Starting phenix.real_space_refine on Thu Mar 5 13:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyc_30496/03_2026/7cyc_30496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyc_30496/03_2026/7cyc_30496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyc_30496/03_2026/7cyc_30496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyc_30496/03_2026/7cyc_30496.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyc_30496/03_2026/7cyc_30496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyc_30496/03_2026/7cyc_30496.cif" } resolution = 3.21 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= 1.000 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 111 5.16 5 C 14151 2.51 5 N 3747 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22521 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7094 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 32, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 224 Chain: "B" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7094 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 32, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 224 Chain: "C" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7094 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 32, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 224 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 5.12, per 1000 atoms: 0.23 Number of scatterers: 22521 At special positions: 0 Unit cell: (131.6, 130.2, 163.8, 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 111 16.00 O 4512 8.00 N 3747 7.00 C 14151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 105 " distance=2.07 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.02 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 320 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 396 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 726 " distance=2.02 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=2.04 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 105 " distance=2.07 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.02 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 396 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 726 " distance=2.02 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=2.04 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 105 " distance=2.07 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.02 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 320 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 630 " distance=2.04 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 726 " distance=2.02 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=2.04 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN D 6 " - " MAN D 7 " " MAN H 4 " - " MAN H 5 " " MAN H 6 " - " MAN H 7 " " MAN L 4 " - " MAN L 5 " " MAN L 6 " - " MAN L 7 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 6 " " BMA L 3 " - " MAN L 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1201 " - " ASN A 98 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 171 " " NAG A1204 " - " ASN A 220 " " NAG A1205 " - " ASN A 326 " " NAG A1206 " - " ASN A 518 " " NAG A1207 " - " ASN A 440 " " NAG A1208 " - " ASN A 464 " " NAG A1209 " - " ASN A 663 " " NAG A1210 " - " ASN A 542 " " NAG A1211 " - " ASN A 568 " " NAG A1212 " - " ASN A 581 " " NAG A1213 " - " ASN A 587 " " NAG A1214 " - " ASN A 671 " " NAG A1215 " - " ASN A1015 " " NAG A1216 " - " ASN A1020 " " NAG B1201 " - " ASN B 98 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 171 " " NAG B1204 " - " ASN B 220 " " NAG B1205 " - " ASN B 326 " " NAG B1206 " - " ASN B 518 " " NAG B1207 " - " ASN B 440 " " NAG B1208 " - " ASN B 464 " " NAG B1209 " - " ASN B 663 " " NAG B1210 " - " ASN B 542 " " NAG B1211 " - " ASN B 568 " " NAG B1212 " - " ASN B 581 " " NAG B1213 " - " ASN B 587 " " NAG B1214 " - " ASN B 671 " " NAG B1215 " - " ASN B1015 " " NAG B1216 " - " ASN B1020 " " NAG C1201 " - " ASN C 98 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 171 " " NAG C1204 " - " ASN C 220 " " NAG C1205 " - " ASN C 326 " " NAG C1206 " - " ASN C 518 " " NAG C1207 " - " ASN C 440 " " NAG C1208 " - " ASN C 464 " " NAG C1209 " - " ASN C 663 " " NAG C1210 " - " ASN C 542 " " NAG C1211 " - " ASN C 568 " " NAG C1212 " - " ASN C 581 " " NAG C1213 " - " ASN C 587 " " NAG C1214 " - " ASN C 671 " " NAG C1215 " - " ASN C1015 " " NAG C1216 " - " ASN C1020 " " NAG D 1 " - " ASN A 62 " " NAG E 1 " - " ASN A 243 " " NAG F 1 " - " ASN A 538 " " NAG G 1 " - " ASN A 930 " " NAG H 1 " - " ASN B 62 " " NAG I 1 " - " ASN B 243 " " NAG J 1 " - " ASN B 538 " " NAG K 1 " - " ASN B 930 " " NAG L 1 " - " ASN C 62 " " NAG M 1 " - " ASN C 243 " " NAG N 1 " - " ASN C 538 " " NAG O 1 " - " ASN C 930 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 884.2 milliseconds 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 26.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 625 removed outlier: 4.135A pdb=" N GLN A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 652 removed outlier: 4.916A pdb=" N THR A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 652 " --> pdb=" O VAL A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 660 removed outlier: 3.760A pdb=" N THR A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 667 removed outlier: 5.487A pdb=" N VAL A 664 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 665 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.629A pdb=" N LYS A 714 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'A' and resid 768 through 781 removed outlier: 3.734A pdb=" N ALA A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 4.037A pdb=" N LYS A 792 " --> pdb=" O GLN A 788 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 797 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 800 " --> pdb=" O ALA A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 848 removed outlier: 4.134A pdb=" N SER A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 870 through 918 removed outlier: 4.068A pdb=" N ASP A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN A 876 " --> pdb=" O ILE A 872 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 887 " --> pdb=" O THR A 883 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 905 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1022 through 1030 removed outlier: 3.607A pdb=" N THR A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 616 through 625 removed outlier: 4.136A pdb=" N GLN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 652 removed outlier: 4.916A pdb=" N THR B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 652 " --> pdb=" O VAL B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 removed outlier: 3.760A pdb=" N THR B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 667 removed outlier: 5.488A pdb=" N VAL B 664 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER B 665 " --> pdb=" O ALA B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 Processing helix chain 'B' and resid 711 through 715 removed outlier: 3.630A pdb=" N LYS B 714 " --> pdb=" O ASP B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 741 through 755 Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.735A pdb=" N ALA B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 780 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 4.038A pdb=" N LYS B 792 " --> pdb=" O GLN B 788 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 795 " --> pdb=" O GLN B 791 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA B 796 " --> pdb=" O LYS B 792 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 797 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 800 " --> pdb=" O ALA B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 848 removed outlier: 4.135A pdb=" N SER B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU B 844 " --> pdb=" O GLN B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 870 through 918 removed outlier: 4.068A pdb=" N ASP B 875 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN B 876 " --> pdb=" O ILE B 872 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 882 " --> pdb=" O VAL B 878 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 887 " --> pdb=" O THR B 883 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 898 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 902 " --> pdb=" O THR B 898 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA B 905 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 906 " --> pdb=" O GLU B 902 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1006 No H-bonds generated for 'chain 'B' and resid 1004 through 1006' Processing helix chain 'B' and resid 1022 through 1030 removed outlier: 3.607A pdb=" N THR B1028 " --> pdb=" O SER B1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 616 through 625 removed outlier: 4.135A pdb=" N GLN C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 removed outlier: 4.916A pdb=" N THR C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 652 " --> pdb=" O VAL C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 660 removed outlier: 3.760A pdb=" N THR C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 667 removed outlier: 5.488A pdb=" N VAL C 664 " --> pdb=" O LEU C 661 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER C 665 " --> pdb=" O ALA C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 700 Processing helix chain 'C' and resid 711 through 715 removed outlier: 3.629A pdb=" N LYS C 714 " --> pdb=" O ASP C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 741 through 755 Processing helix chain 'C' and resid 768 through 781 removed outlier: 3.735A pdb=" N ALA C 772 " --> pdb=" O PRO C 768 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 780 " --> pdb=" O ARG C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 810 removed outlier: 4.037A pdb=" N LYS C 792 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 796 " --> pdb=" O LYS C 792 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 797 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 800 " --> pdb=" O ALA C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 848 removed outlier: 4.135A pdb=" N SER C 843 " --> pdb=" O GLN C 839 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 844 " --> pdb=" O GLN C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 853 Processing helix chain 'C' and resid 861 through 869 Processing helix chain 'C' and resid 870 through 918 removed outlier: 4.068A pdb=" N ASP C 875 " --> pdb=" O ILE C 871 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN C 876 " --> pdb=" O ILE C 872 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 877 " --> pdb=" O GLN C 873 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 882 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 887 " --> pdb=" O THR C 883 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 898 " --> pdb=" O SER C 894 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 902 " --> pdb=" O THR C 898 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 905 " --> pdb=" O THR C 901 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 906 " --> pdb=" O GLU C 902 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 916 " --> pdb=" O GLN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1006 No H-bonds generated for 'chain 'C' and resid 1004 through 1006' Processing helix chain 'C' and resid 1022 through 1030 removed outlier: 3.605A pdb=" N THR C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 8.409A pdb=" N ASP A 239 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TYR A 254 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 241 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN A 243 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 removed outlier: 5.811A pdb=" N GLY A 130 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS A 145 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 5.811A pdb=" N GLY A 130 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS A 145 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 170 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.528A pdb=" N TYR A 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A 201 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 278 removed outlier: 6.851A pdb=" N GLN A 502 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA A 513 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 504 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 534 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 291 removed outlier: 4.556A pdb=" N ILE A 491 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 481 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR A 473 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.735A pdb=" N ILE A 302 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 346 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER A 420 " --> pdb=" O GLY A 383 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY A 422 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS A 381 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 364 removed outlier: 3.651A pdb=" N MET A 398 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 415 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 400 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY A 413 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA A 402 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR A 411 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TRP A 404 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR A 409 " --> pdb=" O TRP A 404 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.664A pdb=" N LEU A 548 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 568 removed outlier: 6.377A pdb=" N ARG A 567 " --> pdb=" O PHE C 654 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 581 through 585 Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 598 removed outlier: 3.727A pdb=" N SER A 591 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 595 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 935 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 952 " --> pdb=" O HIS A 933 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS A 933 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AB5, first strand: chain 'A' and resid 653 through 654 Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1011 Processing sheet with id=AB7, first strand: chain 'A' and resid 981 through 984 removed outlier: 3.717A pdb=" N ILE A 992 " --> pdb=" O ARG A1001 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 70 through 76 removed outlier: 8.409A pdb=" N ASP B 239 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR B 254 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 241 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN B 243 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 94 through 95 removed outlier: 5.810A pdb=" N GLY B 130 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 145 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 94 through 95 removed outlier: 5.810A pdb=" N GLY B 130 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 145 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 170 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.529A pdb=" N TYR B 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 274 through 278 removed outlier: 6.850A pdb=" N GLN B 502 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA B 513 " --> pdb=" O GLN B 502 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 504 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 534 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 288 through 291 removed outlier: 4.557A pdb=" N ILE B 491 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 481 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR B 473 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 301 through 302 removed outlier: 3.736A pdb=" N ILE B 302 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 346 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER B 420 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY B 422 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS B 381 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 364 removed outlier: 3.651A pdb=" N MET B 398 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 415 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 400 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY B 413 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 402 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR B 411 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TRP B 404 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 409 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 548 through 549 removed outlier: 3.664A pdb=" N LEU B 548 " --> pdb=" O VAL B 555 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 581 through 585 Processing sheet with id=AC9, first strand: chain 'B' and resid 588 through 598 removed outlier: 3.726A pdb=" N SER B 591 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 595 " --> pdb=" O PHE B 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 935 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 952 " --> pdb=" O HIS B 933 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS B 933 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 604 through 606 Processing sheet with id=AD2, first strand: chain 'B' and resid 653 through 654 removed outlier: 3.647A pdb=" N PHE B 654 " --> pdb=" O ARG C 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1008 through 1011 Processing sheet with id=AD4, first strand: chain 'B' and resid 981 through 984 removed outlier: 3.717A pdb=" N ILE B 992 " --> pdb=" O ARG B1001 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 70 through 76 removed outlier: 8.409A pdb=" N ASP C 239 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TYR C 254 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 241 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C 243 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 94 through 95 removed outlier: 5.811A pdb=" N GLY C 130 " --> pdb=" O CYS C 145 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS C 145 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 94 through 95 removed outlier: 5.811A pdb=" N GLY C 130 " --> pdb=" O CYS C 145 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS C 145 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 170 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 210 removed outlier: 3.529A pdb=" N TYR C 206 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE C 201 " --> pdb=" O TYR C 208 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 274 through 278 removed outlier: 6.851A pdb=" N GLN C 502 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA C 513 " --> pdb=" O GLN C 502 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 504 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 534 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 288 through 291 removed outlier: 4.556A pdb=" N ILE C 491 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU C 481 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR C 473 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.736A pdb=" N ILE C 302 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 346 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER C 420 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY C 422 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS C 381 " --> pdb=" O GLY C 422 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 360 through 364 removed outlier: 3.650A pdb=" N MET C 398 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 415 " --> pdb=" O MET C 398 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 400 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY C 413 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 402 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR C 411 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TRP C 404 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 409 " --> pdb=" O TRP C 404 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 548 through 549 removed outlier: 3.665A pdb=" N LEU C 548 " --> pdb=" O VAL C 555 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 581 through 585 Processing sheet with id=AE6, first strand: chain 'C' and resid 588 through 598 removed outlier: 3.727A pdb=" N SER C 591 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 595 " --> pdb=" O PHE C 947 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE C 935 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C 952 " --> pdb=" O HIS C 933 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS C 933 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AE8, first strand: chain 'C' and resid 1008 through 1011 Processing sheet with id=AE9, first strand: chain 'C' and resid 981 through 984 removed outlier: 3.716A pdb=" N ILE C 992 " --> pdb=" O ARG C1001 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2415 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: 5.03 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3741 1.32 - 1.45: 6659 1.45 - 1.57: 12433 1.57 - 1.70: 3 1.70 - 1.83: 141 Bond restraints: 22977 Sorted by residual: bond pdb=" C PRO A 272 " pdb=" O PRO A 272 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.16e-02 7.43e+03 1.35e+01 bond pdb=" C PRO B 272 " pdb=" O PRO B 272 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.16e-02 7.43e+03 1.34e+01 bond pdb=" C PRO C 272 " pdb=" O PRO C 272 " ideal model delta sigma weight residual 1.233 1.190 0.042 1.16e-02 7.43e+03 1.34e+01 bond pdb=" C VAL B 271 " pdb=" O VAL B 271 " ideal model delta sigma weight residual 1.248 1.208 0.040 1.27e-02 6.20e+03 9.93e+00 bond pdb=" N ASP B 723 " pdb=" CA ASP B 723 " ideal model delta sigma weight residual 1.453 1.492 -0.038 1.22e-02 6.72e+03 9.87e+00 ... (remaining 22972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 28908 2.34 - 4.67: 1776 4.67 - 7.01: 195 7.01 - 9.35: 48 9.35 - 11.68: 12 Bond angle restraints: 30939 Sorted by residual: angle pdb=" N THR C 716 " pdb=" CA THR C 716 " pdb=" C THR C 716 " ideal model delta sigma weight residual 114.64 102.96 11.68 1.52e+00 4.33e-01 5.91e+01 angle pdb=" N THR A 716 " pdb=" CA THR A 716 " pdb=" C THR A 716 " ideal model delta sigma weight residual 114.64 103.00 11.64 1.52e+00 4.33e-01 5.86e+01 angle pdb=" N THR B 716 " pdb=" CA THR B 716 " pdb=" C THR B 716 " ideal model delta sigma weight residual 114.64 103.03 11.61 1.52e+00 4.33e-01 5.83e+01 angle pdb=" C TYR B 96 " pdb=" CA TYR B 96 " pdb=" CB TYR B 96 " ideal model delta sigma weight residual 111.76 100.56 11.20 1.47e+00 4.63e-01 5.81e+01 angle pdb=" C TYR C 96 " pdb=" CA TYR C 96 " pdb=" CB TYR C 96 " ideal model delta sigma weight residual 111.76 100.56 11.20 1.47e+00 4.63e-01 5.80e+01 ... (remaining 30934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.45: 14169 26.45 - 52.90: 558 52.90 - 79.36: 144 79.36 - 105.81: 51 105.81 - 132.26: 51 Dihedral angle restraints: 14973 sinusoidal: 6600 harmonic: 8373 Sorted by residual: dihedral pdb=" CB CYS C 917 " pdb=" SG CYS C 917 " pdb=" SG CYS C 928 " pdb=" CB CYS C 928 " ideal model delta sinusoidal sigma weight residual 93.00 174.94 -81.94 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS B 917 " pdb=" SG CYS B 917 " pdb=" SG CYS B 928 " pdb=" CB CYS B 928 " ideal model delta sinusoidal sigma weight residual 93.00 174.90 -81.90 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS A 917 " pdb=" SG CYS A 917 " pdb=" SG CYS A 928 " pdb=" CB CYS A 928 " ideal model delta sinusoidal sigma weight residual 93.00 174.90 -81.90 1 1.00e+01 1.00e-02 8.25e+01 ... (remaining 14970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3261 0.189 - 0.378: 115 0.378 - 0.567: 3 0.567 - 0.756: 5 0.756 - 0.945: 9 Chirality restraints: 3393 Sorted by residual: chirality pdb=" C1 MAN D 7 " pdb=" O2 MAN D 6 " pdb=" C2 MAN D 7 " pdb=" O5 MAN D 7 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 MAN H 7 " pdb=" O2 MAN H 6 " pdb=" C2 MAN H 7 " pdb=" O5 MAN H 7 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 MAN L 7 " pdb=" O2 MAN L 6 " pdb=" C2 MAN L 7 " pdb=" O5 MAN L 7 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.96e+03 ... (remaining 3390 not shown) Planarity restraints: 4080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.363 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG L 1 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.553 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.363 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG H 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.553 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.363 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG D 1 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.553 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.164 2.00e-02 2.50e+03 ... (remaining 4077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1203 2.69 - 3.24: 23321 3.24 - 3.80: 33511 3.80 - 4.35: 40182 4.35 - 4.90: 64663 Nonbonded interactions: 162880 Sorted by model distance: nonbonded pdb=" NH2 ARG A 977 " pdb=" OD1 ASP C1007 " model vdw 2.139 3.120 nonbonded pdb=" O MET B 398 " pdb=" O SER B 414 " model vdw 2.207 3.040 nonbonded pdb=" O MET C 398 " pdb=" O SER C 414 " model vdw 2.208 3.040 nonbonded pdb=" O MET A 398 " pdb=" O SER A 414 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASN A 56 " pdb=" NH2 ARG A 191 " model vdw 2.219 3.120 ... (remaining 162875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } 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: 0.620 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.230 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.008 0.153 23091 Z= 0.465 Angle : 1.397 26.089 31260 Z= 0.772 Chirality : 0.093 0.945 3393 Planarity : 0.011 0.311 4020 Dihedral : 17.846 132.261 9546 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.57 % Favored : 93.90 % Rotamer: Outliers : 5.89 % Allowed : 7.31 % Favored : 86.80 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 2853 helix: -0.97 (0.18), residues: 618 sheet: -0.87 (0.23), residues: 507 loop : -2.16 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 991 TYR 0.054 0.003 TYR C 96 PHE 0.035 0.003 PHE C 382 TRP 0.022 0.003 TRP B 57 HIS 0.014 0.003 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00770 (22977) covalent geometry : angle 1.21225 (30939) SS BOND : bond 0.01586 ( 21) SS BOND : angle 4.37935 ( 42) hydrogen bonds : bond 0.16845 ( 823) hydrogen bonds : angle 8.68972 ( 2415) link_ALPHA1-2 : bond 0.01360 ( 6) link_ALPHA1-2 : angle 4.67442 ( 18) link_ALPHA1-3 : bond 0.00255 ( 3) link_ALPHA1-3 : angle 1.35018 ( 9) link_ALPHA1-6 : bond 0.00049 ( 3) link_ALPHA1-6 : angle 0.81677 ( 9) link_BETA1-4 : bond 0.05484 ( 21) link_BETA1-4 : angle 9.59908 ( 63) link_NAG-ASN : bond 0.04772 ( 60) link_NAG-ASN : angle 6.86817 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 729 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.9119 (t) cc_final: 0.8913 (p) REVERT: A 74 PHE cc_start: 0.8289 (m-80) cc_final: 0.8031 (m-80) REVERT: A 96 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 134 PHE cc_start: 0.8087 (m-80) cc_final: 0.7872 (m-10) REVERT: A 135 LYS cc_start: 0.7777 (tttm) cc_final: 0.7150 (tptp) REVERT: A 144 TYR cc_start: 0.5593 (t80) cc_final: 0.5360 (t80) REVERT: A 192 GLU cc_start: 0.7966 (tt0) cc_final: 0.7668 (tt0) REVERT: A 215 GLU cc_start: 0.6893 (tt0) cc_final: 0.6427 (tt0) REVERT: A 246 GLN cc_start: 0.8711 (mt0) cc_final: 0.8406 (mt0) REVERT: A 285 GLU cc_start: 0.8937 (pp20) cc_final: 0.8479 (pp20) REVERT: A 310 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.6935 (Cg_exo) REVERT: A 363 SER cc_start: 0.5602 (OUTLIER) cc_final: 0.4987 (p) REVERT: A 365 ASN cc_start: 0.7890 (m-40) cc_final: 0.7607 (m-40) REVERT: A 370 PRO cc_start: 0.8934 (Cg_exo) cc_final: 0.8437 (Cg_endo) REVERT: A 381 LYS cc_start: 0.7637 (mttp) cc_final: 0.7292 (mmtm) REVERT: A 408 LYS cc_start: 0.7130 (mppt) cc_final: 0.6438 (mttt) REVERT: A 439 MET cc_start: 0.7783 (tpp) cc_final: 0.7466 (mmp) REVERT: A 530 LEU cc_start: 0.7827 (tp) cc_final: 0.7310 (tt) REVERT: A 565 GLN cc_start: 0.8679 (mt0) cc_final: 0.8383 (tm-30) REVERT: A 693 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 741 ASP cc_start: 0.7754 (p0) cc_final: 0.7355 (p0) REVERT: A 839 GLN cc_start: 0.9245 (tp40) cc_final: 0.8948 (tt0) REVERT: A 845 ASN cc_start: 0.7974 (m110) cc_final: 0.7512 (m110) REVERT: A 980 ASN cc_start: 0.8380 (m110) cc_final: 0.8153 (m-40) REVERT: A 986 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 56 ASN cc_start: 0.8029 (m-40) cc_final: 0.7366 (m110) REVERT: B 74 PHE cc_start: 0.8563 (m-80) cc_final: 0.8253 (m-80) REVERT: B 135 LYS cc_start: 0.7681 (tttm) cc_final: 0.7296 (tptp) REVERT: B 192 GLU cc_start: 0.7655 (tt0) cc_final: 0.7389 (tt0) REVERT: B 219 PHE cc_start: 0.8626 (t80) cc_final: 0.8388 (t80) REVERT: B 246 GLN cc_start: 0.8338 (mt0) cc_final: 0.7918 (mm-40) REVERT: B 310 PRO cc_start: 0.7300 (Cg_endo) cc_final: 0.6841 (Cg_exo) REVERT: B 331 ASN cc_start: 0.7758 (t0) cc_final: 0.7360 (t0) REVERT: B 363 SER cc_start: 0.5230 (OUTLIER) cc_final: 0.4861 (p) REVERT: B 371 PHE cc_start: 0.8758 (p90) cc_final: 0.8075 (p90) REVERT: B 375 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7510 (mtpp) REVERT: B 381 LYS cc_start: 0.7863 (mttp) cc_final: 0.7662 (mmtt) REVERT: B 415 LEU cc_start: 0.7781 (mm) cc_final: 0.7455 (tp) REVERT: B 439 MET cc_start: 0.8213 (tpp) cc_final: 0.7926 (mmp) REVERT: B 514 MET cc_start: 0.8251 (mtt) cc_final: 0.7818 (mpp) REVERT: B 530 LEU cc_start: 0.8048 (tp) cc_final: 0.7566 (tt) REVERT: B 586 SER cc_start: 0.4480 (OUTLIER) cc_final: 0.4268 (t) REVERT: B 622 LEU cc_start: 0.9132 (mp) cc_final: 0.8810 (mt) REVERT: B 635 ASP cc_start: 0.8705 (t0) cc_final: 0.8423 (t0) REVERT: B 693 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 723 ASP cc_start: 0.8019 (t0) cc_final: 0.7158 (p0) REVERT: B 724 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (tp) REVERT: B 798 PHE cc_start: 0.9148 (t80) cc_final: 0.8575 (t80) REVERT: B 807 ASP cc_start: 0.8893 (m-30) cc_final: 0.8599 (m-30) REVERT: B 840 GLN cc_start: 0.9381 (tp40) cc_final: 0.9020 (tm-30) REVERT: B 853 GLN cc_start: 0.9153 (pp30) cc_final: 0.8464 (pp30) REVERT: B 868 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8432 (mtp85) REVERT: B 911 GLN cc_start: 0.8542 (tt0) cc_final: 0.8326 (tp-100) REVERT: B 916 GLU cc_start: 0.7780 (tp30) cc_final: 0.7469 (tm-30) REVERT: B 980 ASN cc_start: 0.8693 (m110) cc_final: 0.8162 (m-40) REVERT: B 985 LYS cc_start: 0.8997 (tttt) cc_final: 0.8699 (tttm) REVERT: C 74 PHE cc_start: 0.8792 (m-80) cc_final: 0.8534 (m-80) REVERT: C 79 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.5682 (tp) REVERT: C 88 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6395 (pt) REVERT: C 144 TYR cc_start: 0.5438 (t80) cc_final: 0.5132 (t80) REVERT: C 177 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6798 (tm-30) REVERT: C 192 GLU cc_start: 0.7896 (tt0) cc_final: 0.7293 (tt0) REVERT: C 246 GLN cc_start: 0.8660 (mt0) cc_final: 0.8372 (mp10) REVERT: C 285 GLU cc_start: 0.8881 (pp20) cc_final: 0.8452 (tm-30) REVERT: C 363 SER cc_start: 0.5096 (OUTLIER) cc_final: 0.4576 (p) REVERT: C 365 ASN cc_start: 0.7711 (m-40) cc_final: 0.7511 (m-40) REVERT: C 371 PHE cc_start: 0.8532 (p90) cc_final: 0.8080 (p90) REVERT: C 372 SER cc_start: 0.8696 (p) cc_final: 0.7490 (p) REVERT: C 375 LYS cc_start: 0.8305 (mmtp) cc_final: 0.7969 (mtmm) REVERT: C 381 LYS cc_start: 0.7360 (mttp) cc_final: 0.6969 (mmtt) REVERT: C 439 MET cc_start: 0.7268 (tpp) cc_final: 0.7006 (mmp) REVERT: C 445 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8687 (mmtm) REVERT: C 488 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8656 (mtmm) REVERT: C 515 LEU cc_start: 0.8991 (mp) cc_final: 0.8771 (mp) REVERT: C 595 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7316 (mt-10) REVERT: C 625 GLN cc_start: 0.9067 (pt0) cc_final: 0.8769 (pt0) REVERT: C 639 ASN cc_start: 0.8633 (t0) cc_final: 0.8321 (t0) REVERT: C 693 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 723 ASP cc_start: 0.8153 (t0) cc_final: 0.7890 (t70) REVERT: C 730 TYR cc_start: 0.8927 (m-10) cc_final: 0.8727 (m-80) REVERT: C 741 ASP cc_start: 0.8337 (p0) cc_final: 0.8067 (p0) REVERT: C 774 GLN cc_start: 0.8346 (tp40) cc_final: 0.8097 (tp40) REVERT: C 802 MET cc_start: 0.9091 (mtp) cc_final: 0.8857 (mtp) REVERT: C 830 LEU cc_start: 0.9404 (mt) cc_final: 0.8752 (mt) REVERT: C 844 LEU cc_start: 0.8826 (pp) cc_final: 0.8624 (pp) REVERT: C 845 ASN cc_start: 0.8089 (m110) cc_final: 0.7614 (m110) REVERT: C 853 GLN cc_start: 0.8928 (pp30) cc_final: 0.8379 (pp30) REVERT: C 923 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8617 (mmtp) REVERT: C 978 GLN cc_start: 0.8490 (pm20) cc_final: 0.8052 (pm20) REVERT: C 980 ASN cc_start: 0.8420 (m110) cc_final: 0.8088 (m110) outliers start: 128 outliers final: 87 residues processed: 829 average time/residue: 0.1633 time to fit residues: 203.6754 Evaluate side-chains 643 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 548 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 968 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 331 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 GLN A 731 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 863 GLN ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 331 ASN B 469 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109219 restraints weight = 46656.344| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.02 r_work: 0.3398 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23091 Z= 0.171 Angle : 0.926 17.275 31260 Z= 0.430 Chirality : 0.057 0.831 3393 Planarity : 0.005 0.045 4020 Dihedral : 15.177 113.216 5152 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.24 % Favored : 95.55 % Rotamer: Outliers : 4.64 % Allowed : 14.30 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.15), residues: 2853 helix: 0.00 (0.19), residues: 657 sheet: -0.67 (0.21), residues: 612 loop : -2.12 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 261 TYR 0.034 0.002 TYR C 96 PHE 0.023 0.002 PHE C 219 TRP 0.042 0.004 TRP B 360 HIS 0.009 0.002 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00361 (22977) covalent geometry : angle 0.81461 (30939) SS BOND : bond 0.00620 ( 21) SS BOND : angle 1.54174 ( 42) hydrogen bonds : bond 0.05049 ( 823) hydrogen bonds : angle 6.52043 ( 2415) link_ALPHA1-2 : bond 0.01078 ( 6) link_ALPHA1-2 : angle 5.77781 ( 18) link_ALPHA1-3 : bond 0.00886 ( 3) link_ALPHA1-3 : angle 1.23109 ( 9) link_ALPHA1-6 : bond 0.00027 ( 3) link_ALPHA1-6 : angle 1.94380 ( 9) link_BETA1-4 : bond 0.00440 ( 21) link_BETA1-4 : angle 2.68651 ( 63) link_NAG-ASN : bond 0.01115 ( 60) link_NAG-ASN : angle 5.30454 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 593 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 138 TYR cc_start: 0.6552 (p90) cc_final: 0.5749 (p90) REVERT: A 228 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.4894 (m-30) REVERT: A 363 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7192 (p) REVERT: A 371 PHE cc_start: 0.8920 (p90) cc_final: 0.8612 (p90) REVERT: A 381 LYS cc_start: 0.8313 (mttp) cc_final: 0.7982 (mmtp) REVERT: A 439 MET cc_start: 0.7612 (tpp) cc_final: 0.7158 (mmt) REVERT: A 590 THR cc_start: 0.9490 (m) cc_final: 0.9235 (p) REVERT: A 635 ASP cc_start: 0.8672 (t0) cc_final: 0.8463 (t0) REVERT: A 644 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 655 ASP cc_start: 0.8562 (t0) cc_final: 0.8124 (t0) REVERT: A 723 ASP cc_start: 0.7885 (t0) cc_final: 0.7658 (t0) REVERT: A 734 MET cc_start: 0.8854 (ttm) cc_final: 0.8410 (mtp) REVERT: A 782 LEU cc_start: 0.8455 (mp) cc_final: 0.8112 (tp) REVERT: A 840 GLN cc_start: 0.8980 (tp40) cc_final: 0.8741 (tp40) REVERT: A 845 ASN cc_start: 0.8447 (m110) cc_final: 0.7968 (m110) REVERT: A 856 GLN cc_start: 0.9062 (tp40) cc_final: 0.8825 (mm110) REVERT: A 908 GLN cc_start: 0.9056 (tp40) cc_final: 0.8583 (tm-30) REVERT: A 986 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8463 (tm-30) REVERT: B 78 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 192 GLU cc_start: 0.8554 (tt0) cc_final: 0.8192 (tt0) REVERT: B 338 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: B 363 SER cc_start: 0.7043 (OUTLIER) cc_final: 0.6770 (p) REVERT: B 381 LYS cc_start: 0.8368 (mttp) cc_final: 0.8123 (mmtt) REVERT: B 439 MET cc_start: 0.8261 (tpp) cc_final: 0.7869 (tpp) REVERT: B 514 MET cc_start: 0.8693 (mtt) cc_final: 0.8419 (mpp) REVERT: B 655 ASP cc_start: 0.8596 (t0) cc_final: 0.8247 (t0) REVERT: B 807 ASP cc_start: 0.8969 (m-30) cc_final: 0.8598 (m-30) REVERT: B 840 GLN cc_start: 0.9124 (tp40) cc_final: 0.8528 (tm-30) REVERT: B 853 GLN cc_start: 0.9360 (pp30) cc_final: 0.8673 (pp30) REVERT: B 856 GLN cc_start: 0.9177 (tp40) cc_final: 0.8915 (mm110) REVERT: B 868 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8721 (mtp85) REVERT: C 79 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.5848 (tp) REVERT: C 135 LYS cc_start: 0.7874 (tttm) cc_final: 0.7255 (tptp) REVERT: C 138 TYR cc_start: 0.5981 (p90) cc_final: 0.5548 (p90) REVERT: C 191 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.6950 (mtp-110) REVERT: C 228 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.5477 (m-30) REVERT: C 285 GLU cc_start: 0.9100 (pp20) cc_final: 0.8790 (tm-30) REVERT: C 363 SER cc_start: 0.7137 (OUTLIER) cc_final: 0.6776 (p) REVERT: C 365 ASN cc_start: 0.8589 (m-40) cc_final: 0.8382 (m-40) REVERT: C 369 CYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7597 (m) REVERT: C 375 LYS cc_start: 0.8834 (mmtp) cc_final: 0.8514 (mtmm) REVERT: C 381 LYS cc_start: 0.8152 (mttp) cc_final: 0.7790 (mmtt) REVERT: C 387 PHE cc_start: 0.8306 (m-80) cc_final: 0.8029 (m-80) REVERT: C 595 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 639 ASN cc_start: 0.8764 (t0) cc_final: 0.8460 (t0) REVERT: C 723 ASP cc_start: 0.8457 (t0) cc_final: 0.8248 (t70) REVERT: C 774 GLN cc_start: 0.8933 (tp40) cc_final: 0.8589 (tp40) REVERT: C 845 ASN cc_start: 0.8558 (m110) cc_final: 0.8128 (m110) REVERT: C 867 ASP cc_start: 0.8645 (m-30) cc_final: 0.8366 (m-30) REVERT: C 911 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 920 SER cc_start: 0.9143 (m) cc_final: 0.8751 (p) outliers start: 101 outliers final: 71 residues processed: 657 average time/residue: 0.1510 time to fit residues: 153.9685 Evaluate side-chains 614 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 534 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 978 GLN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 770 SER Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 968 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 249 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 728 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN B 912 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102657 restraints weight = 47551.641| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.94 r_work: 0.3311 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23091 Z= 0.224 Angle : 0.883 17.815 31260 Z= 0.416 Chirality : 0.054 0.551 3393 Planarity : 0.004 0.048 4020 Dihedral : 13.048 116.549 5092 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.04 % Rotamer: Outliers : 5.61 % Allowed : 17.75 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 2853 helix: 0.24 (0.20), residues: 660 sheet: -0.71 (0.20), residues: 612 loop : -2.18 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 191 TYR 0.039 0.002 TYR B 96 PHE 0.030 0.002 PHE A 219 TRP 0.020 0.002 TRP B 360 HIS 0.006 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00489 (22977) covalent geometry : angle 0.78881 (30939) SS BOND : bond 0.00578 ( 21) SS BOND : angle 1.43658 ( 42) hydrogen bonds : bond 0.05329 ( 823) hydrogen bonds : angle 6.11457 ( 2415) link_ALPHA1-2 : bond 0.00959 ( 6) link_ALPHA1-2 : angle 4.69922 ( 18) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 1.30086 ( 9) link_ALPHA1-6 : bond 0.00233 ( 3) link_ALPHA1-6 : angle 2.83349 ( 9) link_BETA1-4 : bond 0.00567 ( 21) link_BETA1-4 : angle 2.62670 ( 63) link_NAG-ASN : bond 0.00788 ( 60) link_NAG-ASN : angle 4.79605 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 515 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6747 (p90) cc_final: 0.5965 (p90) REVERT: A 213 ASN cc_start: 0.8990 (m110) cc_final: 0.8547 (m-40) REVERT: A 228 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.5832 (p0) REVERT: A 371 PHE cc_start: 0.8983 (p90) cc_final: 0.8593 (p90) REVERT: A 381 LYS cc_start: 0.8546 (mttp) cc_final: 0.8186 (mmtt) REVERT: A 439 MET cc_start: 0.7782 (tpp) cc_final: 0.7296 (mmt) REVERT: A 519 PHE cc_start: 0.8599 (t80) cc_final: 0.8363 (t80) REVERT: A 635 ASP cc_start: 0.8813 (t0) cc_final: 0.8569 (t0) REVERT: A 714 LYS cc_start: 0.9294 (mtpp) cc_final: 0.8978 (mtmm) REVERT: A 723 ASP cc_start: 0.8368 (t0) cc_final: 0.8154 (t0) REVERT: A 734 MET cc_start: 0.9050 (ttm) cc_final: 0.8646 (mtp) REVERT: A 789 GLU cc_start: 0.8645 (pp20) cc_final: 0.8119 (pp20) REVERT: A 840 GLN cc_start: 0.8843 (tp40) cc_final: 0.8579 (tp40) REVERT: A 845 ASN cc_start: 0.8528 (m110) cc_final: 0.8063 (m-40) REVERT: A 856 GLN cc_start: 0.9203 (tp40) cc_final: 0.8978 (mm110) REVERT: A 908 GLN cc_start: 0.9118 (tp40) cc_final: 0.8718 (tm-30) REVERT: A 911 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8999 (tp-100) REVERT: A 986 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 74 PHE cc_start: 0.8722 (m-80) cc_final: 0.8497 (m-80) REVERT: B 213 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8551 (m-40) REVERT: B 338 PRO cc_start: 0.8707 (Cg_exo) cc_final: 0.8217 (Cg_endo) REVERT: B 363 SER cc_start: 0.7518 (OUTLIER) cc_final: 0.7292 (p) REVERT: B 381 LYS cc_start: 0.8509 (mttp) cc_final: 0.8230 (mmtt) REVERT: B 514 MET cc_start: 0.9107 (mtt) cc_final: 0.8888 (mpp) REVERT: B 693 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7902 (mt-10) REVERT: B 723 ASP cc_start: 0.8458 (t0) cc_final: 0.8220 (p0) REVERT: B 807 ASP cc_start: 0.8912 (m-30) cc_final: 0.8570 (m-30) REVERT: B 840 GLN cc_start: 0.9024 (tp40) cc_final: 0.8433 (tm-30) REVERT: B 856 GLN cc_start: 0.9260 (tp40) cc_final: 0.9034 (mm110) REVERT: B 866 TYR cc_start: 0.8948 (m-10) cc_final: 0.8669 (m-80) REVERT: B 868 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8778 (mtp85) REVERT: B 908 GLN cc_start: 0.9173 (tp40) cc_final: 0.8904 (tm-30) REVERT: B 912 GLN cc_start: 0.9181 (tt0) cc_final: 0.8862 (tt0) REVERT: C 79 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5253 (tp) REVERT: C 124 GLU cc_start: 0.6142 (mp0) cc_final: 0.5638 (mp0) REVERT: C 135 LYS cc_start: 0.8223 (tttm) cc_final: 0.7406 (tptp) REVERT: C 191 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7132 (mtp-110) REVERT: C 285 GLU cc_start: 0.9063 (pp20) cc_final: 0.8803 (tm-30) REVERT: C 369 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7842 (m) REVERT: C 370 PRO cc_start: 0.9299 (Cg_exo) cc_final: 0.9097 (Cg_endo) REVERT: C 381 LYS cc_start: 0.8350 (mttp) cc_final: 0.7981 (mmtt) REVERT: C 595 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7946 (mt-10) REVERT: C 774 GLN cc_start: 0.9085 (tp40) cc_final: 0.8572 (tp40) REVERT: C 845 ASN cc_start: 0.8620 (m110) cc_final: 0.8225 (m110) REVERT: C 876 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 958 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8481 (ttmm) REVERT: C 969 ASP cc_start: 0.8023 (p0) cc_final: 0.7745 (p0) outliers start: 122 outliers final: 94 residues processed: 596 average time/residue: 0.1417 time to fit residues: 132.9272 Evaluate side-chains 578 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 478 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 978 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 968 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 10 optimal weight: 0.0670 chunk 218 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A 846 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 331 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN C 508 GLN ** C 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105105 restraints weight = 47063.636| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.97 r_work: 0.3348 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23091 Z= 0.135 Angle : 0.788 18.041 31260 Z= 0.369 Chirality : 0.052 0.508 3393 Planarity : 0.004 0.043 4020 Dihedral : 11.775 112.686 5079 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.63 % Favored : 95.16 % Rotamer: Outliers : 5.29 % Allowed : 19.72 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 2853 helix: 0.62 (0.20), residues: 657 sheet: -0.63 (0.21), residues: 609 loop : -2.16 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.032 0.001 TYR B 96 PHE 0.049 0.002 PHE B 219 TRP 0.018 0.002 TRP A 83 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00282 (22977) covalent geometry : angle 0.69915 (30939) SS BOND : bond 0.00744 ( 21) SS BOND : angle 1.11133 ( 42) hydrogen bonds : bond 0.04362 ( 823) hydrogen bonds : angle 5.67366 ( 2415) link_ALPHA1-2 : bond 0.01237 ( 6) link_ALPHA1-2 : angle 4.12137 ( 18) link_ALPHA1-3 : bond 0.01077 ( 3) link_ALPHA1-3 : angle 1.64176 ( 9) link_ALPHA1-6 : bond 0.00466 ( 3) link_ALPHA1-6 : angle 2.85319 ( 9) link_BETA1-4 : bond 0.00541 ( 21) link_BETA1-4 : angle 2.27944 ( 63) link_NAG-ASN : bond 0.00723 ( 60) link_NAG-ASN : angle 4.40537 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 526 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6636 (p90) cc_final: 0.5928 (p90) REVERT: A 228 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.5804 (p0) REVERT: A 371 PHE cc_start: 0.8964 (p90) cc_final: 0.8575 (p90) REVERT: A 381 LYS cc_start: 0.8532 (mttp) cc_final: 0.8066 (mmtt) REVERT: A 439 MET cc_start: 0.7735 (tpp) cc_final: 0.7482 (mmp) REVERT: A 623 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8866 (tt) REVERT: A 631 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8440 (tttp) REVERT: A 644 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8803 (tm-30) REVERT: A 714 LYS cc_start: 0.9279 (mtpp) cc_final: 0.9073 (mtmm) REVERT: A 734 MET cc_start: 0.9019 (ttm) cc_final: 0.8694 (mtp) REVERT: A 789 GLU cc_start: 0.8713 (pp20) cc_final: 0.8179 (pp20) REVERT: A 840 GLN cc_start: 0.8838 (tp40) cc_final: 0.8584 (tp40) REVERT: A 845 ASN cc_start: 0.8642 (m110) cc_final: 0.8173 (m-40) REVERT: A 856 GLN cc_start: 0.9192 (tp40) cc_final: 0.8594 (mm110) REVERT: A 880 ARG cc_start: 0.8626 (ptp-170) cc_final: 0.8283 (ptm160) REVERT: A 908 GLN cc_start: 0.9059 (tp40) cc_final: 0.8754 (tm-30) REVERT: A 911 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8785 (tp-100) REVERT: A 986 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 74 PHE cc_start: 0.8670 (m-80) cc_final: 0.8434 (m-80) REVERT: B 514 MET cc_start: 0.9109 (mtt) cc_final: 0.8879 (mpp) REVERT: B 723 ASP cc_start: 0.8417 (t0) cc_final: 0.8186 (p0) REVERT: B 807 ASP cc_start: 0.8949 (m-30) cc_final: 0.8594 (m-30) REVERT: B 840 GLN cc_start: 0.9055 (tp40) cc_final: 0.8815 (tp-100) REVERT: B 868 ARG cc_start: 0.8935 (mmm-85) cc_final: 0.8679 (mtp85) REVERT: B 908 GLN cc_start: 0.9154 (tp40) cc_final: 0.8892 (tm-30) REVERT: C 79 LEU cc_start: 0.6272 (pt) cc_final: 0.5780 (tp) REVERT: C 135 LYS cc_start: 0.8153 (tttm) cc_final: 0.7359 (tptp) REVERT: C 138 TYR cc_start: 0.6371 (p90) cc_final: 0.5800 (p90) REVERT: C 191 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7179 (mtp-110) REVERT: C 228 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6173 (p0) REVERT: C 285 GLU cc_start: 0.9066 (pp20) cc_final: 0.8786 (tm-30) REVERT: C 369 CYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7545 (m) REVERT: C 381 LYS cc_start: 0.8402 (mttp) cc_final: 0.8149 (mmtt) REVERT: C 390 LYS cc_start: 0.7535 (ptpt) cc_final: 0.7194 (pttt) REVERT: C 571 TYR cc_start: 0.8424 (p90) cc_final: 0.8117 (p90) REVERT: C 595 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7992 (mt-10) REVERT: C 774 GLN cc_start: 0.9075 (tp40) cc_final: 0.8745 (tp40) REVERT: C 832 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8870 (mttm) REVERT: C 845 ASN cc_start: 0.8596 (m110) cc_final: 0.8220 (m-40) REVERT: C 867 ASP cc_start: 0.8746 (m-30) cc_final: 0.8504 (m-30) REVERT: C 876 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8563 (tm-30) REVERT: C 902 GLU cc_start: 0.8862 (pp20) cc_final: 0.8165 (tm-30) REVERT: C 920 SER cc_start: 0.9198 (m) cc_final: 0.8934 (p) REVERT: C 958 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8460 (tttp) outliers start: 115 outliers final: 86 residues processed: 603 average time/residue: 0.1431 time to fit residues: 135.5373 Evaluate side-chains 578 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 487 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 68 optimal weight: 0.0670 chunk 158 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN ** B 978 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 = 0.3653 r_free = 0.3653 target = 0.118490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098929 restraints weight = 47652.679| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.86 r_work: 0.3256 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23091 Z= 0.276 Angle : 0.871 16.974 31260 Z= 0.420 Chirality : 0.055 0.587 3393 Planarity : 0.005 0.049 4020 Dihedral : 11.658 110.698 5068 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.01 % Favored : 92.78 % Rotamer: Outliers : 6.39 % Allowed : 19.40 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.15), residues: 2853 helix: 0.40 (0.20), residues: 660 sheet: -0.72 (0.20), residues: 609 loop : -2.33 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.040 0.002 TYR A 96 PHE 0.038 0.002 PHE B 219 TRP 0.013 0.002 TRP B 419 HIS 0.007 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00608 (22977) covalent geometry : angle 0.79569 (30939) SS BOND : bond 0.00490 ( 21) SS BOND : angle 1.53954 ( 42) hydrogen bonds : bond 0.05370 ( 823) hydrogen bonds : angle 6.04953 ( 2415) link_ALPHA1-2 : bond 0.01089 ( 6) link_ALPHA1-2 : angle 4.06570 ( 18) link_ALPHA1-3 : bond 0.01051 ( 3) link_ALPHA1-3 : angle 1.58253 ( 9) link_ALPHA1-6 : bond 0.00257 ( 3) link_ALPHA1-6 : angle 3.15326 ( 9) link_BETA1-4 : bond 0.00419 ( 21) link_BETA1-4 : angle 2.21148 ( 63) link_NAG-ASN : bond 0.00718 ( 60) link_NAG-ASN : angle 4.29044 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 479 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 PHE cc_start: 0.8991 (p90) cc_final: 0.8617 (p90) REVERT: A 439 MET cc_start: 0.7830 (tpp) cc_final: 0.7486 (mmp) REVERT: A 519 PHE cc_start: 0.8597 (t80) cc_final: 0.8351 (t80) REVERT: A 623 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8961 (tt) REVERT: A 631 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8555 (tttp) REVERT: A 635 ASP cc_start: 0.8813 (t0) cc_final: 0.8573 (t0) REVERT: A 714 LYS cc_start: 0.9231 (mtpp) cc_final: 0.8974 (mtmm) REVERT: A 789 GLU cc_start: 0.8677 (pp20) cc_final: 0.8169 (pp20) REVERT: A 840 GLN cc_start: 0.8816 (tp40) cc_final: 0.8594 (tp40) REVERT: A 845 ASN cc_start: 0.8670 (m110) cc_final: 0.8236 (m-40) REVERT: A 856 GLN cc_start: 0.9217 (tp40) cc_final: 0.8583 (mm110) REVERT: A 880 ARG cc_start: 0.8803 (ptp-170) cc_final: 0.8396 (ptm160) REVERT: A 908 GLN cc_start: 0.9108 (tp40) cc_final: 0.8859 (tm-30) REVERT: A 985 LYS cc_start: 0.9216 (tttt) cc_final: 0.9013 (tttm) REVERT: A 986 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 998 PHE cc_start: 0.8650 (t80) cc_final: 0.8430 (t80) REVERT: B 74 PHE cc_start: 0.8828 (m-80) cc_final: 0.8615 (m-80) REVERT: B 623 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8713 (tp) REVERT: B 693 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 745 MET cc_start: 0.9125 (tpp) cc_final: 0.8901 (tpt) REVERT: B 807 ASP cc_start: 0.8899 (m-30) cc_final: 0.8623 (m-30) REVERT: B 840 GLN cc_start: 0.8972 (tp40) cc_final: 0.8380 (tm-30) REVERT: B 868 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8729 (mtp85) REVERT: B 908 GLN cc_start: 0.9149 (tp40) cc_final: 0.8938 (tm-30) REVERT: C 79 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4893 (tp) REVERT: C 135 LYS cc_start: 0.8264 (tttm) cc_final: 0.7507 (tptp) REVERT: C 285 GLU cc_start: 0.9059 (pp20) cc_final: 0.8780 (pp20) REVERT: C 360 TRP cc_start: 0.6604 (p90) cc_final: 0.6180 (p90) REVERT: C 369 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7774 (m) REVERT: C 381 LYS cc_start: 0.8580 (mttp) cc_final: 0.8319 (mmtt) REVERT: C 390 LYS cc_start: 0.7614 (ptpt) cc_final: 0.7297 (pttt) REVERT: C 445 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8834 (mmtm) REVERT: C 595 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8113 (mt-10) REVERT: C 823 LEU cc_start: 0.7853 (mm) cc_final: 0.7147 (pp) REVERT: C 832 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8920 (mttm) REVERT: C 845 ASN cc_start: 0.8605 (m110) cc_final: 0.8277 (m110) REVERT: C 876 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8562 (tm-30) REVERT: C 908 GLN cc_start: 0.9186 (tp40) cc_final: 0.8654 (tm-30) REVERT: C 958 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8484 (ttmm) outliers start: 139 outliers final: 106 residues processed: 574 average time/residue: 0.1450 time to fit residues: 131.7188 Evaluate side-chains 574 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 463 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 856 GLN Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 266 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 230 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101919 restraints weight = 47265.794| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.89 r_work: 0.3304 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23091 Z= 0.147 Angle : 0.781 17.100 31260 Z= 0.371 Chirality : 0.052 0.524 3393 Planarity : 0.004 0.069 4020 Dihedral : 11.158 108.520 5056 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.33 % Favored : 94.46 % Rotamer: Outliers : 5.43 % Allowed : 21.24 % Favored : 73.33 % 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 are not related in a simple way. whole: -1.79 (0.15), residues: 2853 helix: 0.66 (0.20), residues: 660 sheet: -0.67 (0.21), residues: 591 loop : -2.31 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 72 TYR 0.034 0.002 TYR A 96 PHE 0.045 0.002 PHE C 219 TRP 0.019 0.002 TRP A 419 HIS 0.003 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00312 (22977) covalent geometry : angle 0.70550 (30939) SS BOND : bond 0.00380 ( 21) SS BOND : angle 1.12673 ( 42) hydrogen bonds : bond 0.04464 ( 823) hydrogen bonds : angle 5.62212 ( 2415) link_ALPHA1-2 : bond 0.01323 ( 6) link_ALPHA1-2 : angle 3.49796 ( 18) link_ALPHA1-3 : bond 0.01082 ( 3) link_ALPHA1-3 : angle 1.46733 ( 9) link_ALPHA1-6 : bond 0.00531 ( 3) link_ALPHA1-6 : angle 3.21974 ( 9) link_BETA1-4 : bond 0.00471 ( 21) link_BETA1-4 : angle 1.94696 ( 63) link_NAG-ASN : bond 0.00666 ( 60) link_NAG-ASN : angle 4.12128 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 502 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 PHE cc_start: 0.8946 (p90) cc_final: 0.8539 (p90) REVERT: A 439 MET cc_start: 0.7842 (tpp) cc_final: 0.7537 (mmp) REVERT: A 519 PHE cc_start: 0.8563 (t80) cc_final: 0.8253 (t80) REVERT: A 623 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 631 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8555 (tttm) REVERT: A 714 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8910 (mtmm) REVERT: A 747 MET cc_start: 0.8912 (mtm) cc_final: 0.8655 (mtp) REVERT: A 789 GLU cc_start: 0.8731 (pp20) cc_final: 0.8194 (pp20) REVERT: A 840 GLN cc_start: 0.8753 (tp40) cc_final: 0.8540 (tp40) REVERT: A 845 ASN cc_start: 0.8653 (m110) cc_final: 0.8244 (m-40) REVERT: A 856 GLN cc_start: 0.9210 (tp40) cc_final: 0.8593 (mm110) REVERT: A 867 ASP cc_start: 0.8673 (m-30) cc_final: 0.8419 (m-30) REVERT: A 880 ARG cc_start: 0.8706 (ptp-170) cc_final: 0.8332 (ptm160) REVERT: A 908 GLN cc_start: 0.9061 (tp40) cc_final: 0.8846 (tm-30) REVERT: A 911 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8866 (tp-100) REVERT: A 958 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8667 (ptmm) REVERT: A 985 LYS cc_start: 0.9163 (tttt) cc_final: 0.8950 (tttm) REVERT: A 986 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8473 (tm-30) REVERT: A 998 PHE cc_start: 0.8704 (t80) cc_final: 0.8374 (t80) REVERT: B 74 PHE cc_start: 0.8744 (m-80) cc_final: 0.8535 (m-80) REVERT: B 807 ASP cc_start: 0.8873 (m-30) cc_final: 0.8579 (m-30) REVERT: B 840 GLN cc_start: 0.9045 (tp40) cc_final: 0.8808 (tp-100) REVERT: B 868 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8680 (mtp85) REVERT: B 911 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8800 (tp-100) REVERT: C 79 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5343 (tp) REVERT: C 143 PHE cc_start: 0.8288 (m-80) cc_final: 0.7851 (t80) REVERT: C 228 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6320 (p0) REVERT: C 285 GLU cc_start: 0.9065 (pp20) cc_final: 0.8788 (pp20) REVERT: C 365 ASN cc_start: 0.8825 (m-40) cc_final: 0.8568 (t0) REVERT: C 369 CYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7669 (m) REVERT: C 381 LYS cc_start: 0.8585 (mttp) cc_final: 0.8357 (mmtt) REVERT: C 390 LYS cc_start: 0.7585 (ptpt) cc_final: 0.7278 (pttt) REVERT: C 445 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8821 (mmtm) REVERT: C 595 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8111 (mt-10) REVERT: C 774 GLN cc_start: 0.9039 (tp40) cc_final: 0.8680 (tp40) REVERT: C 823 LEU cc_start: 0.7694 (mm) cc_final: 0.7165 (pp) REVERT: C 832 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8908 (mttm) REVERT: C 845 ASN cc_start: 0.8588 (m110) cc_final: 0.8258 (m110) REVERT: C 876 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8541 (tm-30) REVERT: C 902 GLU cc_start: 0.8877 (pp20) cc_final: 0.8189 (tm-30) REVERT: C 908 GLN cc_start: 0.9124 (tp40) cc_final: 0.8618 (tm-30) REVERT: C 958 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8399 (tttp) outliers start: 118 outliers final: 95 residues processed: 577 average time/residue: 0.1404 time to fit residues: 128.9660 Evaluate side-chains 579 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 477 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 5 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 226 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.0670 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 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 = 0.3737 r_free = 0.3737 target = 0.124412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104712 restraints weight = 47271.348| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.91 r_work: 0.3353 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23091 Z= 0.123 Angle : 0.755 16.901 31260 Z= 0.356 Chirality : 0.051 0.502 3393 Planarity : 0.004 0.070 4020 Dihedral : 10.503 107.535 5052 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.78 % Favored : 94.01 % Rotamer: Outliers : 5.20 % Allowed : 22.30 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 2853 helix: 0.97 (0.21), residues: 642 sheet: -0.79 (0.21), residues: 591 loop : -2.23 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 261 TYR 0.030 0.001 TYR A 96 PHE 0.037 0.001 PHE C 219 TRP 0.017 0.002 TRP A 83 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00256 (22977) covalent geometry : angle 0.68645 (30939) SS BOND : bond 0.00280 ( 21) SS BOND : angle 0.97119 ( 42) hydrogen bonds : bond 0.03750 ( 823) hydrogen bonds : angle 5.20500 ( 2415) link_ALPHA1-2 : bond 0.01530 ( 6) link_ALPHA1-2 : angle 3.10525 ( 18) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 1.34934 ( 9) link_ALPHA1-6 : bond 0.00794 ( 3) link_ALPHA1-6 : angle 3.29817 ( 9) link_BETA1-4 : bond 0.00487 ( 21) link_BETA1-4 : angle 1.75818 ( 63) link_NAG-ASN : bond 0.00708 ( 60) link_NAG-ASN : angle 3.89714 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 513 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6833 (p90) cc_final: 0.6184 (p90) REVERT: A 371 PHE cc_start: 0.8919 (p90) cc_final: 0.8517 (p90) REVERT: A 439 MET cc_start: 0.7685 (tpp) cc_final: 0.7342 (mmp) REVERT: A 519 PHE cc_start: 0.8493 (t80) cc_final: 0.7910 (t80) REVERT: A 623 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8835 (tt) REVERT: A 631 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8384 (tttp) REVERT: A 714 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8901 (mtmm) REVERT: A 747 MET cc_start: 0.8897 (mtm) cc_final: 0.8630 (mtp) REVERT: A 840 GLN cc_start: 0.8686 (tp40) cc_final: 0.8466 (tp40) REVERT: A 845 ASN cc_start: 0.8622 (m110) cc_final: 0.8149 (m-40) REVERT: A 856 GLN cc_start: 0.9206 (tp40) cc_final: 0.8637 (mm110) REVERT: A 867 ASP cc_start: 0.8650 (m-30) cc_final: 0.8404 (m-30) REVERT: A 880 ARG cc_start: 0.8611 (ptp-170) cc_final: 0.8281 (ptm160) REVERT: A 985 LYS cc_start: 0.9122 (tttt) cc_final: 0.8890 (tttm) REVERT: A 986 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 74 PHE cc_start: 0.8669 (m-80) cc_final: 0.8438 (m-80) REVERT: B 365 ASN cc_start: 0.8207 (m-40) cc_final: 0.7988 (m-40) REVERT: B 514 MET cc_start: 0.8849 (mmt) cc_final: 0.8586 (mmm) REVERT: B 530 LEU cc_start: 0.8682 (tt) cc_final: 0.8372 (tp) REVERT: B 807 ASP cc_start: 0.8912 (m-30) cc_final: 0.8589 (m-30) REVERT: B 868 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8677 (mtp85) REVERT: B 911 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8722 (tp-100) REVERT: C 79 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5125 (tp) REVERT: C 228 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6099 (p0) REVERT: C 285 GLU cc_start: 0.9046 (pp20) cc_final: 0.8781 (pp20) REVERT: C 365 ASN cc_start: 0.8769 (m-40) cc_final: 0.8533 (t0) REVERT: C 369 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7524 (m) REVERT: C 390 LYS cc_start: 0.7580 (ptpt) cc_final: 0.7284 (pttt) REVERT: C 445 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8742 (mmtm) REVERT: C 446 CYS cc_start: 0.9149 (m) cc_final: 0.8889 (m) REVERT: C 571 TYR cc_start: 0.8511 (p90) cc_final: 0.8153 (p90) REVERT: C 595 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 774 GLN cc_start: 0.9096 (tp40) cc_final: 0.8852 (tp40) REVERT: C 823 LEU cc_start: 0.7687 (mm) cc_final: 0.7302 (pp) REVERT: C 832 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8740 (mttm) REVERT: C 845 ASN cc_start: 0.8571 (m110) cc_final: 0.8178 (m110) REVERT: C 876 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 908 GLN cc_start: 0.9122 (tp40) cc_final: 0.8783 (tm-30) outliers start: 113 outliers final: 87 residues processed: 584 average time/residue: 0.1400 time to fit residues: 129.7942 Evaluate side-chains 581 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 489 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 130 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 212 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 508 GLN A 978 GLN B 297 HIS B 565 GLN B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 GLN B 911 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C1027 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098112 restraints weight = 47812.881| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.83 r_work: 0.3244 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23091 Z= 0.269 Angle : 0.867 15.913 31260 Z= 0.420 Chirality : 0.056 0.758 3393 Planarity : 0.005 0.071 4020 Dihedral : 10.869 105.308 5046 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 5.61 % Allowed : 22.48 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.15), residues: 2853 helix: 0.77 (0.21), residues: 642 sheet: -0.67 (0.21), residues: 537 loop : -2.30 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 72 TYR 0.035 0.002 TYR C 96 PHE 0.043 0.002 PHE B 219 TRP 0.014 0.002 TRP B 83 HIS 0.006 0.002 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00594 (22977) covalent geometry : angle 0.80523 (30939) SS BOND : bond 0.00759 ( 21) SS BOND : angle 1.54669 ( 42) hydrogen bonds : bond 0.05249 ( 823) hydrogen bonds : angle 5.85427 ( 2415) link_ALPHA1-2 : bond 0.01194 ( 6) link_ALPHA1-2 : angle 3.47131 ( 18) link_ALPHA1-3 : bond 0.00883 ( 3) link_ALPHA1-3 : angle 1.53007 ( 9) link_ALPHA1-6 : bond 0.00482 ( 3) link_ALPHA1-6 : angle 3.28272 ( 9) link_BETA1-4 : bond 0.00381 ( 21) link_BETA1-4 : angle 1.91225 ( 63) link_NAG-ASN : bond 0.00699 ( 60) link_NAG-ASN : angle 3.91160 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 470 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5196 (tp) REVERT: A 371 PHE cc_start: 0.8953 (p90) cc_final: 0.8562 (p90) REVERT: A 410 TYR cc_start: 0.7483 (t80) cc_final: 0.7202 (t80) REVERT: A 439 MET cc_start: 0.7723 (tpp) cc_final: 0.7125 (mmt) REVERT: A 519 PHE cc_start: 0.8431 (t80) cc_final: 0.8058 (t80) REVERT: A 635 ASP cc_start: 0.8739 (t0) cc_final: 0.8464 (t0) REVERT: A 714 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8962 (mtmm) REVERT: A 724 LEU cc_start: 0.8975 (mt) cc_final: 0.8766 (tp) REVERT: A 747 MET cc_start: 0.8970 (mtm) cc_final: 0.8742 (mtm) REVERT: A 840 GLN cc_start: 0.8822 (tp40) cc_final: 0.8605 (tp40) REVERT: A 856 GLN cc_start: 0.9236 (tp40) cc_final: 0.8629 (mm110) REVERT: A 869 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7917 (mm) REVERT: A 880 ARG cc_start: 0.8817 (ptp-170) cc_final: 0.8455 (ptm160) REVERT: A 986 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 74 PHE cc_start: 0.8860 (m-80) cc_final: 0.8650 (m-80) REVERT: B 514 MET cc_start: 0.8893 (mmt) cc_final: 0.8630 (mmm) REVERT: B 807 ASP cc_start: 0.8859 (m-30) cc_final: 0.8598 (m-30) REVERT: B 868 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8742 (mtp85) REVERT: C 79 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5429 (tp) REVERT: C 228 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6327 (p0) REVERT: C 285 GLU cc_start: 0.8972 (pp20) cc_final: 0.8716 (pp20) REVERT: C 360 TRP cc_start: 0.6565 (p90) cc_final: 0.6142 (p90) REVERT: C 365 ASN cc_start: 0.8912 (m-40) cc_final: 0.8675 (t0) REVERT: C 369 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7827 (m) REVERT: C 390 LYS cc_start: 0.7642 (ptpt) cc_final: 0.7346 (pttt) REVERT: C 595 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 845 ASN cc_start: 0.8683 (m110) cc_final: 0.8356 (m110) REVERT: C 876 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 908 GLN cc_start: 0.9118 (tp40) cc_final: 0.8618 (tm-30) REVERT: C 958 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (ttmm) outliers start: 122 outliers final: 98 residues processed: 544 average time/residue: 0.1402 time to fit residues: 122.8088 Evaluate side-chains 562 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 458 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 731 ASN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 728 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102176 restraints weight = 47254.384| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.86 r_work: 0.3311 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23091 Z= 0.138 Angle : 0.783 16.065 31260 Z= 0.375 Chirality : 0.052 0.567 3393 Planarity : 0.004 0.073 4020 Dihedral : 10.467 104.448 5042 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.85 % Favored : 93.94 % Rotamer: Outliers : 4.41 % Allowed : 23.91 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 2853 helix: 0.93 (0.21), residues: 657 sheet: -0.77 (0.21), residues: 576 loop : -2.25 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 261 TYR 0.036 0.001 TYR A 96 PHE 0.040 0.002 PHE B 219 TRP 0.071 0.003 TRP A 360 HIS 0.019 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00297 (22977) covalent geometry : angle 0.72007 (30939) SS BOND : bond 0.00373 ( 21) SS BOND : angle 1.06649 ( 42) hydrogen bonds : bond 0.04191 ( 823) hydrogen bonds : angle 5.39089 ( 2415) link_ALPHA1-2 : bond 0.01592 ( 6) link_ALPHA1-2 : angle 3.18918 ( 18) link_ALPHA1-3 : bond 0.01000 ( 3) link_ALPHA1-3 : angle 1.22405 ( 9) link_ALPHA1-6 : bond 0.00773 ( 3) link_ALPHA1-6 : angle 3.37713 ( 9) link_BETA1-4 : bond 0.00448 ( 21) link_BETA1-4 : angle 1.70819 ( 63) link_NAG-ASN : bond 0.00649 ( 60) link_NAG-ASN : angle 3.79378 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 487 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.5888 (pt) cc_final: 0.5207 (tp) REVERT: A 439 MET cc_start: 0.7717 (tpp) cc_final: 0.7361 (mmp) REVERT: A 623 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8889 (tt) REVERT: A 635 ASP cc_start: 0.8706 (t0) cc_final: 0.8406 (t0) REVERT: A 714 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8878 (mtmm) REVERT: A 747 MET cc_start: 0.8932 (mtm) cc_final: 0.8626 (mtm) REVERT: A 789 GLU cc_start: 0.8569 (pp20) cc_final: 0.8128 (pp20) REVERT: A 840 GLN cc_start: 0.8683 (tp40) cc_final: 0.8481 (tp40) REVERT: A 845 ASN cc_start: 0.9044 (t0) cc_final: 0.8733 (m-40) REVERT: A 856 GLN cc_start: 0.9184 (tp40) cc_final: 0.8646 (mm110) REVERT: A 880 ARG cc_start: 0.8705 (ptp-170) cc_final: 0.8309 (ptm160) REVERT: A 911 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8839 (tp-100) REVERT: A 986 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 74 PHE cc_start: 0.8750 (m-80) cc_final: 0.8546 (m-80) REVERT: B 285 GLU cc_start: 0.9283 (pp20) cc_final: 0.8940 (pp20) REVERT: B 807 ASP cc_start: 0.8855 (m-30) cc_final: 0.8578 (m-30) REVERT: B 868 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8719 (mtp85) REVERT: B 911 GLN cc_start: 0.9132 (tp40) cc_final: 0.8824 (tp-100) REVERT: C 79 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5249 (tp) REVERT: C 138 TYR cc_start: 0.6698 (p90) cc_final: 0.5657 (p90) REVERT: C 213 ASN cc_start: 0.8959 (m-40) cc_final: 0.8587 (m-40) REVERT: C 228 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6290 (p0) REVERT: C 285 GLU cc_start: 0.8983 (pp20) cc_final: 0.8747 (pp20) REVERT: C 369 CYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7614 (m) REVERT: C 390 LYS cc_start: 0.7631 (ptpt) cc_final: 0.7342 (pttt) REVERT: C 595 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8018 (mt-10) REVERT: C 774 GLN cc_start: 0.9123 (tp40) cc_final: 0.8857 (tp40) REVERT: C 845 ASN cc_start: 0.8552 (m110) cc_final: 0.8220 (m110) REVERT: C 876 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8457 (tm-30) REVERT: C 908 GLN cc_start: 0.9075 (tp40) cc_final: 0.8733 (tm-30) outliers start: 96 outliers final: 87 residues processed: 545 average time/residue: 0.1413 time to fit residues: 123.1701 Evaluate side-chains 556 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 465 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 196 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 200 optimal weight: 0.0870 chunk 190 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 4 optimal weight: 0.0870 chunk 168 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102694 restraints weight = 47321.418| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.88 r_work: 0.3321 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23091 Z= 0.137 Angle : 0.780 18.523 31260 Z= 0.373 Chirality : 0.051 0.553 3393 Planarity : 0.004 0.074 4020 Dihedral : 10.221 104.859 5042 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.24 % Favored : 93.55 % Rotamer: Outliers : 4.37 % Allowed : 23.95 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 2853 helix: 0.93 (0.21), residues: 657 sheet: -0.81 (0.21), residues: 585 loop : -2.21 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 261 TYR 0.032 0.001 TYR A 96 PHE 0.041 0.002 PHE C 219 TRP 0.057 0.002 TRP A 360 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00297 (22977) covalent geometry : angle 0.72054 (30939) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.04734 ( 42) hydrogen bonds : bond 0.04013 ( 823) hydrogen bonds : angle 5.29012 ( 2415) link_ALPHA1-2 : bond 0.01631 ( 6) link_ALPHA1-2 : angle 3.16131 ( 18) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 1.22451 ( 9) link_ALPHA1-6 : bond 0.00600 ( 3) link_ALPHA1-6 : angle 3.16345 ( 9) link_BETA1-4 : bond 0.00444 ( 21) link_BETA1-4 : angle 1.68336 ( 63) link_NAG-ASN : bond 0.00629 ( 60) link_NAG-ASN : angle 3.69983 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 483 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.5875 (pt) cc_final: 0.5193 (tp) REVERT: A 192 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8418 (mt-10) REVERT: A 219 PHE cc_start: 0.8478 (t80) cc_final: 0.8251 (t80) REVERT: A 410 TYR cc_start: 0.7108 (t80) cc_final: 0.6871 (t80) REVERT: A 439 MET cc_start: 0.7711 (tpp) cc_final: 0.7361 (mmp) REVERT: A 519 PHE cc_start: 0.8254 (t80) cc_final: 0.7994 (t80) REVERT: A 623 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 635 ASP cc_start: 0.8696 (t0) cc_final: 0.8395 (t0) REVERT: A 650 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 714 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8876 (mtmm) REVERT: A 789 GLU cc_start: 0.8537 (pp20) cc_final: 0.8083 (pp20) REVERT: A 840 GLN cc_start: 0.8649 (tp40) cc_final: 0.8440 (tp40) REVERT: A 856 GLN cc_start: 0.9170 (tp40) cc_final: 0.8757 (mm-40) REVERT: A 869 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7447 (mm) REVERT: A 880 ARG cc_start: 0.8673 (ptp-170) cc_final: 0.8321 (ptm160) REVERT: A 986 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8334 (tm-30) REVERT: B 74 PHE cc_start: 0.8723 (m-80) cc_final: 0.8519 (m-80) REVERT: B 285 GLU cc_start: 0.9272 (pp20) cc_final: 0.8936 (pp20) REVERT: B 365 ASN cc_start: 0.8191 (m-40) cc_final: 0.7978 (m-40) REVERT: B 514 MET cc_start: 0.8831 (mmm) cc_final: 0.8334 (mmm) REVERT: B 807 ASP cc_start: 0.8853 (m-30) cc_final: 0.8574 (m-30) REVERT: B 868 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8717 (mtp85) REVERT: B 911 GLN cc_start: 0.9179 (tp40) cc_final: 0.8902 (tp-100) REVERT: C 79 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5225 (tp) REVERT: C 138 TYR cc_start: 0.6675 (p90) cc_final: 0.5631 (p90) REVERT: C 213 ASN cc_start: 0.8935 (m-40) cc_final: 0.8547 (m-40) REVERT: C 228 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6135 (p0) REVERT: C 285 GLU cc_start: 0.8999 (pp20) cc_final: 0.8755 (pp20) REVERT: C 369 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7592 (m) REVERT: C 390 LYS cc_start: 0.7626 (ptpt) cc_final: 0.7346 (pttt) REVERT: C 595 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7948 (mt-10) REVERT: C 774 GLN cc_start: 0.9158 (tp40) cc_final: 0.8878 (tp40) REVERT: C 845 ASN cc_start: 0.8519 (m110) cc_final: 0.8155 (m-40) REVERT: C 876 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 908 GLN cc_start: 0.9123 (tp40) cc_final: 0.8796 (tm-30) REVERT: C 958 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8432 (tttp) outliers start: 95 outliers final: 86 residues processed: 540 average time/residue: 0.1398 time to fit residues: 121.1018 Evaluate side-chains 566 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 474 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 121 optimal weight: 0.0000 chunk 269 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 252 optimal weight: 0.7980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN B 565 GLN B 728 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 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 = 0.3697 r_free = 0.3697 target = 0.121710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102287 restraints weight = 47352.527| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.87 r_work: 0.3314 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23091 Z= 0.148 Angle : 0.771 15.404 31260 Z= 0.371 Chirality : 0.051 0.532 3393 Planarity : 0.004 0.073 4020 Dihedral : 9.992 104.604 5042 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.48 % Favored : 93.31 % Rotamer: Outliers : 4.74 % Allowed : 23.68 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 2853 helix: 0.96 (0.21), residues: 657 sheet: -0.82 (0.21), residues: 585 loop : -2.20 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 261 TYR 0.031 0.001 TYR A 96 PHE 0.037 0.002 PHE C 219 TRP 0.055 0.002 TRP A 360 HIS 0.005 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00325 (22977) covalent geometry : angle 0.71304 (30939) SS BOND : bond 0.00401 ( 21) SS BOND : angle 1.08436 ( 42) hydrogen bonds : bond 0.04050 ( 823) hydrogen bonds : angle 5.27706 ( 2415) link_ALPHA1-2 : bond 0.01592 ( 6) link_ALPHA1-2 : angle 3.16091 ( 18) link_ALPHA1-3 : bond 0.00857 ( 3) link_ALPHA1-3 : angle 1.19052 ( 9) link_ALPHA1-6 : bond 0.00811 ( 3) link_ALPHA1-6 : angle 3.30718 ( 9) link_BETA1-4 : bond 0.00430 ( 21) link_BETA1-4 : angle 1.66206 ( 63) link_NAG-ASN : bond 0.00587 ( 60) link_NAG-ASN : angle 3.61599 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4750.68 seconds wall clock time: 82 minutes 11.66 seconds (4931.66 seconds total)