Starting phenix.real_space_refine on Sat Jul 4 19:00:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cyc_30496/07_2026/7cyc_30496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyc_30496/07_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_30496/07_2026/7cyc_30496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyc_30496/07_2026/7cyc_30496.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyc_30496/07_2026/7cyc_30496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyc_30496/07_2026/7cyc_30496.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cyc_30496/07_2026/7cyc_30496.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cyc_30496/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 16 Time building chain proxies: 5.27, 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.02 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: 5.23 Time building geometry restraints manager: 2.99 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 - 16.39: 11829 16.39 - 32.78: 941 32.78 - 49.16: 214 49.16 - 65.55: 52 65.55 - 81.94: 26 Dihedral angle restraints: 13062 sinusoidal: 4689 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 13059 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.250 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 13.046 76.367 7635 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/Z covalent geometry : bond 0.00770 / 0.44 (22977) covalent geometry : angle 1.21225 / 0.74 (30939) SS BOND : bond 0.01586 / 0.96 ( 21) SS BOND : angle 4.37935 / 2.82 ( 42) hydrogen bonds : bond 0.16845 / 11.28 ( 823) hydrogen bonds : angle 8.68972 / 6.14 ( 2415) link_ALPHA1-2 : bond 0.01360 / 0.67 ( 6) link_ALPHA1-2 : angle 4.67442 / 3.09 ( 18) link_ALPHA1-3 : bond 0.00255 / 0.12 ( 3) link_ALPHA1-3 : angle 1.35018 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00049 / 0.02 ( 3) link_ALPHA1-6 : angle 0.81677 / 0.43 ( 9) link_BETA1-4 : bond 0.05484 / 3.49 ( 21) link_BETA1-4 : angle 9.59908 / 6.38 ( 63) link_NAG-ASN : bond 0.04772 / 3.28 ( 60) link_NAG-ASN : angle 6.86817 / 4.95 ( 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 : 0.827 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: 0.1758 time to fit residues: 220.3408 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 : 0.808 ------------------------------------------------------------------------------- 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... 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 = 0.3801 r_free = 0.3801 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109275 restraints weight = 46597.452| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.00 r_work: 0.3398 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23091 Z= 0.173 Angle : 0.916 17.790 31260 Z= 0.428 Chirality : 0.055 0.754 3393 Planarity : 0.004 0.043 4020 Dihedral : 7.372 59.644 3241 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.21 % Favored : 95.58 % Rotamer: Outliers : 4.87 % Allowed : 14.21 % Favored : 80.92 % 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: -0.62 (0.21), residues: 603 loop : -2.13 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 261 TYR 0.038 0.002 TYR C 96 PHE 0.024 0.002 PHE C 219 TRP 0.042 0.003 TRP B 360 HIS 0.010 0.002 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (22977) covalent geometry : angle 0.81326 / 0.41 (30939) SS BOND : bond 0.00991 / 0.68 ( 21) SS BOND : angle 1.51415 / 1.00 ( 42) hydrogen bonds : bond 0.05157 / 3.44 ( 823) hydrogen bonds : angle 6.59645 / 4.66 ( 2415) link_ALPHA1-2 : bond 0.00556 / 0.30 ( 6) link_ALPHA1-2 : angle 3.79718 / 3.27 ( 18) link_ALPHA1-3 : bond 0.00074 / 0.03 ( 3) link_ALPHA1-3 : angle 1.65729 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00169 / 0.08 ( 3) link_ALPHA1-6 : angle 0.93124 / 0.49 ( 9) link_BETA1-4 : bond 0.00465 / 0.29 ( 21) link_BETA1-4 : angle 2.11679 / 1.36 ( 63) link_NAG-ASN : bond 0.00926 / 0.58 ( 60) link_NAG-ASN : angle 5.33044 / 3.87 ( 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 698 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 592 time to evaluate : 0.820 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 78 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7896 (mm) REVERT: A 138 TYR cc_start: 0.6524 (p90) cc_final: 0.5727 (p90) REVERT: A 228 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.4879 (m-30) REVERT: A 363 SER cc_start: 0.7494 (OUTLIER) cc_final: 0.7190 (p) REVERT: A 370 PRO cc_start: 0.9063 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: A 371 PHE cc_start: 0.8924 (p90) cc_final: 0.8617 (p90) REVERT: A 381 LYS cc_start: 0.8294 (mttp) cc_final: 0.7991 (mmmt) REVERT: A 439 MET cc_start: 0.7628 (tpp) cc_final: 0.7200 (mmt) REVERT: A 631 LYS cc_start: 0.8808 (tttp) cc_final: 0.8460 (tttp) REVERT: A 635 ASP cc_start: 0.8665 (t0) cc_final: 0.8433 (t0) REVERT: A 655 ASP cc_start: 0.8542 (t0) cc_final: 0.8114 (t0) REVERT: A 723 ASP cc_start: 0.7916 (t0) cc_final: 0.7703 (t0) REVERT: A 734 MET cc_start: 0.8856 (ttm) cc_final: 0.8391 (mtp) REVERT: A 782 LEU cc_start: 0.8485 (mp) cc_final: 0.8143 (tp) REVERT: A 840 GLN cc_start: 0.8987 (tp40) cc_final: 0.8746 (tp40) REVERT: A 845 ASN cc_start: 0.8450 (m110) cc_final: 0.7987 (m110) REVERT: A 856 GLN cc_start: 0.9057 (tp40) cc_final: 0.8819 (mm110) REVERT: A 908 GLN cc_start: 0.9055 (tp40) cc_final: 0.8588 (tm-30) REVERT: A 986 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8461 (tm-30) REVERT: A 1018 PHE cc_start: 0.7992 (m-10) cc_final: 0.7751 (m-80) REVERT: B 192 GLU cc_start: 0.8535 (tt0) cc_final: 0.8172 (tt0) REVERT: B 228 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5892 (p0) REVERT: B 338 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8418 (Cg_endo) REVERT: B 363 SER cc_start: 0.7068 (OUTLIER) cc_final: 0.6790 (p) REVERT: B 381 LYS cc_start: 0.8353 (mttp) cc_final: 0.8125 (mmtt) REVERT: B 514 MET cc_start: 0.8697 (mtt) cc_final: 0.8418 (mpp) REVERT: B 655 ASP cc_start: 0.8520 (t0) cc_final: 0.8157 (t0) REVERT: B 807 ASP cc_start: 0.8963 (m-30) cc_final: 0.8593 (m-30) REVERT: B 840 GLN cc_start: 0.9122 (tp40) cc_final: 0.8536 (tm-30) REVERT: B 853 GLN cc_start: 0.9362 (pp30) cc_final: 0.8672 (pp30) REVERT: B 856 GLN cc_start: 0.9174 (tp40) cc_final: 0.8908 (mm110) REVERT: B 868 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8719 (mtp85) REVERT: C 79 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.5851 (tp) REVERT: C 135 LYS cc_start: 0.7879 (tttm) cc_final: 0.7254 (tptp) REVERT: C 138 TYR cc_start: 0.5943 (p90) cc_final: 0.5562 (p90) REVERT: C 191 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.6919 (mtp-110) REVERT: C 228 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.5491 (m-30) REVERT: C 285 GLU cc_start: 0.9097 (pp20) cc_final: 0.8783 (tm-30) REVERT: C 363 SER cc_start: 0.7142 (OUTLIER) cc_final: 0.6781 (p) REVERT: C 365 ASN cc_start: 0.8599 (m-40) cc_final: 0.8390 (m-40) REVERT: C 375 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8515 (mtmm) REVERT: C 381 LYS cc_start: 0.8122 (mttp) cc_final: 0.7645 (mmtt) REVERT: C 387 PHE cc_start: 0.8267 (m-80) cc_final: 0.8007 (m-80) REVERT: C 595 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 639 ASN cc_start: 0.8779 (t0) cc_final: 0.8483 (t0) REVERT: C 774 GLN cc_start: 0.8931 (tp40) cc_final: 0.8577 (tp40) REVERT: C 845 ASN cc_start: 0.8553 (m110) cc_final: 0.8123 (m110) REVERT: C 867 ASP cc_start: 0.8686 (m-30) cc_final: 0.8401 (m-30) REVERT: C 877 GLN cc_start: 0.8556 (tt0) cc_final: 0.8314 (tt0) REVERT: C 911 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8813 (tm-30) REVERT: C 920 SER cc_start: 0.9137 (m) cc_final: 0.8743 (p) outliers start: 106 outliers final: 75 residues processed: 661 average time/residue: 0.1602 time to fit residues: 164.6385 Evaluate side-chains 617 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 534 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 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 392 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 555 VAL 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 117 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 183 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 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 392 ILE 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 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: 6.9990 chunk 280 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 403 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101826 restraints weight = 47612.078| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.92 r_work: 0.3297 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23091 Z= 0.245 Angle : 0.900 19.547 31260 Z= 0.429 Chirality : 0.053 0.551 3393 Planarity : 0.005 0.048 4020 Dihedral : 6.697 59.368 3189 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.78 % Favored : 94.01 % Rotamer: Outliers : 5.84 % Allowed : 17.89 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.21 (0.20), residues: 660 sheet: -0.74 (0.20), residues: 612 loop : -2.19 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 197 TYR 0.040 0.002 TYR B 96 PHE 0.031 0.002 PHE A 219 TRP 0.022 0.003 TRP B 360 HIS 0.006 0.002 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (22977) covalent geometry : angle 0.81184 / 0.41 (30939) SS BOND : bond 0.00541 / 0.39 ( 21) SS BOND : angle 1.95663 / 0.98 ( 42) hydrogen bonds : bond 0.05480 / 3.64 ( 823) hydrogen bonds : angle 6.24698 / 4.40 ( 2415) link_ALPHA1-2 : bond 0.00386 / 0.23 ( 6) link_ALPHA1-2 : angle 3.31001 / 2.77 ( 18) link_ALPHA1-3 : bond 0.00329 / 0.15 ( 3) link_ALPHA1-3 : angle 1.32628 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00136 / 0.06 ( 3) link_ALPHA1-6 : angle 1.27562 / 0.67 ( 9) link_BETA1-4 : bond 0.00495 / 0.31 ( 21) link_BETA1-4 : angle 2.03118 / 1.37 ( 63) link_NAG-ASN : bond 0.00767 / 0.45 ( 60) link_NAG-ASN : angle 4.87995 / 3.61 ( 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 642 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 515 time to evaluate : 0.865 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 138 TYR cc_start: 0.6778 (p90) cc_final: 0.5996 (p90) REVERT: A 213 ASN cc_start: 0.9012 (m110) cc_final: 0.8579 (m-40) REVERT: A 228 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5857 (p0) REVERT: A 371 PHE cc_start: 0.8911 (p90) cc_final: 0.8610 (p90) REVERT: A 375 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8595 (mmmm) REVERT: A 381 LYS cc_start: 0.8568 (mttp) cc_final: 0.8211 (mmtt) REVERT: A 439 MET cc_start: 0.7808 (tpp) cc_final: 0.7332 (mmt) REVERT: A 519 PHE cc_start: 0.8603 (t80) cc_final: 0.8369 (t80) REVERT: A 635 ASP cc_start: 0.8839 (t0) cc_final: 0.8636 (t0) REVERT: A 714 LYS cc_start: 0.9302 (mtpp) cc_final: 0.8972 (mtmm) REVERT: A 723 ASP cc_start: 0.8367 (t0) cc_final: 0.8159 (t0) REVERT: A 789 GLU cc_start: 0.8682 (pp20) cc_final: 0.8156 (pp20) REVERT: A 840 GLN cc_start: 0.8841 (tp40) cc_final: 0.8577 (tp40) REVERT: A 845 ASN cc_start: 0.8498 (m110) cc_final: 0.8055 (m-40) REVERT: A 856 GLN cc_start: 0.9204 (tp40) cc_final: 0.8988 (mm110) REVERT: A 908 GLN cc_start: 0.9118 (tp40) cc_final: 0.8714 (tm-30) REVERT: A 911 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9015 (tp-100) REVERT: A 985 LYS cc_start: 0.9211 (tttt) cc_final: 0.8951 (tttm) REVERT: A 986 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 213 ASN cc_start: 0.9164 (OUTLIER) cc_final: 0.8567 (m-40) REVERT: B 338 PRO cc_start: 0.8746 (Cg_exo) cc_final: 0.8320 (Cg_endo) REVERT: B 363 SER cc_start: 0.7522 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 381 LYS cc_start: 0.8523 (mttp) cc_final: 0.8250 (mmtt) REVERT: B 514 MET cc_start: 0.9096 (mtt) cc_final: 0.8878 (mpp) REVERT: B 693 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 723 ASP cc_start: 0.8457 (t0) cc_final: 0.8250 (p0) REVERT: B 807 ASP cc_start: 0.8930 (m-30) cc_final: 0.8593 (m-30) REVERT: B 840 GLN cc_start: 0.9029 (tp40) cc_final: 0.8450 (tm-30) REVERT: B 856 GLN cc_start: 0.9266 (tp40) cc_final: 0.9053 (mm110) REVERT: B 866 TYR cc_start: 0.9049 (m-10) cc_final: 0.8742 (m-80) REVERT: B 868 ARG cc_start: 0.9058 (mmm-85) cc_final: 0.8779 (mtp85) REVERT: B 908 GLN cc_start: 0.9168 (tp40) cc_final: 0.8914 (tm-30) REVERT: B 912 GLN cc_start: 0.9192 (tt0) cc_final: 0.8968 (tt0) REVERT: C 79 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4895 (tp) REVERT: C 135 LYS cc_start: 0.8250 (tttm) cc_final: 0.7429 (tptp) REVERT: C 191 ARG cc_start: 0.8205 (mtp-110) cc_final: 0.7087 (mtp-110) REVERT: C 285 GLU cc_start: 0.9060 (pp20) cc_final: 0.8780 (tm-30) REVERT: C 369 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7780 (m) REVERT: C 370 PRO cc_start: 0.9301 (Cg_exo) cc_final: 0.9100 (Cg_endo) REVERT: C 381 LYS cc_start: 0.8371 (mttp) cc_final: 0.7994 (mmtt) REVERT: C 595 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7963 (mt-10) REVERT: C 774 GLN cc_start: 0.9093 (tp40) cc_final: 0.8565 (tp40) REVERT: C 845 ASN cc_start: 0.8643 (m110) cc_final: 0.8250 (m110) REVERT: C 876 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 958 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8479 (ttmm) outliers start: 127 outliers final: 96 residues processed: 597 average time/residue: 0.1556 time to fit residues: 146.4784 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 : 0.877 ------------------------------------------------------------------------------- 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 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 88 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 142 VAL 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 630 CYS 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 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 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 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 700 LEU 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: 10.0000 chunk 218 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103639 restraints weight = 47106.938| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.94 r_work: 0.3324 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3696 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= 0.152 Angle : 0.794 18.086 31260 Z= 0.376 Chirality : 0.050 0.493 3393 Planarity : 0.004 0.050 4020 Dihedral : 6.180 58.562 3169 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % Rotamer: Outliers : 5.20 % Allowed : 20.09 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.73 (0.15), residues: 2853 helix: 0.59 (0.20), residues: 657 sheet: -0.69 (0.20), residues: 612 loop : -2.19 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.035 0.002 TYR B 96 PHE 0.047 0.002 PHE A 219 TRP 0.016 0.002 TRP B 360 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (22977) covalent geometry : angle 0.71388 / 0.36 (30939) SS BOND : bond 0.00443 / 0.33 ( 21) SS BOND : angle 1.69182 / 0.87 ( 42) hydrogen bonds : bond 0.04586 / 3.06 ( 823) hydrogen bonds : angle 5.77965 / 4.07 ( 2415) link_ALPHA1-2 : bond 0.00453 / 0.26 ( 6) link_ALPHA1-2 : angle 2.81143 / 2.26 ( 18) link_ALPHA1-3 : bond 0.00342 / 0.16 ( 3) link_ALPHA1-3 : angle 1.12252 / 0.60 ( 9) link_ALPHA1-6 : bond 0.00255 / 0.12 ( 3) link_ALPHA1-6 : angle 1.26991 / 0.67 ( 9) link_BETA1-4 : bond 0.00469 / 0.29 ( 21) link_BETA1-4 : angle 1.73547 / 1.18 ( 63) link_NAG-ASN : bond 0.00693 / 0.41 ( 60) link_NAG-ASN : angle 4.39185 / 3.18 ( 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 635 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 522 time to evaluate : 0.894 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: 0.6709 (p90) cc_final: 0.5991 (p90) REVERT: A 228 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.5835 (p0) REVERT: A 371 PHE cc_start: 0.8968 (p90) cc_final: 0.8620 (p90) REVERT: A 375 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8618 (mmmm) REVERT: A 381 LYS cc_start: 0.8542 (mttp) cc_final: 0.8063 (mmtt) REVERT: A 439 MET cc_start: 0.7772 (tpp) cc_final: 0.7478 (mmp) REVERT: A 519 PHE cc_start: 0.8568 (t80) cc_final: 0.8233 (t80) REVERT: A 634 GLU cc_start: 0.7950 (pt0) cc_final: 0.7721 (mt-10) REVERT: A 635 ASP cc_start: 0.8803 (t0) cc_final: 0.8508 (t0) REVERT: A 644 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8834 (tm-30) REVERT: A 714 LYS cc_start: 0.9277 (mtpp) cc_final: 0.9057 (mtmm) REVERT: A 789 GLU cc_start: 0.8663 (pp20) cc_final: 0.8110 (pp20) REVERT: A 840 GLN cc_start: 0.8808 (tp40) cc_final: 0.8567 (tp40) REVERT: A 845 ASN cc_start: 0.8673 (m110) cc_final: 0.8209 (m-40) REVERT: A 880 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8388 (ptm160) REVERT: A 908 GLN cc_start: 0.9090 (tp40) cc_final: 0.8784 (tm-30) REVERT: A 911 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8804 (tp-100) REVERT: A 986 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 333 ASN cc_start: 0.7528 (t0) cc_final: 0.7230 (t0) REVERT: B 514 MET cc_start: 0.9093 (mtt) cc_final: 0.8769 (mpp) REVERT: B 723 ASP cc_start: 0.8457 (t0) cc_final: 0.8234 (p0) REVERT: B 736 LEU cc_start: 0.9352 (mt) cc_final: 0.9098 (mt) REVERT: B 807 ASP cc_start: 0.8922 (m-30) cc_final: 0.8580 (m-30) REVERT: B 840 GLN cc_start: 0.9068 (tp40) cc_final: 0.8826 (tp-100) REVERT: B 866 TYR cc_start: 0.9046 (m-10) cc_final: 0.8833 (m-80) REVERT: B 868 ARG cc_start: 0.8983 (mmm-85) cc_final: 0.8727 (mtp85) REVERT: B 908 GLN cc_start: 0.9152 (tp40) cc_final: 0.8877 (tm-30) REVERT: B 912 GLN cc_start: 0.8798 (tt0) cc_final: 0.8574 (tt0) REVERT: C 79 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5181 (tp) REVERT: C 135 LYS cc_start: 0.8213 (tttm) cc_final: 0.7403 (tptp) REVERT: C 228 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6057 (p0) REVERT: C 285 GLU cc_start: 0.9079 (pp20) cc_final: 0.8803 (pp20) REVERT: C 369 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7588 (m) REVERT: C 381 LYS cc_start: 0.8437 (mttp) cc_final: 0.8171 (mmtt) REVERT: C 390 LYS cc_start: 0.7554 (ptpt) cc_final: 0.7207 (pttt) REVERT: C 571 TYR cc_start: 0.8361 (p90) cc_final: 0.7993 (p90) REVERT: C 595 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7989 (mt-10) REVERT: C 717 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8808 (mmmt) REVERT: C 774 GLN cc_start: 0.9085 (tp40) cc_final: 0.8663 (tp40) REVERT: C 823 LEU cc_start: 0.7821 (mm) cc_final: 0.7273 (pp) REVERT: C 832 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8878 (mttm) REVERT: C 845 ASN cc_start: 0.8580 (m110) cc_final: 0.8221 (m110) REVERT: C 876 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8589 (tm-30) REVERT: C 902 GLU cc_start: 0.8887 (pp20) cc_final: 0.8190 (tm-30) REVERT: C 920 SER cc_start: 0.9243 (m) cc_final: 0.8921 (p) REVERT: C 958 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8481 (tttp) outliers start: 113 outliers final: 89 residues processed: 598 average time/residue: 0.1554 time to fit residues: 146.2694 Evaluate side-chains 585 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 491 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 573 SER Chi-restraints excluded: chain A residue 577 ILE 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 834 GLN Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 877 GLN 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 221 VAL 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 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 396 CYS Chi-restraints excluded: chain B residue 414 SER 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 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 968 VAL Chi-restraints excluded: chain C residue 65 SER 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 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 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 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 634 GLU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 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 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: 6.9990 chunk 158 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS B 75 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN C 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099105 restraints weight = 47551.725| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.82 r_work: 0.3261 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23091 Z= 0.246 Angle : 0.848 17.245 31260 Z= 0.409 Chirality : 0.052 0.525 3393 Planarity : 0.004 0.049 4020 Dihedral : 6.257 59.453 3158 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.87 % Favored : 92.92 % Rotamer: Outliers : 6.48 % Allowed : 19.77 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.82 (0.15), residues: 2853 helix: 0.50 (0.20), residues: 660 sheet: -0.54 (0.21), residues: 567 loop : -2.30 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 72 TYR 0.041 0.002 TYR A 96 PHE 0.043 0.002 PHE C 219 TRP 0.019 0.002 TRP A 419 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (22977) covalent geometry : angle 0.77633 / 0.39 (30939) SS BOND : bond 0.00653 / 0.44 ( 21) SS BOND : angle 1.69371 / 0.91 ( 42) hydrogen bonds : bond 0.05185 / 3.45 ( 823) hydrogen bonds : angle 5.96757 / 4.19 ( 2415) link_ALPHA1-2 : bond 0.00260 / 0.15 ( 6) link_ALPHA1-2 : angle 3.09660 / 2.45 ( 18) link_ALPHA1-3 : bond 0.00408 / 0.18 ( 3) link_ALPHA1-3 : angle 0.99702 / 0.54 ( 9) link_ALPHA1-6 : bond 0.00183 / 0.08 ( 3) link_ALPHA1-6 : angle 1.45811 / 0.76 ( 9) link_BETA1-4 : bond 0.00406 / 0.24 ( 21) link_BETA1-4 : angle 1.87030 / 1.28 ( 63) link_NAG-ASN : bond 0.00676 / 0.38 ( 60) link_NAG-ASN : angle 4.26168 / 3.08 ( 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 615 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 474 time to evaluate : 0.864 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: A 371 PHE cc_start: 0.8960 (p90) cc_final: 0.8581 (p90) REVERT: A 439 MET cc_start: 0.7989 (tpp) cc_final: 0.7690 (mmp) REVERT: A 623 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8931 (tt) REVERT: A 635 ASP cc_start: 0.8829 (t0) cc_final: 0.8538 (t0) REVERT: A 714 LYS cc_start: 0.9227 (mtpp) cc_final: 0.9021 (mtmm) REVERT: A 789 GLU cc_start: 0.8770 (pp20) cc_final: 0.8250 (pp20) REVERT: A 840 GLN cc_start: 0.8789 (tp40) cc_final: 0.8566 (tp40) REVERT: A 845 ASN cc_start: 0.8669 (m110) cc_final: 0.8235 (m-40) REVERT: A 880 ARG cc_start: 0.8821 (ptm160) cc_final: 0.8410 (ptm160) REVERT: A 908 GLN cc_start: 0.9096 (tp40) cc_final: 0.8844 (tm-30) REVERT: A 986 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 567 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8387 (ttt-90) REVERT: B 623 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8796 (tp) REVERT: B 807 ASP cc_start: 0.8909 (m-30) cc_final: 0.8627 (m-30) REVERT: B 840 GLN cc_start: 0.8980 (tp40) cc_final: 0.8406 (tm-30) REVERT: B 868 ARG cc_start: 0.9021 (mmm-85) cc_final: 0.8752 (mtp85) REVERT: B 908 GLN cc_start: 0.9145 (tp40) cc_final: 0.8930 (tm-30) REVERT: C 72 ARG cc_start: 0.8572 (ptt180) cc_final: 0.8281 (ptt180) REVERT: C 79 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5424 (tp) REVERT: C 125 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 135 LYS cc_start: 0.8263 (tttm) cc_final: 0.7363 (tptp) REVERT: C 285 GLU cc_start: 0.9067 (pp20) cc_final: 0.8781 (pp20) REVERT: C 360 TRP cc_start: 0.6679 (p90) cc_final: 0.6270 (p90) REVERT: C 369 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7728 (m) REVERT: C 381 LYS cc_start: 0.8592 (mttp) cc_final: 0.8313 (mmtt) REVERT: C 390 LYS cc_start: 0.7620 (ptpt) cc_final: 0.7300 (pttt) REVERT: C 595 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 823 LEU cc_start: 0.7827 (mm) cc_final: 0.7185 (pp) REVERT: C 832 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8901 (mttm) REVERT: C 845 ASN cc_start: 0.8603 (m110) cc_final: 0.8277 (m110) REVERT: C 876 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 908 GLN cc_start: 0.9170 (tp40) cc_final: 0.8644 (tm-30) REVERT: C 958 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8475 (ttmm) outliers start: 141 outliers final: 111 residues processed: 573 average time/residue: 0.1491 time to fit residues: 135.3957 Evaluate side-chains 575 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 458 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 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 571 TYR 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 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 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 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 302 ILE 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 443 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 623 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 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 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 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 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 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 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 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: 3.9990 chunk 108 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 230 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 333 ASN B 508 GLN B 728 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 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 = 0.3705 r_free = 0.3705 target = 0.122224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.102644 restraints weight = 47371.822| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.89 r_work: 0.3320 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23091 Z= 0.129 Angle : 0.758 17.187 31260 Z= 0.361 Chirality : 0.050 0.477 3393 Planarity : 0.004 0.070 4020 Dihedral : 5.753 55.644 3147 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 5.33 % Allowed : 21.38 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.92 (0.21), residues: 639 sheet: -0.68 (0.21), residues: 543 loop : -2.19 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.033 0.001 TYR A 96 PHE 0.036 0.002 PHE C 219 TRP 0.018 0.002 TRP A 419 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (22977) covalent geometry : angle 0.68850 / 0.35 (30939) SS BOND : bond 0.00627 / 0.45 ( 21) SS BOND : angle 1.12508 / 0.68 ( 42) hydrogen bonds : bond 0.04242 / 2.84 ( 823) hydrogen bonds : angle 5.47475 / 3.86 ( 2415) link_ALPHA1-2 : bond 0.00588 / 0.33 ( 6) link_ALPHA1-2 : angle 2.39752 / 1.82 ( 18) link_ALPHA1-3 : bond 0.00422 / 0.19 ( 3) link_ALPHA1-3 : angle 1.05475 / 0.56 ( 9) link_ALPHA1-6 : bond 0.00352 / 0.16 ( 3) link_ALPHA1-6 : angle 1.33846 / 0.71 ( 9) link_BETA1-4 : bond 0.00482 / 0.29 ( 21) link_BETA1-4 : angle 1.59578 / 1.10 ( 63) link_NAG-ASN : bond 0.00676 / 0.39 ( 60) link_NAG-ASN : angle 4.04917 / 2.92 ( 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 621 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 505 time to evaluate : 0.850 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: A 371 PHE cc_start: 0.8923 (p90) cc_final: 0.8528 (p90) REVERT: A 375 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8665 (mmmm) REVERT: A 439 MET cc_start: 0.7985 (tpp) cc_final: 0.7714 (mmp) REVERT: A 519 PHE cc_start: 0.8522 (t80) cc_final: 0.8023 (t80) REVERT: A 623 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 624 LYS cc_start: 0.8976 (tptp) cc_final: 0.8647 (tptp) REVERT: A 714 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8898 (mtmm) REVERT: A 789 GLU cc_start: 0.8688 (pp20) cc_final: 0.8048 (pp20) REVERT: A 840 GLN cc_start: 0.8725 (tp40) cc_final: 0.8520 (tp40) REVERT: A 845 ASN cc_start: 0.8633 (m110) cc_final: 0.8215 (m-40) REVERT: A 880 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8268 (ptm160) REVERT: A 908 GLN cc_start: 0.9047 (tp40) cc_final: 0.8846 (tm-30) REVERT: A 911 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8857 (tp-100) REVERT: A 945 LEU cc_start: 0.9124 (mp) cc_final: 0.8812 (mt) REVERT: A 986 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 530 LEU cc_start: 0.8460 (tt) cc_final: 0.8041 (tp) REVERT: B 533 PHE cc_start: 0.7705 (p90) cc_final: 0.7346 (p90) REVERT: B 623 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8708 (tp) REVERT: B 807 ASP cc_start: 0.8876 (m-30) cc_final: 0.8572 (m-30) REVERT: B 840 GLN cc_start: 0.9048 (tp40) cc_final: 0.8822 (tp-100) REVERT: B 868 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8696 (mtp85) REVERT: B 911 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8767 (tp-100) REVERT: C 79 LEU cc_start: 0.5777 (pt) cc_final: 0.5303 (tp) REVERT: C 125 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 135 LYS cc_start: 0.8177 (tttm) cc_final: 0.7436 (tptp) REVERT: C 228 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6278 (p0) REVERT: C 285 GLU cc_start: 0.9070 (pp20) cc_final: 0.8799 (pp20) REVERT: C 369 CYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7598 (m) REVERT: C 390 LYS cc_start: 0.7570 (ptpt) cc_final: 0.7267 (pttt) REVERT: C 571 TYR cc_start: 0.8511 (p90) cc_final: 0.8080 (p90) REVERT: C 595 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8089 (mt-10) REVERT: C 774 GLN cc_start: 0.9042 (tp40) cc_final: 0.8674 (tp40) REVERT: C 823 LEU cc_start: 0.7793 (mm) cc_final: 0.7334 (pp) REVERT: C 832 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8869 (mttm) REVERT: C 845 ASN cc_start: 0.8610 (m110) cc_final: 0.8280 (m110) REVERT: C 876 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8527 (tm-30) REVERT: C 902 GLU cc_start: 0.8882 (pp20) cc_final: 0.8180 (tm-30) REVERT: C 908 GLN cc_start: 0.9114 (tp40) cc_final: 0.8753 (tm-30) outliers start: 116 outliers final: 90 residues processed: 577 average time/residue: 0.1538 time to fit residues: 140.0647 Evaluate side-chains 577 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 483 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 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 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 698 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 67 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 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 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 435 VAL Chi-restraints excluded: chain B residue 451 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 714 LYS Chi-restraints excluded: chain B residue 773 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 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 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 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 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 635 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 5 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 220 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 731 ASN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** 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 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 = 0.3712 r_free = 0.3712 target = 0.122864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103302 restraints weight = 47536.050| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.90 r_work: 0.3328 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4465 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= 0.129 Angle : 0.747 16.766 31260 Z= 0.356 Chirality : 0.049 0.487 3393 Planarity : 0.004 0.070 4020 Dihedral : 5.491 58.587 3141 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.96 % Favored : 93.83 % Rotamer: Outliers : 5.15 % Allowed : 22.21 % Favored : 72.64 % 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: -1.64 (0.15), residues: 2853 helix: 0.95 (0.21), residues: 642 sheet: -0.74 (0.21), residues: 573 loop : -2.18 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 72 TYR 0.030 0.001 TYR A 96 PHE 0.033 0.001 PHE C 219 TRP 0.016 0.002 TRP A 83 HIS 0.003 0.001 HIS B 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (22977) covalent geometry : angle 0.68242 / 0.34 (30939) SS BOND : bond 0.00319 / 0.23 ( 21) SS BOND : angle 1.15869 / 0.68 ( 42) hydrogen bonds : bond 0.03994 / 2.67 ( 823) hydrogen bonds : angle 5.30086 / 3.73 ( 2415) link_ALPHA1-2 : bond 0.00508 / 0.29 ( 6) link_ALPHA1-2 : angle 2.14300 / 1.58 ( 18) link_ALPHA1-3 : bond 0.00360 / 0.16 ( 3) link_ALPHA1-3 : angle 1.13012 / 0.60 ( 9) link_ALPHA1-6 : bond 0.00381 / 0.18 ( 3) link_ALPHA1-6 : angle 1.35993 / 0.72 ( 9) link_BETA1-4 : bond 0.00427 / 0.25 ( 21) link_BETA1-4 : angle 1.54628 / 1.06 ( 63) link_NAG-ASN : bond 0.00647 / 0.37 ( 60) link_NAG-ASN : angle 3.87796 / 2.78 ( 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 624 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 512 time to evaluate : 0.891 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: 0.8897 (p90) cc_final: 0.8520 (p90) REVERT: A 375 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8650 (mmmm) REVERT: A 439 MET cc_start: 0.7860 (tpp) cc_final: 0.7549 (mmp) REVERT: A 519 PHE cc_start: 0.8407 (t80) cc_final: 0.8086 (t80) REVERT: A 635 ASP cc_start: 0.8697 (t0) cc_final: 0.8416 (t0) REVERT: A 747 MET cc_start: 0.8901 (ttm) cc_final: 0.8689 (mtp) REVERT: A 789 GLU cc_start: 0.8592 (pp20) cc_final: 0.7925 (pp20) REVERT: A 840 GLN cc_start: 0.8724 (tp40) cc_final: 0.8509 (tp40) REVERT: A 845 ASN cc_start: 0.8635 (m110) cc_final: 0.8159 (m-40) REVERT: A 880 ARG cc_start: 0.8663 (ptm160) cc_final: 0.8281 (ptm160) REVERT: A 945 LEU cc_start: 0.9135 (mp) cc_final: 0.8852 (mt) REVERT: A 986 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 390 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7554 (ttpp) REVERT: B 514 MET cc_start: 0.8850 (mmm) cc_final: 0.8499 (mmm) REVERT: B 807 ASP cc_start: 0.8877 (m-30) cc_final: 0.8571 (m-30) REVERT: B 868 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8708 (mtp85) REVERT: B 911 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8744 (tp-100) REVERT: C 79 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5171 (tp) REVERT: C 125 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 135 LYS cc_start: 0.8228 (tttm) cc_final: 0.7427 (tptp) REVERT: C 138 TYR cc_start: 0.6555 (p90) cc_final: 0.5620 (p90) REVERT: C 285 GLU cc_start: 0.9039 (pp20) cc_final: 0.8766 (pp20) REVERT: C 369 CYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7551 (m) REVERT: C 390 LYS cc_start: 0.7558 (ptpt) cc_final: 0.7266 (pttt) REVERT: C 595 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8021 (mt-10) REVERT: C 774 GLN cc_start: 0.9026 (tp40) cc_final: 0.8609 (tp40) REVERT: C 823 LEU cc_start: 0.7739 (mm) cc_final: 0.7348 (pp) REVERT: C 832 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8834 (mttm) REVERT: C 845 ASN cc_start: 0.8597 (m110) cc_final: 0.8255 (m110) REVERT: C 876 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8516 (tm-30) REVERT: C 902 GLU cc_start: 0.8896 (pp20) cc_final: 0.8228 (tm-30) REVERT: C 908 GLN cc_start: 0.9095 (tp40) cc_final: 0.8768 (tm-30) outliers start: 112 outliers final: 96 residues processed: 586 average time/residue: 0.1534 time to fit residues: 142.5338 Evaluate side-chains 589 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 491 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 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 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 573 SER Chi-restraints excluded: chain A residue 577 ILE 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 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 67 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 279 SER Chi-restraints excluded: chain B residue 302 ILE 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 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 634 GLU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 692 ILE 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 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 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 203 ILE 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 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: 4.9990 chunk 263 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 chunk 119 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 GLN 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 = 0.118654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099397 restraints weight = 47836.718| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.81 r_work: 0.3263 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23091 Z= 0.217 Angle : 0.813 15.920 31260 Z= 0.395 Chirality : 0.052 0.680 3393 Planarity : 0.004 0.070 4020 Dihedral : 5.693 59.510 3139 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.69 % Favored : 93.09 % Rotamer: Outliers : 5.61 % Allowed : 22.67 % Favored : 71.72 % 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: 0.87 (0.21), residues: 642 sheet: -0.92 (0.19), residues: 657 loop : -2.30 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.033 0.002 TYR C 96 PHE 0.046 0.002 PHE B 219 TRP 0.017 0.002 TRP B 83 HIS 0.005 0.001 HIS B 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (22977) covalent geometry : angle 0.75432 / 0.38 (30939) SS BOND : bond 0.00676 / 0.46 ( 21) SS BOND : angle 1.35543 / 0.77 ( 42) hydrogen bonds : bond 0.04846 / 3.21 ( 823) hydrogen bonds : angle 5.65348 / 3.97 ( 2415) link_ALPHA1-2 : bond 0.00365 / 0.20 ( 6) link_ALPHA1-2 : angle 2.61015 / 1.92 ( 18) link_ALPHA1-3 : bond 0.00442 / 0.20 ( 3) link_ALPHA1-3 : angle 1.01051 / 0.55 ( 9) link_ALPHA1-6 : bond 0.00283 / 0.13 ( 3) link_ALPHA1-6 : angle 1.52287 / 0.80 ( 9) link_BETA1-4 : bond 0.00393 / 0.23 ( 21) link_BETA1-4 : angle 1.70345 / 1.18 ( 63) link_NAG-ASN : bond 0.00642 / 0.37 ( 60) link_NAG-ASN : angle 3.83568 / 2.75 ( 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 593 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 471 time to evaluate : 0.848 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 79 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5214 (tp) REVERT: A 371 PHE cc_start: 0.8924 (p90) cc_final: 0.8543 (p90) REVERT: A 439 MET cc_start: 0.7805 (tpp) cc_final: 0.7450 (mmp) REVERT: A 519 PHE cc_start: 0.8458 (t80) cc_final: 0.8144 (t80) REVERT: A 635 ASP cc_start: 0.8752 (t0) cc_final: 0.8382 (t0) REVERT: A 789 GLU cc_start: 0.8707 (pp20) cc_final: 0.7995 (pp20) REVERT: A 840 GLN cc_start: 0.8786 (tp40) cc_final: 0.8572 (tp40) REVERT: A 845 ASN cc_start: 0.8652 (m110) cc_final: 0.8237 (m-40) REVERT: A 869 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7906 (mm) REVERT: A 880 ARG cc_start: 0.8764 (ptm160) cc_final: 0.8513 (ptm160) REVERT: A 957 TYR cc_start: 0.9254 (m-80) cc_final: 0.8950 (m-80) REVERT: A 986 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 439 MET cc_start: 0.7925 (tpp) cc_final: 0.7563 (mmp) REVERT: B 807 ASP cc_start: 0.8850 (m-30) cc_final: 0.8573 (m-30) REVERT: B 868 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8745 (mtp85) REVERT: B 911 GLN cc_start: 0.9173 (tp40) cc_final: 0.8758 (tp-100) REVERT: C 79 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.4914 (tp) REVERT: C 285 GLU cc_start: 0.8982 (pp20) cc_final: 0.8741 (pp20) REVERT: C 360 TRP cc_start: 0.6657 (p90) cc_final: 0.6260 (p90) REVERT: C 369 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7726 (m) REVERT: C 390 LYS cc_start: 0.7612 (ptpt) cc_final: 0.7325 (pttt) REVERT: C 595 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8028 (mt-10) REVERT: C 774 GLN cc_start: 0.9157 (tp40) cc_final: 0.8635 (tp40) REVERT: C 845 ASN cc_start: 0.8679 (m110) cc_final: 0.8363 (m110) REVERT: C 876 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 902 GLU cc_start: 0.8905 (pp20) cc_final: 0.8202 (tm-30) REVERT: C 908 GLN cc_start: 0.9078 (tp40) cc_final: 0.8723 (tm-30) REVERT: C 958 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8431 (tttp) outliers start: 122 outliers final: 98 residues processed: 549 average time/residue: 0.1507 time to fit residues: 132.1170 Evaluate side-chains 565 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 462 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 264 CYS 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 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 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 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 877 GLN 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 A residue 992 ILE Chi-restraints excluded: chain B residue 67 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 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 302 ILE 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 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 414 SER 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 634 GLU Chi-restraints excluded: chain B residue 692 ILE 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 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 = 0.3678 r_free = 0.3678 target = 0.120321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101016 restraints weight = 47621.874| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.85 r_work: 0.3291 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23091 Z= 0.159 Angle : 0.779 15.782 31260 Z= 0.378 Chirality : 0.051 0.541 3393 Planarity : 0.004 0.072 4020 Dihedral : 5.486 57.860 3133 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.13 % Favored : 93.66 % Rotamer: Outliers : 5.06 % Allowed : 23.17 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 2853 helix: 1.01 (0.21), residues: 639 sheet: -0.89 (0.21), residues: 582 loop : -2.17 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.034 0.002 TYR A 96 PHE 0.038 0.002 PHE B 219 TRP 0.016 0.002 TRP B 360 HIS 0.004 0.001 HIS B 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (22977) covalent geometry : angle 0.72187 / 0.37 (30939) SS BOND : bond 0.00407 / 0.31 ( 21) SS BOND : angle 1.23101 / 0.68 ( 42) hydrogen bonds : bond 0.04350 / 2.88 ( 823) hydrogen bonds : angle 5.42917 / 3.82 ( 2415) link_ALPHA1-2 : bond 0.00444 / 0.25 ( 6) link_ALPHA1-2 : angle 2.27665 / 1.64 ( 18) link_ALPHA1-3 : bond 0.00449 / 0.20 ( 3) link_ALPHA1-3 : angle 1.00821 / 0.54 ( 9) link_ALPHA1-6 : bond 0.00320 / 0.15 ( 3) link_ALPHA1-6 : angle 1.47768 / 0.78 ( 9) link_BETA1-4 : bond 0.00421 / 0.25 ( 21) link_BETA1-4 : angle 1.56137 / 1.09 ( 63) link_NAG-ASN : bond 0.00583 / 0.33 ( 60) link_NAG-ASN : angle 3.74730 / 2.70 ( 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 585 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 475 time to evaluate : 0.836 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: A 79 LEU cc_start: 0.5928 (pt) cc_final: 0.5167 (tp) REVERT: A 219 PHE cc_start: 0.8914 (t80) cc_final: 0.8612 (t80) REVERT: A 371 PHE cc_start: 0.8899 (p90) cc_final: 0.8493 (p90) REVERT: A 439 MET cc_start: 0.7769 (tpp) cc_final: 0.7406 (mmp) REVERT: A 635 ASP cc_start: 0.8646 (t0) cc_final: 0.8298 (t0) REVERT: A 840 GLN cc_start: 0.8762 (tp40) cc_final: 0.8558 (tp40) REVERT: A 845 ASN cc_start: 0.8671 (m110) cc_final: 0.8264 (m-40) REVERT: A 880 ARG cc_start: 0.8727 (ptm160) cc_final: 0.8458 (ptm160) REVERT: A 957 TYR cc_start: 0.9199 (m-80) cc_final: 0.8873 (m-80) REVERT: B 125 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 285 GLU cc_start: 0.9278 (pp20) cc_final: 0.8932 (pp20) REVERT: B 514 MET cc_start: 0.8877 (tpp) cc_final: 0.8390 (mmm) REVERT: B 807 ASP cc_start: 0.8835 (m-30) cc_final: 0.8567 (m-30) REVERT: B 868 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8742 (mtp85) REVERT: B 911 GLN cc_start: 0.9159 (tp40) cc_final: 0.8860 (tp-100) REVERT: C 79 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5279 (tp) REVERT: C 369 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7661 (m) REVERT: C 390 LYS cc_start: 0.7598 (ptpt) cc_final: 0.7315 (pttt) REVERT: C 595 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 774 GLN cc_start: 0.9160 (tp40) cc_final: 0.8668 (tp40) REVERT: C 845 ASN cc_start: 0.8684 (m110) cc_final: 0.8347 (m110) REVERT: C 876 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8501 (tm-30) REVERT: C 902 GLU cc_start: 0.8944 (pp20) cc_final: 0.8255 (tm-30) REVERT: C 908 GLN cc_start: 0.9064 (tp40) cc_final: 0.8732 (tm-30) REVERT: C 958 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8388 (tttp) outliers start: 110 outliers final: 99 residues processed: 546 average time/residue: 0.1502 time to fit residues: 131.1137 Evaluate side-chains 567 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 465 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 571 TYR 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 698 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 844 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 A residue 992 ILE Chi-restraints excluded: chain B residue 67 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 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 414 SER 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 565 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 634 GLU 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 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 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 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 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 196 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 162 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 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 = 0.3684 r_free = 0.3684 target = 0.120776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101446 restraints weight = 47752.482| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.86 r_work: 0.3299 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23091 Z= 0.148 Angle : 0.774 15.439 31260 Z= 0.376 Chirality : 0.050 0.519 3393 Planarity : 0.004 0.074 4020 Dihedral : 5.385 54.319 3131 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.48 % Favored : 93.31 % Rotamer: Outliers : 4.74 % Allowed : 23.59 % 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: 0.99 (0.21), residues: 642 sheet: -0.87 (0.21), residues: 582 loop : -2.18 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 72 TYR 0.033 0.001 TYR A 96 PHE 0.040 0.002 PHE C 219 TRP 0.022 0.002 TRP A 83 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (22977) covalent geometry : angle 0.71992 / 0.37 (30939) SS BOND : bond 0.00399 / 0.31 ( 21) SS BOND : angle 1.10521 / 0.66 ( 42) hydrogen bonds : bond 0.04201 / 2.80 ( 823) hydrogen bonds : angle 5.35193 / 3.77 ( 2415) link_ALPHA1-2 : bond 0.00438 / 0.25 ( 6) link_ALPHA1-2 : angle 2.13511 / 1.49 ( 18) link_ALPHA1-3 : bond 0.00468 / 0.22 ( 3) link_ALPHA1-3 : angle 1.03926 / 0.56 ( 9) link_ALPHA1-6 : bond 0.00361 / 0.17 ( 3) link_ALPHA1-6 : angle 1.44099 / 0.77 ( 9) link_BETA1-4 : bond 0.00404 / 0.24 ( 21) link_BETA1-4 : angle 1.52412 / 1.06 ( 63) link_NAG-ASN : bond 0.00572 / 0.32 ( 60) link_NAG-ASN : angle 3.65293 / 2.63 ( 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 573 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 470 time to evaluate : 0.772 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: A 79 LEU cc_start: 0.5913 (pt) cc_final: 0.5225 (tp) REVERT: A 371 PHE cc_start: 0.8880 (p90) cc_final: 0.8472 (p90) REVERT: A 439 MET cc_start: 0.7756 (tpp) cc_final: 0.7392 (mmp) REVERT: A 519 PHE cc_start: 0.8308 (t80) cc_final: 0.8047 (t80) REVERT: A 635 ASP cc_start: 0.8652 (t0) cc_final: 0.8305 (t0) REVERT: A 650 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 789 GLU cc_start: 0.8573 (pp20) cc_final: 0.8120 (pp20) REVERT: A 840 GLN cc_start: 0.8694 (tp40) cc_final: 0.8486 (tp40) REVERT: A 845 ASN cc_start: 0.8654 (m110) cc_final: 0.8229 (m-40) REVERT: A 869 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7725 (mm) REVERT: A 880 ARG cc_start: 0.8708 (ptm160) cc_final: 0.8441 (ptm160) REVERT: A 957 TYR cc_start: 0.9192 (m-80) cc_final: 0.8889 (m-80) REVERT: A 986 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 125 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 192 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 390 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7667 (ttpp) REVERT: B 514 MET cc_start: 0.8792 (tpp) cc_final: 0.8353 (mmm) REVERT: B 807 ASP cc_start: 0.8825 (m-30) cc_final: 0.8555 (m-30) REVERT: B 868 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8755 (mtp85) REVERT: B 911 GLN cc_start: 0.9151 (tp40) cc_final: 0.8862 (tp-100) REVERT: B 912 GLN cc_start: 0.8800 (tt0) cc_final: 0.8586 (tt0) REVERT: C 79 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5264 (tp) REVERT: C 138 TYR cc_start: 0.6687 (p90) cc_final: 0.5640 (p90) REVERT: C 228 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6067 (p0) REVERT: C 369 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7657 (m) REVERT: C 390 LYS cc_start: 0.7635 (ptpt) cc_final: 0.7356 (pttt) REVERT: C 595 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7967 (mt-10) REVERT: C 774 GLN cc_start: 0.9169 (tp40) cc_final: 0.8776 (tp40) REVERT: C 845 ASN cc_start: 0.8683 (m110) cc_final: 0.8351 (m110) REVERT: C 876 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 902 GLU cc_start: 0.8885 (pp20) cc_final: 0.8219 (tm-30) REVERT: C 908 GLN cc_start: 0.9089 (tp40) cc_final: 0.8773 (tm-30) REVERT: C 958 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8393 (tttp) outliers start: 103 outliers final: 96 residues processed: 537 average time/residue: 0.1376 time to fit residues: 118.6415 Evaluate side-chains 564 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 463 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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 573 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 844 LEU 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 A residue 992 ILE Chi-restraints excluded: chain B residue 67 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 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 414 SER 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 565 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 634 GLU 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 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 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 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 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: 0.8980 chunk 22 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 121 optimal weight: 0.0870 chunk 269 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 260 optimal weight: 0.0370 chunk 217 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103718 restraints weight = 47245.910| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.86 r_work: 0.3341 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23091 Z= 0.126 Angle : 0.762 18.051 31260 Z= 0.368 Chirality : 0.049 0.475 3393 Planarity : 0.004 0.074 4020 Dihedral : 5.195 55.411 3131 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.89 % Favored : 93.90 % Rotamer: Outliers : 4.28 % Allowed : 24.46 % Favored : 71.26 % 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: -1.57 (0.15), residues: 2853 helix: 1.09 (0.21), residues: 639 sheet: -0.66 (0.22), residues: 555 loop : -2.17 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 261 TYR 0.029 0.001 TYR A 96 PHE 0.044 0.001 PHE A 219 TRP 0.016 0.002 TRP B 360 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22977) covalent geometry : angle 0.71094 / 0.36 (30939) SS BOND : bond 0.00479 / 0.26 ( 21) SS BOND : angle 1.01505 / 0.63 ( 42) hydrogen bonds : bond 0.03712 / 2.49 ( 823) hydrogen bonds : angle 5.14536 / 3.62 ( 2415) link_ALPHA1-2 : bond 0.00636 / 0.36 ( 6) link_ALPHA1-2 : angle 1.76946 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00394 / 0.18 ( 3) link_ALPHA1-3 : angle 1.14285 / 0.61 ( 9) link_ALPHA1-6 : bond 0.00465 / 0.21 ( 3) link_ALPHA1-6 : angle 1.40022 / 0.74 ( 9) link_BETA1-4 : bond 0.00458 / 0.28 ( 21) link_BETA1-4 : angle 1.40156 / 0.98 ( 63) link_NAG-ASN : bond 0.00624 / 0.36 ( 60) link_NAG-ASN : angle 3.52984 / 2.53 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5036.24 seconds wall clock time: 87 minutes 25.05 seconds (5245.05 seconds total)