Starting phenix.real_space_refine on Mon Aug 25 19:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r50_18889/08_2025/8r50_18889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r50_18889/08_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_18889/08_2025/8r50_18889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r50_18889/08_2025/8r50_18889.map" model { file = "/net/cci-nas-00/data/ceres_data/8r50_18889/08_2025/8r50_18889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r50_18889/08_2025/8r50_18889.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 20, 'GLN:plan1': 13, 'ASP:plan': 18, 'ASN:plan1': 7, 'PHE:plan': 2, 'ARG:plan': 6, 'TRP:plan': 1} 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: {'GLU:plan': 20, 'GLN:plan1': 13, 'ASP:plan': 18, 'ASN:plan1': 7, 'PHE:plan': 2, 'ARG:plan': 6, 'TRP:plan': 1} 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: 6.30, per 1000 atoms: 0.21 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: 2.07 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.42 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: 11.69 Time building geometry restraints manager: 2.82 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.880 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- 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 : 9.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (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 ARG 0.003 0.000 ARG B2672 TYR 0.016 0.001 TYR A1314 PHE 0.007 0.001 PHE A1811 TRP 0.006 0.001 TRP B2460 HIS 0.004 0.000 HIS A2281 Details of bonding type rmsd covalent geometry : bond 0.00281 (30386) covalent geometry : angle 0.50980 (41286) SS BOND : bond 0.00091 ( 18) SS BOND : angle 0.59988 ( 36) hydrogen bonds : bond 0.26177 ( 961) hydrogen bonds : angle 10.18738 ( 2817) link_BETA1-4 : bond 0.01049 ( 8) link_BETA1-4 : angle 2.73464 ( 24) link_NAG-ASN : bond 0.00611 ( 22) link_NAG-ASN : angle 2.58033 ( 66) *********************** 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 : 0.735 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 146 average time/residue: 0.1364 time to fit residues: 35.2023 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 : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** B2051 ASN ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2294 GLN B2534 ASN B2563 HIS A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2051 ASN ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2294 GLN A2534 ASN A2563 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.108836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085869 restraints weight = 61592.667| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.78 r_work: 0.3270 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30434 Z= 0.136 Angle : 0.566 10.128 41412 Z= 0.292 Chirality : 0.046 0.340 4726 Planarity : 0.004 0.062 5270 Dihedral : 7.378 82.593 4826 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.43 % Allowed : 27.30 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3716 helix: 0.60 (0.37), residues: 222 sheet: -0.71 (0.15), residues: 1212 loop : -0.80 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1981 TYR 0.017 0.001 TYR B1716 PHE 0.008 0.001 PHE B2368 TRP 0.008 0.001 TRP B2460 HIS 0.005 0.001 HIS B2096 Details of bonding type rmsd covalent geometry : bond 0.00300 (30386) covalent geometry : angle 0.55252 (41286) SS BOND : bond 0.00162 ( 18) SS BOND : angle 0.58701 ( 36) hydrogen bonds : bond 0.04717 ( 961) hydrogen bonds : angle 6.82461 ( 2817) link_BETA1-4 : bond 0.00847 ( 8) link_BETA1-4 : angle 2.70550 ( 24) link_NAG-ASN : bond 0.00731 ( 22) link_NAG-ASN : angle 2.71234 ( 66) *********************** 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 265 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 159 time to evaluate : 1.160 Fit side-chains REVERT: B 1524 MET cc_start: 0.8306 (mpt) cc_final: 0.7931 (mpp) REVERT: B 2065 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7652 (pt) REVERT: A 1524 MET cc_start: 0.8290 (mpt) cc_final: 0.7933 (mpp) REVERT: A 2065 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7627 (pt) outliers start: 106 outliers final: 59 residues processed: 255 average time/residue: 0.1325 time to fit residues: 59.1195 Evaluate side-chains 203 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 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 947 VAL Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1385 THR Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1655 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 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 2084 GLN 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 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 2575 LEU Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain A residue 802 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 947 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1655 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 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 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 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 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 268 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 chunk 82 optimal weight: 0.0170 chunk 192 optimal weight: 30.0000 chunk 228 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 361 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.4024 ------------------------------------------------------------------------------- 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 B2622 HIS A 936 HIS A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2615 GLN A2622 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.107648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084511 restraints weight = 61916.588| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.80 r_work: 0.3245 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30434 Z= 0.162 Angle : 0.567 10.506 41412 Z= 0.288 Chirality : 0.046 0.348 4726 Planarity : 0.004 0.053 5270 Dihedral : 6.682 69.123 4826 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.92 % Allowed : 27.88 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3716 helix: 0.62 (0.37), residues: 222 sheet: -0.67 (0.15), residues: 1224 loop : -0.82 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1922 TYR 0.019 0.001 TYR B1716 PHE 0.013 0.001 PHE B 926 TRP 0.011 0.001 TRP B2460 HIS 0.003 0.001 HIS A2281 Details of bonding type rmsd covalent geometry : bond 0.00371 (30386) covalent geometry : angle 0.55241 (41286) SS BOND : bond 0.00165 ( 18) SS BOND : angle 0.54283 ( 36) hydrogen bonds : bond 0.04302 ( 961) hydrogen bonds : angle 6.25551 ( 2817) link_BETA1-4 : bond 0.00909 ( 8) link_BETA1-4 : angle 2.67458 ( 24) link_NAG-ASN : bond 0.00702 ( 22) link_NAG-ASN : angle 2.78852 ( 66) *********************** 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 281 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 160 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1524 MET cc_start: 0.8330 (mpt) cc_final: 0.7953 (mpp) REVERT: B 2065 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7647 (pt) REVERT: B 2339 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: A 1524 MET cc_start: 0.8329 (mpt) cc_final: 0.7964 (mpp) REVERT: A 2339 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7679 (mp0) outliers start: 121 outliers final: 76 residues processed: 269 average time/residue: 0.1302 time to fit residues: 61.4523 Evaluate side-chains 224 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 145 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 802 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 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 1246 VAL Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1576 ASN Chi-restraints excluded: chain B residue 1635 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 1848 ILE 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 2084 GLN 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 2575 LEU Chi-restraints excluded: chain B residue 2593 VAL Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain A residue 802 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 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 1246 VAL Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 THR 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 1848 ILE Chi-restraints excluded: chain A residue 1862 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 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 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 2556 THR Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2593 VAL Chi-restraints excluded: chain A residue 2595 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 143 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 329 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 267 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.107574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084557 restraints weight = 61468.496| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.79 r_work: 0.3247 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30434 Z= 0.142 Angle : 0.558 10.495 41412 Z= 0.281 Chirality : 0.045 0.356 4726 Planarity : 0.003 0.051 5270 Dihedral : 6.050 55.786 4826 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.27 % Allowed : 27.88 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.14), residues: 3716 helix: 0.64 (0.36), residues: 234 sheet: -0.61 (0.15), residues: 1218 loop : -0.79 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 761 TYR 0.019 0.001 TYR B1716 PHE 0.009 0.001 PHE A2368 TRP 0.023 0.001 TRP B1103 HIS 0.003 0.001 HIS A2281 Details of bonding type rmsd covalent geometry : bond 0.00325 (30386) covalent geometry : angle 0.54332 (41286) SS BOND : bond 0.00140 ( 18) SS BOND : angle 0.49643 ( 36) hydrogen bonds : bond 0.03811 ( 961) hydrogen bonds : angle 5.92208 ( 2817) link_BETA1-4 : bond 0.00904 ( 8) link_BETA1-4 : angle 2.65401 ( 24) link_NAG-ASN : bond 0.00701 ( 22) link_NAG-ASN : angle 2.77483 ( 66) *********************** 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 285 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 153 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1524 MET cc_start: 0.8305 (mpt) cc_final: 0.7959 (mpp) REVERT: B 2065 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7619 (pt) REVERT: B 2070 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: B 2339 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: A 1524 MET cc_start: 0.8315 (mpt) cc_final: 0.7987 (mpp) REVERT: A 2065 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7696 (pt) REVERT: A 2070 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 2339 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7667 (mp0) outliers start: 132 outliers final: 94 residues processed: 272 average time/residue: 0.1430 time to fit residues: 67.5738 Evaluate side-chains 241 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 141 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 802 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 1029 ILE 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 1246 VAL Chi-restraints excluded: chain B residue 1351 MET 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 1747 VAL Chi-restraints excluded: chain B residue 1776 VAL Chi-restraints excluded: chain B residue 1813 LEU Chi-restraints excluded: chain B residue 1847 SER Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1862 GLN 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 2070 GLU Chi-restraints excluded: chain B residue 2163 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 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 2595 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 802 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 932 LEU Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1029 ILE 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 1246 VAL Chi-restraints excluded: chain A residue 1351 MET 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 1664 VAL 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 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 2070 GLU Chi-restraints excluded: chain A residue 2163 ILE Chi-restraints excluded: chain A residue 2164 MET 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 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 2569 THR Chi-restraints excluded: chain A residue 2575 LEU Chi-restraints excluded: chain A residue 2595 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 344 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 122 optimal weight: 0.0010 chunk 252 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 936 HIS ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084926 restraints weight = 61821.434| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.82 r_work: 0.3248 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30434 Z= 0.134 Angle : 0.549 10.480 41412 Z= 0.277 Chirality : 0.045 0.359 4726 Planarity : 0.003 0.050 5270 Dihedral : 5.549 55.716 4826 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.94 % Favored : 93.03 % Rotamer: Outliers : 4.86 % Allowed : 26.81 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3716 helix: 0.89 (0.37), residues: 220 sheet: -0.61 (0.15), residues: 1228 loop : -0.76 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2672 TYR 0.019 0.001 TYR A1716 PHE 0.009 0.001 PHE A2368 TRP 0.011 0.001 TRP B1103 HIS 0.002 0.001 HIS A2281 Details of bonding type rmsd covalent geometry : bond 0.00305 (30386) covalent geometry : angle 0.53433 (41286) SS BOND : bond 0.00136 ( 18) SS BOND : angle 0.48717 ( 36) hydrogen bonds : bond 0.03586 ( 961) hydrogen bonds : angle 5.71545 ( 2817) link_BETA1-4 : bond 0.00965 ( 8) link_BETA1-4 : angle 2.65305 ( 24) link_NAG-ASN : bond 0.00693 ( 22) link_NAG-ASN : angle 2.78422 ( 66) *********************** 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 299 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 149 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1524 MET cc_start: 0.8316 (mpt) cc_final: 0.7972 (mpp) REVERT: B 2339 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: B 2664 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6167 (ttt90) REVERT: A 1524 MET cc_start: 0.8338 (mpt) cc_final: 0.8010 (mpp) REVERT: A 2065 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7714 (pt) REVERT: A 2339 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 2664 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6138 (ttt90) outliers start: 150 outliers final: 110 residues processed: 284 average time/residue: 0.1383 time to fit residues: 68.4407 Evaluate side-chains 258 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 143 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 802 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 932 LEU Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1029 ILE 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 1155 VAL Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1351 MET 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 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 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 1862 GLN 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 2124 ASN Chi-restraints excluded: chain B residue 2163 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 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 2569 THR 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 802 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 932 LEU Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1029 ILE 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 1155 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1351 MET 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 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 1862 GLN Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1941 ILE 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 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 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 2569 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 39 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 337 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 375 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 GLN A2263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081595 restraints weight = 61816.945| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.98 r_work: 0.3188 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30434 Z= 0.263 Angle : 0.634 11.423 41412 Z= 0.320 Chirality : 0.048 0.389 4726 Planarity : 0.004 0.052 5270 Dihedral : 5.519 56.016 4826 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.60 % Allowed : 26.23 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.14), residues: 3716 helix: 0.54 (0.35), residues: 234 sheet: -0.71 (0.14), residues: 1240 loop : -0.85 (0.14), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1584 TYR 0.026 0.002 TYR B1716 PHE 0.014 0.002 PHE A2368 TRP 0.029 0.002 TRP A1103 HIS 0.004 0.001 HIS B 860 Details of bonding type rmsd covalent geometry : bond 0.00618 (30386) covalent geometry : angle 0.61828 (41286) SS BOND : bond 0.00269 ( 18) SS BOND : angle 0.72122 ( 36) hydrogen bonds : bond 0.04110 ( 961) hydrogen bonds : angle 5.79773 ( 2817) link_BETA1-4 : bond 0.00832 ( 8) link_BETA1-4 : angle 2.88878 ( 24) link_NAG-ASN : bond 0.00720 ( 22) link_NAG-ASN : angle 3.08071 ( 66) *********************** 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 317 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 144 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 862 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 945 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8398 (t80) REVERT: B 1252 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6905 (mmt90) REVERT: B 1524 MET cc_start: 0.8382 (mpt) cc_final: 0.7982 (mpp) REVERT: B 2028 MET cc_start: 0.8089 (mmt) cc_final: 0.7701 (mmp) REVERT: B 2065 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7722 (pt) REVERT: B 2339 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 2664 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6290 (ttt90) REVERT: A 862 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7909 (tp) REVERT: A 945 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8318 (t80) REVERT: A 1252 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6867 (mmt90) REVERT: A 1524 MET cc_start: 0.8383 (mpt) cc_final: 0.7975 (mpp) REVERT: A 2028 MET cc_start: 0.8092 (mmt) cc_final: 0.7691 (mmp) REVERT: A 2339 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: A 2664 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6272 (ttt90) outliers start: 173 outliers final: 139 residues processed: 299 average time/residue: 0.1377 time to fit residues: 70.7298 Evaluate side-chains 289 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 139 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 904 THR 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 1029 ILE 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 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 1246 VAL Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1273 VAL Chi-restraints excluded: chain B residue 1299 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 1454 ILE 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 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 1763 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 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 2094 THR 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 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 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 2569 THR Chi-restraints excluded: chain B residue 2570 THR Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2593 VAL Chi-restraints excluded: chain B residue 2628 THR 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 862 LEU 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 932 LEU Chi-restraints excluded: chain A residue 945 PHE 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 1029 ILE 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 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 1246 VAL Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1299 LEU 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 1454 ILE Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1635 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 1763 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 1854 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 2094 THR 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 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 2569 THR Chi-restraints excluded: chain A residue 2570 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 365 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 368 optimal weight: 4.9990 chunk 326 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** 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 = 0.3713 r_free = 0.3713 target = 0.104986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082042 restraints weight = 61979.130| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.77 r_work: 0.3198 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30434 Z= 0.219 Angle : 0.607 11.330 41412 Z= 0.308 Chirality : 0.047 0.386 4726 Planarity : 0.004 0.061 5270 Dihedral : 5.355 55.848 4826 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.38 % Allowed : 26.42 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.14), residues: 3716 helix: 0.60 (0.36), residues: 220 sheet: -0.78 (0.14), residues: 1274 loop : -0.85 (0.14), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B2672 TYR 0.025 0.002 TYR A1716 PHE 0.011 0.001 PHE B2368 TRP 0.019 0.002 TRP A2460 HIS 0.003 0.001 HIS B2277 Details of bonding type rmsd covalent geometry : bond 0.00512 (30386) covalent geometry : angle 0.59103 (41286) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.67320 ( 36) hydrogen bonds : bond 0.03879 ( 961) hydrogen bonds : angle 5.74090 ( 2817) link_BETA1-4 : bond 0.00856 ( 8) link_BETA1-4 : angle 2.86287 ( 24) link_NAG-ASN : bond 0.00710 ( 22) link_NAG-ASN : angle 3.05338 ( 66) *********************** 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 320 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 154 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 862 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7875 (tp) REVERT: B 945 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8752 (t80) REVERT: B 1222 ASP cc_start: 0.4798 (OUTLIER) cc_final: 0.4553 (t0) REVERT: B 1252 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6879 (mmt90) REVERT: B 2065 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7746 (pt) REVERT: B 2339 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: B 2664 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6283 (ttt90) REVERT: A 862 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7880 (tp) REVERT: A 945 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8669 (t80) REVERT: A 1222 ASP cc_start: 0.4683 (OUTLIER) cc_final: 0.4397 (t0) REVERT: A 1252 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6881 (mmt90) REVERT: A 2339 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: A 2664 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6250 (ttt90) outliers start: 166 outliers final: 130 residues processed: 302 average time/residue: 0.1523 time to fit residues: 80.1571 Evaluate side-chains 282 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 139 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 904 THR 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 1029 ILE Chi-restraints excluded: chain B residue 1035 VAL Chi-restraints excluded: chain B residue 1050 VAL 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 1246 VAL Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1273 VAL 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 1454 ILE Chi-restraints excluded: chain B residue 1635 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 1763 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 1854 SER Chi-restraints excluded: chain B residue 1862 GLN 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 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 2569 THR Chi-restraints excluded: chain B residue 2570 THR Chi-restraints excluded: chain B residue 2575 LEU Chi-restraints excluded: chain B residue 2593 VAL Chi-restraints excluded: chain B residue 2628 THR 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 862 LEU 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 932 LEU Chi-restraints excluded: chain A residue 945 PHE 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 1246 VAL Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1273 VAL 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 1454 ILE Chi-restraints excluded: chain A residue 1635 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 1763 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 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 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 2569 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 89 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 326 optimal weight: 0.0000 chunk 237 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.107235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084333 restraints weight = 61458.555| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.78 r_work: 0.3242 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30434 Z= 0.116 Angle : 0.559 11.843 41412 Z= 0.281 Chirality : 0.046 0.366 4726 Planarity : 0.003 0.048 5270 Dihedral : 4.993 55.401 4826 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 4.02 % Allowed : 27.66 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3716 helix: 0.75 (0.36), residues: 222 sheet: -0.61 (0.15), residues: 1196 loop : -0.76 (0.14), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2672 TYR 0.017 0.001 TYR A1716 PHE 0.008 0.001 PHE B2565 TRP 0.013 0.001 TRP B2117 HIS 0.003 0.001 HIS B2281 Details of bonding type rmsd covalent geometry : bond 0.00259 (30386) covalent geometry : angle 0.54417 (41286) SS BOND : bond 0.00566 ( 18) SS BOND : angle 0.59701 ( 36) hydrogen bonds : bond 0.03310 ( 961) hydrogen bonds : angle 5.54204 ( 2817) link_BETA1-4 : bond 0.00964 ( 8) link_BETA1-4 : angle 2.72216 ( 24) link_NAG-ASN : bond 0.00707 ( 22) link_NAG-ASN : angle 2.84700 ( 66) *********************** 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 279 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 155 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 862 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7871 (tp) REVERT: B 1222 ASP cc_start: 0.4702 (OUTLIER) cc_final: 0.4415 (t0) REVERT: B 1252 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6878 (mmt90) REVERT: B 1299 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8030 (mp) REVERT: B 1524 MET cc_start: 0.8349 (mpt) cc_final: 0.7972 (mpp) REVERT: B 2065 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7750 (pt) REVERT: B 2664 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6155 (ttt90) REVERT: A 862 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7865 (tp) REVERT: A 1222 ASP cc_start: 0.4649 (OUTLIER) cc_final: 0.4361 (t0) REVERT: A 1524 MET cc_start: 0.8359 (mpt) cc_final: 0.8008 (mpp) REVERT: A 2065 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7719 (pt) REVERT: A 2664 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6119 (ttt90) outliers start: 124 outliers final: 90 residues processed: 264 average time/residue: 0.1480 time to fit residues: 67.5885 Evaluate side-chains 241 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 141 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 932 LEU Chi-restraints excluded: chain B residue 945 PHE Chi-restraints excluded: chain B residue 977 SER 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 1222 ASP Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1252 ARG Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1454 ILE 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 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 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 2177 LEU 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 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 2538 ILE 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 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 945 PHE Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1246 VAL 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 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL 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 1941 ILE 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 2163 ILE Chi-restraints excluded: chain A residue 2177 LEU 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 2325 ASN 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 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 2538 ILE Chi-restraints excluded: chain A residue 2570 THR Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 202 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 318 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 B2325 ASN A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3733 r_free = 0.3733 target = 0.106234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083362 restraints weight = 61403.051| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.76 r_work: 0.3223 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30434 Z= 0.170 Angle : 0.582 10.827 41412 Z= 0.294 Chirality : 0.046 0.370 4726 Planarity : 0.004 0.058 5270 Dihedral : 5.002 55.828 4826 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.30 % Rotamer: Outliers : 4.37 % Allowed : 27.01 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.14), residues: 3716 helix: 0.80 (0.36), residues: 222 sheet: -0.64 (0.15), residues: 1224 loop : -0.75 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1584 TYR 0.022 0.001 TYR A1716 PHE 0.016 0.001 PHE A 852 TRP 0.018 0.001 TRP B1103 HIS 0.002 0.001 HIS B 860 Details of bonding type rmsd covalent geometry : bond 0.00395 (30386) covalent geometry : angle 0.56632 (41286) SS BOND : bond 0.00197 ( 18) SS BOND : angle 0.85342 ( 36) hydrogen bonds : bond 0.03504 ( 961) hydrogen bonds : angle 5.51321 ( 2817) link_BETA1-4 : bond 0.00910 ( 8) link_BETA1-4 : angle 2.77341 ( 24) link_NAG-ASN : bond 0.00697 ( 22) link_NAG-ASN : angle 2.91936 ( 66) *********************** 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 280 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 145 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 862 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 1222 ASP cc_start: 0.4695 (OUTLIER) cc_final: 0.4376 (t0) REVERT: B 1252 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6873 (mmt90) REVERT: B 2664 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6151 (ttt90) REVERT: A 862 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 1222 ASP cc_start: 0.4654 (OUTLIER) cc_final: 0.4333 (t0) REVERT: A 1252 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6875 (mmt90) REVERT: A 2664 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6144 (ttt90) outliers start: 135 outliers final: 106 residues processed: 268 average time/residue: 0.1568 time to fit residues: 72.2325 Evaluate side-chains 254 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 140 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 932 LEU 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 1089 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1246 VAL 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 1474 CYS 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 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 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 2177 LEU Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2317 THR Chi-restraints excluded: chain B residue 2325 ASN 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 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 2628 THR 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 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 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 1246 VAL Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1366 ILE 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 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL 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 1941 ILE 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 2177 LEU 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 2538 ILE Chi-restraints excluded: chain A residue 2570 THR Chi-restraints excluded: chain A residue 2628 THR Chi-restraints excluded: chain A residue 2664 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 234 optimal weight: 10.0000 chunk 267 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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** A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082220 restraints weight = 61472.887| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.81 r_work: 0.3202 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30434 Z= 0.218 Angle : 0.613 11.063 41412 Z= 0.311 Chirality : 0.047 0.380 4726 Planarity : 0.004 0.092 5270 Dihedral : 5.122 55.924 4826 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.18 % Favored : 91.77 % Rotamer: Outliers : 4.27 % Allowed : 27.10 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.14), residues: 3716 helix: 0.75 (0.37), residues: 220 sheet: -0.67 (0.15), residues: 1240 loop : -0.80 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B2672 TYR 0.024 0.002 TYR B1716 PHE 0.015 0.001 PHE B 852 TRP 0.018 0.001 TRP A2460 HIS 0.003 0.001 HIS B 860 Details of bonding type rmsd covalent geometry : bond 0.00510 (30386) covalent geometry : angle 0.59782 (41286) SS BOND : bond 0.00239 ( 18) SS BOND : angle 0.82429 ( 36) hydrogen bonds : bond 0.03729 ( 961) hydrogen bonds : angle 5.56415 ( 2817) link_BETA1-4 : bond 0.00854 ( 8) link_BETA1-4 : angle 2.83208 ( 24) link_NAG-ASN : bond 0.00716 ( 22) link_NAG-ASN : angle 3.02504 ( 66) ********************** 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 279 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 147 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 862 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7886 (tp) REVERT: B 1222 ASP cc_start: 0.4628 (OUTLIER) cc_final: 0.4316 (t0) REVERT: B 1252 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6796 (mmt90) REVERT: B 1299 LEU cc_start: 0.8335 (mp) cc_final: 0.8113 (mp) REVERT: B 2664 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6222 (ttt90) REVERT: A 862 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 1222 ASP cc_start: 0.4644 (OUTLIER) cc_final: 0.4328 (t0) REVERT: A 1252 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6777 (mmt90) REVERT: A 2664 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6144 (ttt90) outliers start: 132 outliers final: 115 residues processed: 268 average time/residue: 0.1840 time to fit residues: 84.2854 Evaluate side-chains 264 residues out of total 3308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 141 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 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 1000 LEU Chi-restraints excluded: chain B residue 1029 ILE 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 1246 VAL 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 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 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 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 2177 LEU 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 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 2569 THR Chi-restraints excluded: chain B residue 2628 THR 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 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 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 1246 VAL Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1366 ILE 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 1716 TYR Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1776 VAL 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 1877 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 2163 ILE Chi-restraints excluded: chain A residue 2177 LEU 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 2570 THR 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 113 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 374 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** A1576 ASN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.105483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083101 restraints weight = 61855.350| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.71 r_work: 0.3212 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30434 Z= 0.192 Angle : 0.606 11.069 41412 Z= 0.307 Chirality : 0.047 0.379 4726 Planarity : 0.004 0.070 5270 Dihedral : 5.122 55.823 4826 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.02 % Favored : 91.93 % Rotamer: Outliers : 4.37 % Allowed : 26.94 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3716 helix: 0.76 (0.36), residues: 220 sheet: -0.69 (0.14), residues: 1244 loop : -0.80 (0.14), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B2672 TYR 0.023 0.001 TYR B1716 PHE 0.016 0.001 PHE B 852 TRP 0.017 0.001 TRP A2460 HIS 0.003 0.001 HIS A 860 Details of bonding type rmsd covalent geometry : bond 0.00448 (30386) covalent geometry : angle 0.59017 (41286) SS BOND : bond 0.00230 ( 18) SS BOND : angle 0.79754 ( 36) hydrogen bonds : bond 0.03648 ( 961) hydrogen bonds : angle 5.56686 ( 2817) link_BETA1-4 : bond 0.00919 ( 8) link_BETA1-4 : angle 2.84700 ( 24) link_NAG-ASN : bond 0.00711 ( 22) link_NAG-ASN : angle 3.00076 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5596.81 seconds wall clock time: 97 minutes 11.79 seconds (5831.79 seconds total)