3, first strand: chain 'A' and resid 911 through 912 removed outlier: 3.716A pdb=" N PHE A 912 " --> pdb=" O GLY A 878 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 878 " --> pdb=" O PHE A 912 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 915 through 917 Processing sheet with id=AD5, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AD6, first strand: chain 'A' and resid 974 through 977 Processing sheet with id=AD7, first strand: chain 'A' and resid 1001 through 1003 Processing sheet with id=AD8, first strand: chain 'A' and resid 1054 through 1059 removed outlier: 3.509A pdb=" N LYS A1042 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A1102 " --> pdb=" O TYR A1092 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1130 through 1132 Processing sheet with id=AE1, first strand: chain 'A' and resid 1154 through 1159 removed outlier: 5.769A pdb=" N VAL A1155 " --> pdb=" O SER A1515 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER A1515 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER A1157 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A1513 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A1502 " --> pdb=" O LEU A1493 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1493 " --> pdb=" O TYR A1502 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A1504 " --> pdb=" O SER A1491 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1174 through 1175 Processing sheet with id=AE3, first strand: chain 'A' and resid 1195 through 1197 removed outlier: 6.531A pdb=" N VAL A1203 " --> pdb=" O VAL A1215 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1235 through 1237 removed outlier: 5.583A pdb=" N LEU A1244 " --> pdb=" O PRO A1257 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A1253 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A1254 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1302 through 1307 removed outlier: 5.075A pdb=" N GLY A1304 " --> pdb=" O VAL A1316 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A1315 " --> pdb=" O ARG A1322 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1361 through 1366 removed outlier: 3.762A pdb=" N ASP A1363 " --> pdb=" O LEU A1376 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1381 " --> pdb=" O ALA A1393 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1421 through 1426 removed outlier: 5.097A pdb=" N ALA A1421 " --> pdb=" O THR A1437 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR A1437 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A1423 " --> pdb=" O THR A1435 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A1445 " --> pdb=" O VAL A1457 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1527 through 1531 removed outlier: 3.568A pdb=" N TYR A1548 " --> pdb=" O ILE A1539 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN A1547 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A1560 " --> pdb=" O GLN A1547 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A1549 " --> pdb=" O LEU A1558 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1571 " --> pdb=" O SER A1562 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR A1570 " --> pdb=" O ILE A1582 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A1574 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASN A1578 " --> pdb=" O ASP A1574 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A1592 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS A1612 " --> pdb=" O PHE A1624 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A1622 " --> pdb=" O MET A1614 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A1621 " --> pdb=" O ASP A1638 " (cutoff:3.500A) removed outlier: 4.705A 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: 4.212A pdb=" N LYS A1636 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR A1625 " --> pdb=" O ALA A1634 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA A1634 " --> pdb=" O PHE A1646 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP A1638 " --> pdb=" O TRP A1642 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TRP A1642 " --> pdb=" O ASP A1638 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR A1655 " --> pdb=" O LEU A1667 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 1698 through 1704 removed outlier: 3.820A pdb=" N LYS A1749 " --> pdb=" O GLN A1733 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU A1735 " --> pdb=" O VAL A1747 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A1747 " --> pdb=" O GLU A1735 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N THR A1746 " --> pdb=" O PHE A1767 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N PHE A1767 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA A1748 " --> pdb=" O TRP A1765 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU A1764 " --> pdb=" O LEU A1783 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU A1783 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ARG A1766 " --> pdb=" O ARG A1781 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG A1781 " --> pdb=" O ARG A1766 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG A1768 " --> pdb=" O PHE A1779 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A1779 " --> pdb=" O ARG A1768 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A1770 " --> pdb=" O ASN A1777 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A1785 " --> pdb=" O ASN A1789 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU A1812 " --> pdb=" O PRO A1828 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A1814 " --> pdb=" O TRP A1826 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TRP A1826 " --> pdb=" O ARG A1814 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A1816 " --> pdb=" O THR A1824 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR A1824 " --> pdb=" O VAL A1837 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA A1846 " --> pdb=" O VAL A1857 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1877 through 1879 removed outlier: 3.574A pdb=" N MET A1885 " --> pdb=" O PHE A1897 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1907 " --> pdb=" O GLU A1898 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A1906 " --> pdb=" O MET A1918 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A1952 " --> pdb=" O ASP A1943 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A1951 " --> pdb=" O PHE A1964 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A1963 " --> pdb=" O ILE A1975 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A1975 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A1965 " --> pdb=" O SER A1973 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS A2005 " --> pdb=" O LEU A1998 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A2012 " --> pdb=" O ILE A2016 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE A2016 " --> pdb=" O ILE A2012 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N LEU A2015 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N TYR A2037 " --> pdb=" O LEU A2015 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A2017 " --> pdb=" O TYR A2035 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A2045 " --> pdb=" O SER A2036 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1877 through 1879 removed outlier: 3.574A pdb=" N MET A1885 " --> pdb=" O PHE A1897 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1907 " --> pdb=" O GLU A1898 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A1906 " --> pdb=" O MET A1918 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A1952 " --> pdb=" O ASP A1943 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A1951 " --> pdb=" O PHE A1964 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A1963 " --> pdb=" O ILE A1975 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A1975 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A1965 " --> pdb=" O SER A1973 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS A2005 " --> pdb=" O LEU A1998 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A2012 " --> pdb=" O ILE A2016 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE A2016 " --> pdb=" O ILE A2012 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N LEU A2015 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N TYR A2037 " --> pdb=" O LEU A2015 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A2017 " --> pdb=" O TYR A2035 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A2045 " --> pdb=" O SER A2036 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 2061 through 2062 removed outlier: 5.101A pdb=" N GLU A2070 " --> pdb=" O VAL A2077 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A2076 " --> pdb=" O SER A2087 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A2109 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS A2104 " --> pdb=" O THR A2119 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A2119 " --> pdb=" O LYS A2104 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A2106 " --> pdb=" O TRP A2117 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP A2117 " --> pdb=" O ILE A2106 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A2108 " --> pdb=" O MET A2115 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 2145 through 2148 removed outlier: 3.968A pdb=" N TRP A2165 " --> pdb=" O VAL A2157 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A2159 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE A2163 " --> pdb=" O LEU A2159 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 2168 through 2169 removed outlier: 6.397A pdb=" N ASN A2168 " --> pdb=" O HIS A2176 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS A2176 " --> pdb=" O LEU A2189 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A2178 " --> pdb=" O THR A2187 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU A2200 " --> pdb=" O PRO A2188 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG A2190 " --> pdb=" O THR A2198 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A2198 " --> pdb=" O TYR A2205 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG A2214 " --> pdb=" O PHE A2221 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A2231 " --> pdb=" O GLU A2222 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR A2230 " --> pdb=" O TYR A2243 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL A2252 " --> pdb=" O PHE A2264 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A2299 " --> pdb=" O TYR A2290 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A2298 " --> pdb=" O ILE A2310 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A2306 " --> pdb=" O ILE A2302 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A2342 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 2358 through 2360 removed outlier: 3.722A pdb=" N LEU A2365 " --> pdb=" O ASP A2360 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 2684 through 2687 1099 hydrogen bonds defined for protein. 2817 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: 23.82 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9682 1.34 - 1.46: 7096 1.46 - 1.58: 13402 1.58 - 1.69: 2 1.69 - 1.81: 204 Bond restraints: 30386 Sorted by residual: bond pdb=" N PRO A1586 " pdb=" CD PRO A1586 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.75e+01 bond pdb=" N PRO B1586 " pdb=" CD PRO B1586 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C1 NAG B2805 " pdb=" O5 NAG B2805 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" CB PRO B2054 " pdb=" CG PRO B2054 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.80e+00 ... (remaining 30381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 40679 1.79 - 3.58: 519 3.58 - 5.37: 60 5.37 - 7.16: 20 7.16 - 8.95: 8 Bond angle restraints: 41286 Sorted by residual: angle pdb=" N PRO B1586 " pdb=" CA PRO B1586 " pdb=" C PRO B1586 " ideal model delta sigma weight residual 114.27 106.59 7.68 1.35e+00 5.49e-01 3.23e+01 angle pdb=" N PRO A1586 " pdb=" CA PRO A1586 " pdb=" C PRO A1586 " ideal model delta sigma weight residual 114.27 106.61 7.66 1.35e+00 5.49e-01 3.22e+01 angle pdb=" N SER A1979 " pdb=" CA SER A1979 " pdb=" CB SER A1979 " ideal model delta sigma weight residual 110.88 103.63 7.25 1.38e+00 5.25e-01 2.76e+01 angle pdb=" N SER B1979 " pdb=" CA SER B1979 " pdb=" CB SER B1979 " ideal model delta sigma weight residual 110.88 103.63 7.25 1.38e+00 5.25e-01 2.76e+01 angle pdb=" CA PRO A2054 " pdb=" N PRO A2054 " pdb=" CD PRO A2054 " ideal model delta sigma weight residual 112.00 105.08 6.92 1.40e+00 5.10e-01 2.44e+01 ... (remaining 41281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 16305 21.22 - 42.43: 1727 42.43 - 63.65: 324 63.65 - 84.87: 58 84.87 - 106.09: 20 Dihedral angle restraints: 18434 sinusoidal: 7468 harmonic: 10966 Sorted by residual: dihedral pdb=" CB CYS B1169 " pdb=" SG CYS B1169 " pdb=" SG CYS B1172 " pdb=" CB CYS B1172 " ideal model delta sinusoidal sigma weight residual 93.00 9.58 83.42 1 1.00e+01 1.00e-02 8.50e+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 9.58 83.42 1 1.00e+01 1.00e-02 8.50e+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 93.00 174.91 -81.91 1 1.00e+01 1.00e-02 8.25e+01 ... (remaining 18431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4085 0.062 - 0.124: 605 0.124 - 0.187: 26 0.187 - 0.249: 0 0.249 - 0.311: 10 Chirality restraints: 4726 Sorted by residual: chirality pdb=" CA ASN A 869 " pdb=" N ASN A 869 " pdb=" C ASN A 869 " pdb=" CB ASN A 869 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B1656 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1656 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4723 not shown) Planarity restraints: 5292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1585 " -0.069 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO B1586 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B1586 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B1586 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1585 " -0.069 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A1586 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A1586 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1586 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B2053 " -0.059 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B2054 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B2054 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B2054 " -0.047 5.00e-02 4.00e+02 ... (remaining 5289 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1718 2.73 - 3.27: 28572 3.27 - 3.81: 49052 3.81 - 4.36: 59427 4.36 - 4.90: 105328 Nonbonded interactions: 244097 Sorted by model distance: nonbonded pdb=" OD1 ASP B1074 " pdb=" N ALA B1075 " model vdw 2.186 3.120 nonbonded pdb=" OD1 ASP A1074 " pdb=" N ALA A1075 " model vdw 2.187 3.120 nonbonded pdb=" OE1 GLN A2019 " pdb=" OH TYR A2035 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN B2019 " pdb=" OH TYR B2035 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B2116 " pdb=" O SER B2312 " model vdw 2.237 3.040 ... (remaining 244092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 79.340 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.097 30434 Z= 0.130 Angle : 0.524 9.692 41412 Z= 0.266 Chirality : 0.045 0.311 4726 Planarity : 0.004 0.100 5270 Dihedral : 17.302 106.086 11360 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.95 % Rotamer: Outliers : 0.16 % Allowed : 30.44 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3716 helix: 0.06 (0.34), residues: 232 sheet: -0.55 (0.16), residues: 1158 loop : -0.98 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2460 HIS 0.004 0.000 HIS A2281 PHE 0.007 0.001 PHE A1811 TYR 0.016 0.001 TYR A1314 ARG 0.003 0.000 ARG B2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 22) link_NAG-ASN : angle 2.58033 ( 66) link_BETA1-4 : bond 0.01049 ( 8) link_BETA1-4 : angle 2.73464 ( 24) hydrogen bonds : bond 0.26177 ( 961) hydrogen bonds : angle 10.18738 ( 2817) SS BOND : bond 0.00091 ( 18) SS BOND : angle 0.59988 ( 36) covalent geometry : bond 0.00281 (30386) covalent geometry : angle 0.50980 (41286) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 3.094 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 146 average time/residue: 0.3457 time to fit residues: 88.7105 Evaluate side-chains 136 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 192 optimal weight: 30.0000 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1576 ASN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 GLN B2051 ASN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2294 GLN B2534 ASN B2563 HIS B2622 HIS A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 GLN A2051 ASN ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2294 GLN A2534 ASN A2563 HIS A2622 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082353 restraints weight = 62082.609| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.74 r_work: 0.3195 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 30434 Z= 0.301 Angle : 0.684 11.544 41412 Z= 0.353 Chirality : 0.050 0.369 4726 Planarity : 0.005 0.063 5270 Dihedral : 7.788 86.067 4826 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.31 % Allowed : 26.68 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3716 helix: 0.39 (0.36), residues: 224 sheet: -0.85 (0.15), residues: 1212 loop : -0.94 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B2460 HIS 0.005 0.001 HIS A2277 PHE 0.015 0.002 PHE A2368 TYR 0.029 0.002 TYR B1716 ARG 0.005 0.001 ARG B1981 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 22) link_NAG-ASN : angle 3.10590 ( 66) link_BETA1-4 : bond 0.00542 ( 8) link_BETA1-4 : angle 3.06201 ( 24) hydrogen bonds : bond 0.04835 ( 961) hydrogen bonds : angle 6.70010 ( 2817) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.86182 ( 36) covalent geometry : bond 0.00708 (30386) covalent geometry : angle 0.66899 (41286) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 156 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7753 (mp) REVERT: B 945 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8262 (t80) REVERT: B 2339 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: A 830 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7762 (mp) REVERT: A 945 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 2339 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7695 (mp0) outliers start: 164 outliers final: 101 residues processed: 308 average time/residue: 0.3557 time to fit residues: 190.0931 Evaluate side-chains 250 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 143 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1035 VAL Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1671 MET Chi-restraints excluded: chain B residue 1675 ILE Chi-restraints excluded: chain B residue 1694 LEU Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1739 LEU Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1763 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1832 LEU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1854 SER Chi-restraints excluded: chain B residue 1877 SER Chi-restraints excluded: chain B residue 1942 THR Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1972 LEU Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2084 GLN Chi-restraints excluded: chain B residue 2094 THR Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2327 LEU Chi-restraints excluded: chain B residue 2339 GLU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2394 ASP Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2569 THR Chi-restraints excluded: chain B residue 2570 THR Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2628 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1739 LEU Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1854 SER Chi-restraints excluded: chain A residue 1877 SER Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2094 THR Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2327 LEU Chi-restraints excluded: chain A residue 2339 GLU Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2394 ASP Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2569 THR Chi-restraints excluded: chain A residue 2570 THR Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2595 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 296 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 326 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 936 HIS B1576 ASN B1744 ASN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 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 = 0.3763 r_free = 0.3763 target = 0.108130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085238 restraints weight = 61324.351| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.79 r_work: 0.3261 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30434 Z= 0.107 Angle : 0.551 10.344 41412 Z= 0.280 Chirality : 0.045 0.343 4726 Planarity : 0.003 0.050 5270 Dihedral : 6.684 68.776 4826 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.69 % Allowed : 28.21 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3716 helix: 0.55 (0.37), residues: 222 sheet: -0.71 (0.15), residues: 1204 loop : -0.80 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2117 HIS 0.005 0.001 HIS A1808 PHE 0.008 0.001 PHE A2565 TYR 0.015 0.001 TYR B1716 ARG 0.004 0.000 ARG B2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 22) link_NAG-ASN : angle 2.72277 ( 66) link_BETA1-4 : bond 0.01016 ( 8) link_BETA1-4 : angle 2.69317 ( 24) hydrogen bonds : bond 0.03988 ( 961) hydrogen bonds : angle 6.12638 ( 2817) SS BOND : bond 0.00110 ( 18) SS BOND : angle 0.44238 ( 36) covalent geometry : bond 0.00227 (30386) covalent geometry : angle 0.53666 (41286) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 163 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1049 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8683 (t) REVERT: B 1524 MET cc_start: 0.8332 (mpt) cc_final: 0.7943 (mpp) REVERT: B 2065 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7700 (pt) REVERT: B 2070 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: B 2664 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6176 (ttt90) REVERT: A 1524 MET cc_start: 0.8346 (mpt) cc_final: 0.7970 (mpp) REVERT: A 2065 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7715 (pt) REVERT: A 2070 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: A 2664 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6154 (ttt90) REVERT: A 2705 GLN cc_start: 0.7929 (tt0) cc_final: 0.7662 (pt0) outliers start: 114 outliers final: 66 residues processed: 265 average time/residue: 0.3819 time to fit residues: 173.1708 Evaluate side-chains 220 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1646 PHE Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1733 GLN Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1862 GLN Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2070 GLU Chi-restraints excluded: chain B residue 2084 GLN Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2327 LEU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2593 VAL Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2637 LEU Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1733 GLN Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2070 GLU Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2327 LEU Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 371 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 229 optimal weight: 0.0070 chunk 208 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 58 optimal weight: 0.0000 chunk 102 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 overall best weight: 1.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 936 HIS B1576 ASN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2615 GLN A 936 HIS A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2615 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.107529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084561 restraints weight = 61905.674| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.79 r_work: 0.3246 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30434 Z= 0.135 Angle : 0.551 10.531 41412 Z= 0.278 Chirality : 0.045 0.357 4726 Planarity : 0.003 0.049 5270 Dihedral : 6.071 55.777 4826 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.31 % Allowed : 27.98 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3716 helix: 0.59 (0.36), residues: 234 sheet: -0.69 (0.14), residues: 1232 loop : -0.80 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2460 HIS 0.003 0.001 HIS B2281 PHE 0.010 0.001 PHE A2368 TYR 0.019 0.001 TYR A1716 ARG 0.007 0.000 ARG B 761 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 22) link_NAG-ASN : angle 2.79212 ( 66) link_BETA1-4 : bond 0.00898 ( 8) link_BETA1-4 : angle 2.69701 ( 24) hydrogen bonds : bond 0.03692 ( 961) hydrogen bonds : angle 5.81914 ( 2817) SS BOND : bond 0.00134 ( 18) SS BOND : angle 0.51922 ( 36) covalent geometry : bond 0.00309 (30386) covalent geometry : angle 0.53641 (41286) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 154 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 1524 MET cc_start: 0.8332 (mpt) cc_final: 0.7977 (mpp) REVERT: B 2065 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7759 (pt) REVERT: B 2664 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6173 (ttt90) REVERT: B 2705 GLN cc_start: 0.7892 (tt0) cc_final: 0.7667 (pt0) REVERT: A 830 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 1524 MET cc_start: 0.8325 (mpt) cc_final: 0.7997 (mpp) REVERT: A 2065 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7739 (pt) REVERT: A 2664 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6148 (ttt90) REVERT: A 2705 GLN cc_start: 0.7900 (tt0) cc_final: 0.7681 (pt0) outliers start: 133 outliers final: 90 residues processed: 274 average time/residue: 0.4020 time to fit residues: 193.1122 Evaluate side-chains 242 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 146 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2124 ASN Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2327 LEU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2593 VAL Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2453 GLU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2593 VAL Chi-restraints excluded: chain A residue 2628 THR Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 135 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 329 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 338 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 936 HIS B1744 ASN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082068 restraints weight = 61947.997| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.81 r_work: 0.3200 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30434 Z= 0.235 Angle : 0.611 11.193 41412 Z= 0.308 Chirality : 0.047 0.379 4726 Planarity : 0.004 0.051 5270 Dihedral : 5.876 55.954 4826 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.21 % Allowed : 27.01 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3716 helix: 0.53 (0.36), residues: 222 sheet: -0.77 (0.14), residues: 1254 loop : -0.82 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B2460 HIS 0.003 0.001 HIS B 860 PHE 0.013 0.001 PHE B 926 TYR 0.025 0.002 TYR A1716 ARG 0.006 0.000 ARG B 761 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 22) link_NAG-ASN : angle 3.00926 ( 66) link_BETA1-4 : bond 0.00895 ( 8) link_BETA1-4 : angle 2.84040 ( 24) hydrogen bonds : bond 0.04019 ( 961) hydrogen bonds : angle 5.80091 ( 2817) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.65814 ( 36) covalent geometry : bond 0.00550 (30386) covalent geometry : angle 0.59595 (41286) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 150 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 862 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7926 (tp) REVERT: B 945 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8751 (t80) REVERT: B 1524 MET cc_start: 0.8367 (mpt) cc_final: 0.7981 (mpp) REVERT: B 2028 MET cc_start: 0.8078 (mmt) cc_final: 0.7690 (mmp) REVERT: B 2065 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7705 (pt) REVERT: B 2664 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6278 (ttt90) REVERT: A 830 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 862 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 1252 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6955 (mmt90) REVERT: A 1524 MET cc_start: 0.8362 (mpt) cc_final: 0.7980 (mpp) REVERT: A 2028 MET cc_start: 0.8084 (mmt) cc_final: 0.7684 (mmp) REVERT: A 2065 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7713 (pt) REVERT: A 2339 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 2664 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6235 (ttt90) outliers start: 161 outliers final: 116 residues processed: 292 average time/residue: 0.3686 time to fit residues: 184.8636 Evaluate side-chains 269 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 142 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1435 THR Chi-restraints excluded: chain B residue 1454 ILE Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1692 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1739 LEU Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1825 LEU Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2124 ASN Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2254 SER Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2327 LEU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2593 VAL Chi-restraints excluded: chain B residue 2637 LEU Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1454 ILE Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1739 LEU Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2254 SER Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2327 LEU Chi-restraints excluded: chain A residue 2339 GLU Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2453 GLU Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2593 VAL Chi-restraints excluded: chain A residue 2628 THR Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 284 optimal weight: 0.9990 chunk 324 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 310 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 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 = 0.3741 r_free = 0.3741 target = 0.106817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084026 restraints weight = 61748.233| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.73 r_work: 0.3240 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30434 Z= 0.133 Angle : 0.558 10.742 41412 Z= 0.279 Chirality : 0.046 0.368 4726 Planarity : 0.003 0.047 5270 Dihedral : 5.437 55.433 4826 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.50 % Allowed : 27.91 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3716 helix: 0.63 (0.36), residues: 220 sheet: -0.71 (0.14), residues: 1226 loop : -0.81 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2460 HIS 0.003 0.001 HIS B2281 PHE 0.011 0.001 PHE B 852 TYR 0.018 0.001 TYR A1716 ARG 0.010 0.000 ARG A2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 22) link_NAG-ASN : angle 2.86305 ( 66) link_BETA1-4 : bond 0.00990 ( 8) link_BETA1-4 : angle 2.74501 ( 24) hydrogen bonds : bond 0.03498 ( 961) hydrogen bonds : angle 5.62611 ( 2817) SS BOND : bond 0.00159 ( 18) SS BOND : angle 0.51968 ( 36) covalent geometry : bond 0.00302 (30386) covalent geometry : angle 0.54268 (41286) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 159 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 862 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7860 (tp) REVERT: B 1222 ASP cc_start: 0.4671 (OUTLIER) cc_final: 0.4432 (t0) REVERT: B 1252 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6962 (mmt90) REVERT: B 1524 MET cc_start: 0.8338 (mpt) cc_final: 0.7982 (mpp) REVERT: B 2038 ASP cc_start: 0.6219 (p0) cc_final: 0.5966 (p0) REVERT: B 2065 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7717 (pt) REVERT: B 2339 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: B 2664 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6206 (ttt90) REVERT: B 2705 GLN cc_start: 0.7924 (tt0) cc_final: 0.7702 (pt0) REVERT: A 830 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 862 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7855 (tp) REVERT: A 1222 ASP cc_start: 0.4650 (OUTLIER) cc_final: 0.4375 (t0) REVERT: A 1252 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6870 (mmt90) REVERT: A 1524 MET cc_start: 0.8338 (mpt) cc_final: 0.7970 (mpp) REVERT: A 2038 ASP cc_start: 0.6291 (p0) cc_final: 0.6073 (p0) REVERT: A 2065 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7745 (pt) REVERT: A 2664 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6163 (ttt90) REVERT: A 2705 GLN cc_start: 0.7926 (tt0) cc_final: 0.7708 (pt0) outliers start: 139 outliers final: 97 residues processed: 282 average time/residue: 0.3532 time to fit residues: 171.1509 Evaluate side-chains 257 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 147 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1035 VAL Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1454 ILE Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1646 PHE Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1692 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1733 GLN Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2327 LEU Chi-restraints excluded: chain B residue 2339 GLU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2410 SER Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2637 LEU Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1454 ILE Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2453 GLU Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 52 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 355 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 269 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 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 = 0.3753 r_free = 0.3753 target = 0.107558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084751 restraints weight = 61360.331| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.78 r_work: 0.3249 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30434 Z= 0.111 Angle : 0.549 11.939 41412 Z= 0.273 Chirality : 0.045 0.358 4726 Planarity : 0.003 0.045 5270 Dihedral : 4.970 55.518 4826 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.10 % Favored : 92.87 % Rotamer: Outliers : 4.34 % Allowed : 27.91 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3716 helix: 0.77 (0.37), residues: 222 sheet: -0.62 (0.14), residues: 1226 loop : -0.77 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1765 HIS 0.003 0.001 HIS B2281 PHE 0.010 0.001 PHE B 852 TYR 0.017 0.001 TYR B1716 ARG 0.005 0.000 ARG B 761 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 22) link_NAG-ASN : angle 2.78659 ( 66) link_BETA1-4 : bond 0.00945 ( 8) link_BETA1-4 : angle 2.67828 ( 24) hydrogen bonds : bond 0.03247 ( 961) hydrogen bonds : angle 5.45954 ( 2817) SS BOND : bond 0.00125 ( 18) SS BOND : angle 0.47064 ( 36) covalent geometry : bond 0.00249 (30386) covalent geometry : angle 0.53403 (41286) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 153 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 862 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7867 (tp) REVERT: B 1222 ASP cc_start: 0.4631 (OUTLIER) cc_final: 0.4343 (t0) REVERT: B 1252 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6864 (mmt90) REVERT: B 1524 MET cc_start: 0.8310 (mpt) cc_final: 0.7966 (mpp) REVERT: B 2038 ASP cc_start: 0.6237 (p0) cc_final: 0.6002 (p0) REVERT: B 2065 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7757 (pt) REVERT: B 2664 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6115 (ttt90) REVERT: A 830 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7746 (mp) REVERT: A 862 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 1222 ASP cc_start: 0.4636 (OUTLIER) cc_final: 0.4353 (t0) REVERT: A 1524 MET cc_start: 0.8310 (mpt) cc_final: 0.7981 (mpp) REVERT: A 2065 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7780 (pt) REVERT: A 2664 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6085 (ttt90) outliers start: 134 outliers final: 108 residues processed: 273 average time/residue: 0.3700 time to fit residues: 171.0909 Evaluate side-chains 264 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 145 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1385 THR Chi-restraints excluded: chain B residue 1454 ILE Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1646 PHE Chi-restraints excluded: chain B residue 1692 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1825 LEU Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1941 ILE Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2124 ASN Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2254 SER Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2410 SER Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain B residue 2702 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1454 ILE Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2254 SER Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2453 GLU Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 185 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 313 optimal weight: 0.0470 chunk 372 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 overall best weight: 2.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1576 ASN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2263 GLN A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2263 GLN ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083568 restraints weight = 61754.005| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.79 r_work: 0.3226 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30434 Z= 0.155 Angle : 0.564 10.635 41412 Z= 0.283 Chirality : 0.046 0.366 4726 Planarity : 0.004 0.052 5270 Dihedral : 4.905 55.760 4826 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.51 % Favored : 92.47 % Rotamer: Outliers : 5.05 % Allowed : 27.33 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3716 helix: 0.78 (0.37), residues: 220 sheet: -0.63 (0.14), residues: 1236 loop : -0.82 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2460 HIS 0.002 0.001 HIS B 860 PHE 0.011 0.001 PHE B2368 TYR 0.021 0.001 TYR A1716 ARG 0.010 0.000 ARG B2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 22) link_NAG-ASN : angle 2.87296 ( 66) link_BETA1-4 : bond 0.00948 ( 8) link_BETA1-4 : angle 2.74588 ( 24) hydrogen bonds : bond 0.03455 ( 961) hydrogen bonds : angle 5.44342 ( 2817) SS BOND : bond 0.00176 ( 18) SS BOND : angle 0.49890 ( 36) covalent geometry : bond 0.00357 (30386) covalent geometry : angle 0.54869 (41286) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 153 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7725 (mp) REVERT: B 862 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 1222 ASP cc_start: 0.4614 (OUTLIER) cc_final: 0.4292 (t0) REVERT: B 1252 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6841 (mmt90) REVERT: B 1351 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6692 (pmm) REVERT: B 1524 MET cc_start: 0.8357 (mpt) cc_final: 0.7965 (mpp) REVERT: B 2038 ASP cc_start: 0.6296 (p0) cc_final: 0.6082 (p0) REVERT: B 2065 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7727 (pt) REVERT: B 2091 MET cc_start: 0.7477 (tmm) cc_final: 0.6995 (ttm) REVERT: B 2339 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: B 2664 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6160 (ttt90) REVERT: A 830 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 862 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7860 (tp) REVERT: A 1222 ASP cc_start: 0.4680 (OUTLIER) cc_final: 0.4375 (t0) REVERT: A 1252 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6863 (mmt90) REVERT: A 1351 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6719 (pmm) REVERT: A 1524 MET cc_start: 0.8358 (mpt) cc_final: 0.7993 (mpp) REVERT: A 2038 ASP cc_start: 0.6256 (p0) cc_final: 0.6039 (p0) REVERT: A 2065 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7749 (pt) REVERT: A 2664 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6137 (ttt90) outliers start: 156 outliers final: 128 residues processed: 293 average time/residue: 0.3639 time to fit residues: 184.3973 Evaluate side-chains 287 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 144 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1035 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1385 THR Chi-restraints excluded: chain B residue 1435 THR Chi-restraints excluded: chain B residue 1454 ILE Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1646 PHE Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1692 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1825 LEU Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2124 ASN Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2254 SER Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2339 GLU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2410 SER Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2621 LEU Chi-restraints excluded: chain B residue 2637 LEU Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain B residue 2702 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1454 ILE Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2254 SER Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2453 GLU Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2621 LEU Chi-restraints excluded: chain A residue 2628 THR Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain A residue 2664 ARG Chi-restraints excluded: chain A residue 2702 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 230 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080566 restraints weight = 62046.865| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.80 r_work: 0.3167 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 30434 Z= 0.325 Angle : 0.688 11.689 41412 Z= 0.351 Chirality : 0.050 0.394 4726 Planarity : 0.005 0.053 5270 Dihedral : 5.426 56.474 4826 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.88 % Favored : 91.04 % Rotamer: Outliers : 5.21 % Allowed : 27.40 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3716 helix: 0.51 (0.36), residues: 222 sheet: -0.80 (0.14), residues: 1268 loop : -0.96 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2460 HIS 0.004 0.001 HIS A 860 PHE 0.015 0.002 PHE A2368 TYR 0.030 0.002 TYR A1716 ARG 0.008 0.001 ARG B2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 22) link_NAG-ASN : angle 3.27721 ( 66) link_BETA1-4 : bond 0.00789 ( 8) link_BETA1-4 : angle 3.04539 ( 24) hydrogen bonds : bond 0.04305 ( 961) hydrogen bonds : angle 5.74568 ( 2817) SS BOND : bond 0.00510 ( 18) SS BOND : angle 0.79262 ( 36) covalent geometry : bond 0.00762 (30386) covalent geometry : angle 0.67167 (41286) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 146 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 862 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7915 (tp) REVERT: B 945 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8098 (t80) REVERT: B 1031 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7038 (mmt) REVERT: B 1222 ASP cc_start: 0.4625 (OUTLIER) cc_final: 0.4316 (t0) REVERT: B 1252 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6775 (mmt90) REVERT: B 1351 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6368 (pmm) REVERT: B 1556 ASP cc_start: 0.7594 (m-30) cc_final: 0.7140 (p0) REVERT: B 2339 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: B 2664 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6274 (ttt90) REVERT: A 862 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 1031 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7057 (mmt) REVERT: A 1222 ASP cc_start: 0.4632 (OUTLIER) cc_final: 0.4327 (t0) REVERT: A 1252 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6764 (mmt90) REVERT: A 1351 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6354 (pmm) REVERT: A 1556 ASP cc_start: 0.7611 (m-30) cc_final: 0.7151 (p0) REVERT: A 2664 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6271 (ttt90) outliers start: 161 outliers final: 125 residues processed: 290 average time/residue: 0.3779 time to fit residues: 186.3976 Evaluate side-chains 282 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 143 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1035 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1435 THR Chi-restraints excluded: chain B residue 1454 ILE Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1591 VAL Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1692 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1739 LEU Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1825 LEU Chi-restraints excluded: chain B residue 1832 LEU Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2124 ASN Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2254 SER Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2327 LEU Chi-restraints excluded: chain B residue 2339 GLU Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2410 SER Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2621 LEU Chi-restraints excluded: chain B residue 2637 LEU Chi-restraints excluded: chain B residue 2664 ARG Chi-restraints excluded: chain B residue 2702 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1454 ILE Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2254 SER Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2621 LEU Chi-restraints excluded: chain A residue 2628 THR Chi-restraints excluded: chain A residue 2664 ARG Chi-restraints excluded: chain A residue 2702 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 341 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 0.0870 chunk 188 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 313 optimal weight: 6.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1576 ASN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 GLN ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.106309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083417 restraints weight = 61535.351| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.77 r_work: 0.3222 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30434 Z= 0.134 Angle : 0.577 10.980 41412 Z= 0.291 Chirality : 0.046 0.372 4726 Planarity : 0.004 0.048 5270 Dihedral : 5.080 55.339 4826 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 4.63 % Allowed : 28.08 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3716 helix: 0.77 (0.36), residues: 220 sheet: -0.75 (0.14), residues: 1244 loop : -0.82 (0.14), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2460 HIS 0.003 0.001 HIS A2281 PHE 0.013 0.001 PHE B 852 TYR 0.023 0.001 TYR A1314 ARG 0.007 0.000 ARG B2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 22) link_NAG-ASN : angle 2.94118 ( 66) link_BETA1-4 : bond 0.00921 ( 8) link_BETA1-4 : angle 2.80009 ( 24) hydrogen bonds : bond 0.03405 ( 961) hydrogen bonds : angle 5.56211 ( 2817) SS BOND : bond 0.00178 ( 18) SS BOND : angle 0.88851 ( 36) covalent geometry : bond 0.00304 (30386) covalent geometry : angle 0.56154 (41286) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 148 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 830 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 862 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7894 (tp) REVERT: B 1222 ASP cc_start: 0.4663 (OUTLIER) cc_final: 0.4375 (t0) REVERT: B 1252 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6778 (mmt90) REVERT: B 1524 MET cc_start: 0.8369 (mpt) cc_final: 0.8000 (mpp) REVERT: B 2065 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7751 (pt) REVERT: B 2091 MET cc_start: 0.7335 (tmm) cc_final: 0.6850 (ttm) REVERT: A 830 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 862 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7884 (tp) REVERT: A 1222 ASP cc_start: 0.4629 (OUTLIER) cc_final: 0.4322 (t0) REVERT: A 1252 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6785 (mmt90) REVERT: A 1524 MET cc_start: 0.8376 (mpt) cc_final: 0.8000 (mpp) REVERT: A 2065 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7749 (pt) outliers start: 143 outliers final: 119 residues processed: 274 average time/residue: 0.3696 time to fit residues: 173.4314 Evaluate side-chains 273 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 144 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 860 HIS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 898 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1035 VAL Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1435 THR Chi-restraints excluded: chain B residue 1474 CYS Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1591 VAL Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1692 SER Chi-restraints excluded: chain B residue 1716 TYR Chi-restraints excluded: chain B residue 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1824 THR Chi-restraints excluded: chain B residue 1825 LEU Chi-restraints excluded: chain B residue 1832 LEU Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1886 VAL Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 1952 GLN Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 ILE Chi-restraints excluded: chain B residue 2124 ASN Chi-restraints excluded: chain B residue 2163 ILE Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2254 SER Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2379 ARG Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2410 SER Chi-restraints excluded: chain B residue 2453 GLU Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2489 VAL Chi-restraints excluded: chain B residue 2511 LEU Chi-restraints excluded: chain B residue 2512 ILE Chi-restraints excluded: chain B residue 2518 LEU Chi-restraints excluded: chain B residue 2529 VAL Chi-restraints excluded: chain B residue 2537 CYS Chi-restraints excluded: chain B residue 2538 ILE Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2621 LEU Chi-restraints excluded: chain B residue 2702 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1474 CYS Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1824 THR Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2065 ILE Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2254 SER Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2379 ARG Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2453 GLU Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2489 VAL Chi-restraints excluded: chain A residue 2511 LEU Chi-restraints excluded: chain A residue 2512 ILE Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2529 VAL Chi-restraints excluded: chain A residue 2537 CYS Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2593 VAL Chi-restraints excluded: chain A residue 2621 LEU Chi-restraints excluded: chain A residue 2628 THR Chi-restraints excluded: chain A residue 2702 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 74 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 320 optimal weight: 8.9990 chunk 304 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1576 ASN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083047 restraints weight = 61676.493| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.78 r_work: 0.3218 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30434 Z= 0.153 Angle : 0.576 10.905 41412 Z= 0.291 Chirality : 0.046 0.372 4726 Planarity : 0.005 0.137 5270 Dihedral : 5.051 55.757 4826 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.64 % Favored : 92.25 % Rotamer: Outliers : 4.60 % Allowed : 27.91 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3716 helix: 0.77 (0.37), residues: 220 sheet: -0.70 (0.14), residues: 1244 loop : -0.81 (0.14), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2460 HIS 0.003 0.001 HIS B2281 PHE 0.013 0.001 PHE B 852 TYR 0.021 0.001 TYR A1716 ARG 0.025 0.000 ARG B2672 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 22) link_NAG-ASN : angle 2.95126 ( 66) link_BETA1-4 : bond 0.00913 ( 8) link_BETA1-4 : angle 2.80509 ( 24) hydrogen bonds : bond 0.03485 ( 961) hydrogen bonds : angle 5.50670 ( 2817) SS BOND : bond 0.00168 ( 18) SS BOND : angle 0.75259 ( 36) covalent geometry : bond 0.00355 (30386) covalent geometry : angle 0.56040 (41286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12167.24 seconds wall clock time: 212 minutes 54.29 seconds (12774.29 seconds total)