Starting phenix.real_space_refine on Sun Feb 18 17:10:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyc_30496/02_2024/7cyc_30496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyc_30496/02_2024/7cyc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyc_30496/02_2024/7cyc_30496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyc_30496/02_2024/7cyc_30496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyc_30496/02_2024/7cyc_30496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyc_30496/02_2024/7cyc_30496.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B GLU 916": "OE1" <-> "OE2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B GLU 1032": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 685": "NH1" <-> "NH2" Residue "C TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 916": "OE1" <-> "OE2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C GLU 1032": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22521 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7094 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 32, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 224 Chain: "B" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7094 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 32, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 224 Chain: "C" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7094 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 32, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 224 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 11.97, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 10.05 Conformation dependent library (CDL) restraints added in 3.8 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: 2.61 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: 9.10 Time building geometry restraints manager: 10.71 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: 99.85 - 106.69: 634 106.69 - 113.53: 12219 113.53 - 120.38: 8877 120.38 - 127.22: 9036 127.22 - 134.06: 173 Bond angle restraints: 30939 Sorted by residual: angle pdb=" N THR C 716 " pdb=" CA THR C 716 " pdb=" C THR C 716 " ideal model delta sigma weight residual 114.64 102.96 11.68 1.52e+00 4.33e-01 5.91e+01 angle pdb=" N THR A 716 " pdb=" CA THR A 716 " pdb=" C THR A 716 " ideal model delta sigma weight residual 114.64 103.00 11.64 1.52e+00 4.33e-01 5.86e+01 angle pdb=" N THR B 716 " pdb=" CA THR B 716 " pdb=" C THR B 716 " ideal model delta sigma weight residual 114.64 103.03 11.61 1.52e+00 4.33e-01 5.83e+01 angle pdb=" C TYR B 96 " pdb=" CA TYR B 96 " pdb=" CB TYR B 96 " ideal model delta sigma weight residual 111.76 100.56 11.20 1.47e+00 4.63e-01 5.81e+01 angle pdb=" C TYR C 96 " pdb=" CA TYR C 96 " pdb=" CB TYR C 96 " ideal model delta sigma weight residual 111.76 100.56 11.20 1.47e+00 4.63e-01 5.80e+01 ... (remaining 30934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.45: 14169 26.45 - 52.90: 558 52.90 - 79.36: 144 79.36 - 105.81: 51 105.81 - 132.26: 51 Dihedral angle restraints: 14973 sinusoidal: 6600 harmonic: 8373 Sorted by residual: dihedral pdb=" CB CYS C 917 " pdb=" SG CYS C 917 " pdb=" SG CYS C 928 " pdb=" CB CYS C 928 " ideal model delta sinusoidal sigma weight residual 93.00 174.94 -81.94 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS B 917 " pdb=" SG CYS B 917 " pdb=" SG CYS B 928 " pdb=" CB CYS B 928 " ideal model delta sinusoidal sigma weight residual 93.00 174.90 -81.90 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS A 917 " pdb=" SG CYS A 917 " pdb=" SG CYS A 928 " pdb=" CB CYS A 928 " ideal model delta sinusoidal sigma weight residual 93.00 174.90 -81.90 1 1.00e+01 1.00e-02 8.25e+01 ... (remaining 14970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3261 0.189 - 0.378: 115 0.378 - 0.567: 3 0.567 - 0.756: 5 0.756 - 0.945: 9 Chirality restraints: 3393 Sorted by residual: chirality pdb=" C1 MAN D 7 " pdb=" O2 MAN D 6 " pdb=" C2 MAN D 7 " pdb=" O5 MAN D 7 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 MAN H 7 " pdb=" O2 MAN H 6 " pdb=" C2 MAN H 7 " pdb=" O5 MAN H 7 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 MAN L 7 " pdb=" O2 MAN L 6 " pdb=" C2 MAN L 7 " pdb=" O5 MAN L 7 " both_signs ideal model delta sigma weight residual False 2.40 1.51 0.89 2.00e-02 2.50e+03 1.96e+03 ... (remaining 3390 not shown) Planarity restraints: 4080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.363 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG L 1 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.553 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.363 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG H 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.553 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.363 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG D 1 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.553 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.164 2.00e-02 2.50e+03 ... (remaining 4077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1203 2.69 - 3.24: 23321 3.24 - 3.80: 33511 3.80 - 4.35: 40182 4.35 - 4.90: 64663 Nonbonded interactions: 162880 Sorted by model distance: nonbonded pdb=" NH2 ARG A 977 " pdb=" OD1 ASP C1007 " model vdw 2.139 2.520 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 2.520 ... (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 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.980 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 60.240 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.230 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 22977 Z= 0.509 Angle : 1.212 11.682 30939 Z= 0.737 Chirality : 0.093 0.945 3393 Planarity : 0.011 0.311 4020 Dihedral : 17.846 132.261 9546 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.57 % Favored : 93.90 % Rotamer: Outliers : 5.89 % Allowed : 7.31 % Favored : 86.80 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP B 57 HIS 0.014 0.003 HIS C 299 PHE 0.035 0.003 PHE C 382 TYR 0.054 0.003 TYR C 96 ARG 0.010 0.001 ARG C 991 *********************** 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 fitting. rotamer outliers: 128 poor density : 729 time to evaluate : 2.561 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: 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: 0.8028 (m-80) REVERT: A 96 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: A 134 PHE cc_start: 0.8087 (m-80) cc_final: 0.7870 (m-10) REVERT: A 135 LYS cc_start: 0.7777 (tttm) cc_final: 0.7148 (tptp) REVERT: A 144 TYR cc_start: 0.5593 (t80) cc_final: 0.5312 (t80) REVERT: A 192 GLU cc_start: 0.7966 (tt0) cc_final: 0.7669 (tt0) REVERT: A 215 GLU cc_start: 0.6893 (tt0) cc_final: 0.6421 (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: 0.8480 (pp20) REVERT: A 310 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.6933 (Cg_exo) REVERT: A 363 SER cc_start: 0.5602 (OUTLIER) cc_final: 0.4984 (p) REVERT: A 365 ASN cc_start: 0.7890 (m-40) cc_final: 0.7610 (m-40) REVERT: A 370 PRO cc_start: 0.8934 (Cg_exo) cc_final: 0.8442 (Cg_endo) REVERT: A 381 LYS cc_start: 0.7637 (mttp) cc_final: 0.7290 (mmtm) REVERT: A 408 LYS cc_start: 0.7130 (mppt) cc_final: 0.6440 (mttt) REVERT: A 439 MET cc_start: 0.7783 (tpp) cc_final: 0.7470 (mmp) REVERT: A 530 LEU cc_start: 0.7827 (tp) cc_final: 0.7312 (tt) REVERT: A 565 GLN cc_start: 0.8679 (mt0) cc_final: 0.8385 (tm-30) REVERT: A 693 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 741 ASP cc_start: 0.7754 (p0) cc_final: 0.7287 (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: 0.7506 (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: 0.8300 (tm-30) REVERT: B 56 ASN cc_start: 0.8029 (m-40) cc_final: 0.7365 (m110) REVERT: B 74 PHE cc_start: 0.8563 (m-80) cc_final: 0.8249 (m-80) REVERT: B 135 LYS cc_start: 0.7681 (tttm) cc_final: 0.7299 (tptp) REVERT: B 192 GLU cc_start: 0.7655 (tt0) cc_final: 0.7386 (tt0) REVERT: B 219 PHE cc_start: 0.8626 (t80) cc_final: 0.8390 (t80) REVERT: B 246 GLN cc_start: 0.8338 (mt0) cc_final: 0.7915 (mm-40) REVERT: B 310 PRO cc_start: 0.7300 (Cg_endo) cc_final: 0.6837 (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: 0.4856 (p) REVERT: B 371 PHE cc_start: 0.8758 (p90) cc_final: 0.8076 (p90) REVERT: B 375 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7508 (mtpp) REVERT: B 381 LYS cc_start: 0.7863 (mttp) cc_final: 0.7658 (mmtt) REVERT: B 415 LEU cc_start: 0.7781 (mm) cc_final: 0.7454 (tp) REVERT: B 439 MET cc_start: 0.8213 (tpp) cc_final: 0.7928 (mmp) REVERT: B 514 MET cc_start: 0.8251 (mtt) cc_final: 0.7826 (mpp) REVERT: B 530 LEU cc_start: 0.8048 (tp) cc_final: 0.7562 (tt) REVERT: B 586 SER cc_start: 0.4480 (OUTLIER) cc_final: 0.4267 (t) REVERT: B 622 LEU cc_start: 0.9132 (mp) cc_final: 0.8811 (mt) REVERT: B 635 ASP cc_start: 0.8705 (t0) cc_final: 0.8412 (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: 0.7148 (p0) REVERT: B 724 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8066 (tp) REVERT: B 798 PHE cc_start: 0.9148 (t80) cc_final: 0.8576 (t80) REVERT: B 807 ASP cc_start: 0.8893 (m-30) cc_final: 0.8596 (m-30) REVERT: B 840 GLN cc_start: 0.9381 (tp40) cc_final: 0.9023 (tm-30) REVERT: B 853 GLN cc_start: 0.9153 (pp30) cc_final: 0.8462 (pp30) REVERT: B 868 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8433 (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: 0.7467 (tm-30) REVERT: B 980 ASN cc_start: 0.8693 (m110) cc_final: 0.8164 (m-40) REVERT: B 985 LYS cc_start: 0.8997 (tttt) cc_final: 0.8700 (tttm) REVERT: C 74 PHE cc_start: 0.8792 (m-80) cc_final: 0.8532 (m-80) REVERT: C 79 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.5687 (tp) REVERT: C 88 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6393 (pt) REVERT: C 138 TYR cc_start: 0.5693 (p90) cc_final: 0.5493 (p90) REVERT: C 144 TYR cc_start: 0.5438 (t80) cc_final: 0.5131 (t80) REVERT: C 177 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6797 (tm-30) REVERT: C 192 GLU cc_start: 0.7896 (tt0) cc_final: 0.7295 (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: 0.8449 (tm-30) REVERT: C 363 SER cc_start: 0.5096 (OUTLIER) cc_final: 0.4576 (p) REVERT: C 371 PHE cc_start: 0.8532 (p90) cc_final: 0.8082 (p90) REVERT: C 372 SER cc_start: 0.8696 (p) cc_final: 0.7489 (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: 0.6964 (mmtt) REVERT: C 439 MET cc_start: 0.7268 (tpp) cc_final: 0.7007 (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: 0.8654 (mtmm) REVERT: C 515 LEU cc_start: 0.8991 (mp) cc_final: 0.8769 (mp) REVERT: C 595 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7313 (mt-10) REVERT: C 625 GLN cc_start: 0.9067 (pt0) cc_final: 0.8768 (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: 0.8021 (mm-30) REVERT: C 723 ASP cc_start: 0.8153 (t0) cc_final: 0.7883 (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: 0.8127 (p0) REVERT: C 774 GLN cc_start: 0.8346 (tp40) cc_final: 0.8095 (tp40) REVERT: C 802 MET cc_start: 0.9091 (mtp) cc_final: 0.8855 (mtp) REVERT: C 830 LEU cc_start: 0.9404 (mt) cc_final: 0.8743 (mt) REVERT: C 844 LEU cc_start: 0.8826 (pp) cc_final: 0.8619 (pp) REVERT: C 845 ASN cc_start: 0.8089 (m110) cc_final: 0.7608 (m110) REVERT: C 853 GLN cc_start: 0.8928 (pp30) cc_final: 0.8378 (pp30) REVERT: C 923 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8615 (mmtp) REVERT: C 978 GLN cc_start: 0.8490 (pm20) cc_final: 0.8051 (pm20) REVERT: C 980 ASN cc_start: 0.8420 (m110) cc_final: 0.8088 (m110) outliers start: 128 outliers final: 90 residues processed: 829 average time/residue: 0.3684 time to fit residues: 453.4469 Evaluate side-chains 653 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 555 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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 270 ASP 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 270 ASP 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 270 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 240 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 258 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 824 GLN A 863 GLN ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 80 ASN B 213 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 469 ASN B 728 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 297 HIS C 333 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 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 ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22977 Z= 0.207 Angle : 0.776 11.747 30939 Z= 0.386 Chirality : 0.057 0.926 3393 Planarity : 0.004 0.047 4020 Dihedral : 15.356 112.988 5158 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 5.01 % Allowed : 14.25 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 2853 helix: 0.05 (0.20), residues: 657 sheet: -0.57 (0.21), residues: 597 loop : -2.08 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 360 HIS 0.009 0.002 HIS A 299 PHE 0.025 0.002 PHE C 219 TYR 0.036 0.002 TYR C 96 ARG 0.008 0.001 ARG B 261 *********************** 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 704 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 595 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8295 (m-80) cc_final: 0.7982 (m-80) REVERT: A 78 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7001 (mm) REVERT: A 135 LYS cc_start: 0.7862 (tttm) cc_final: 0.7293 (tptp) REVERT: A 215 GLU cc_start: 0.6465 (tt0) cc_final: 0.6057 (tt0) REVERT: A 228 ASP cc_start: 0.4844 (OUTLIER) cc_final: 0.3528 (m-30) REVERT: A 371 PHE cc_start: 0.8860 (p90) cc_final: 0.8580 (p90) REVERT: A 381 LYS cc_start: 0.7805 (mttp) cc_final: 0.7426 (mmtp) REVERT: A 439 MET cc_start: 0.7082 (tpp) cc_final: 0.6717 (mmt) REVERT: A 507 GLN cc_start: 0.8783 (tp40) cc_final: 0.8040 (mp10) REVERT: A 517 GLU cc_start: 0.8699 (tp30) cc_final: 0.8408 (tp30) REVERT: A 530 LEU cc_start: 0.8017 (tp) cc_final: 0.7790 (tt) REVERT: A 635 ASP cc_start: 0.8297 (t0) cc_final: 0.8015 (t0) REVERT: A 644 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 655 ASP cc_start: 0.7967 (t0) cc_final: 0.7618 (t0) REVERT: A 723 ASP cc_start: 0.7720 (t0) cc_final: 0.7393 (t0) REVERT: A 728 GLN cc_start: 0.8445 (mt0) cc_final: 0.8181 (mt0) REVERT: A 782 LEU cc_start: 0.8194 (mp) cc_final: 0.7738 (tp) REVERT: A 840 GLN cc_start: 0.9217 (tp40) cc_final: 0.8978 (tp40) REVERT: A 845 ASN cc_start: 0.8021 (m110) cc_final: 0.7526 (m110) REVERT: A 856 GLN cc_start: 0.9065 (tp40) cc_final: 0.8531 (mm-40) REVERT: A 873 GLN cc_start: 0.8706 (pm20) cc_final: 0.8498 (mp10) REVERT: A 908 GLN cc_start: 0.8899 (tp40) cc_final: 0.8292 (tm-30) REVERT: A 958 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8163 (tttp) REVERT: A 986 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 135 LYS cc_start: 0.7532 (tttm) cc_final: 0.7309 (tptp) REVERT: B 192 GLU cc_start: 0.7957 (tt0) cc_final: 0.7106 (tt0) REVERT: B 331 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7694 (t0) REVERT: B 363 SER cc_start: 0.4987 (OUTLIER) cc_final: 0.4763 (p) REVERT: B 381 LYS cc_start: 0.7831 (mttp) cc_final: 0.7588 (mmtt) REVERT: B 439 MET cc_start: 0.7866 (tpp) cc_final: 0.7586 (mmp) REVERT: B 445 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8608 (mmmm) REVERT: B 514 MET cc_start: 0.8282 (mtt) cc_final: 0.7992 (mpp) REVERT: B 530 LEU cc_start: 0.8136 (tp) cc_final: 0.7878 (tt) REVERT: B 647 ASP cc_start: 0.8863 (t0) cc_final: 0.8527 (t0) REVERT: B 693 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 807 ASP cc_start: 0.8910 (m-30) cc_final: 0.8486 (m-30) REVERT: B 840 GLN cc_start: 0.9352 (tp40) cc_final: 0.8977 (tm-30) REVERT: B 853 GLN cc_start: 0.9054 (pp30) cc_final: 0.8303 (pp30) REVERT: B 856 GLN cc_start: 0.9223 (tp40) cc_final: 0.8854 (mm110) REVERT: B 868 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8391 (mtp85) REVERT: B 876 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8702 (tm-30) REVERT: B 877 GLN cc_start: 0.8609 (tt0) cc_final: 0.8373 (tt0) REVERT: B 911 GLN cc_start: 0.8631 (tt0) cc_final: 0.8288 (tp-100) REVERT: B 916 GLU cc_start: 0.7678 (tp30) cc_final: 0.7258 (tp30) REVERT: B 980 ASN cc_start: 0.8505 (m110) cc_final: 0.8232 (m-40) REVERT: B 985 LYS cc_start: 0.8982 (tttt) cc_final: 0.8669 (tttm) REVERT: C 74 PHE cc_start: 0.8767 (m-80) cc_final: 0.8334 (m-80) REVERT: C 78 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7149 (mm) REVERT: C 135 LYS cc_start: 0.7286 (tttm) cc_final: 0.6844 (tptp) REVERT: C 138 TYR cc_start: 0.5764 (p90) cc_final: 0.5421 (p90) REVERT: C 191 ARG cc_start: 0.7226 (mtp-110) cc_final: 0.6045 (mtp-110) REVERT: C 192 GLU cc_start: 0.7879 (tt0) cc_final: 0.7632 (tt0) REVERT: C 215 GLU cc_start: 0.6323 (tt0) cc_final: 0.6053 (tt0) REVERT: C 228 ASP cc_start: 0.5170 (OUTLIER) cc_final: 0.4701 (p0) REVERT: C 285 GLU cc_start: 0.9002 (pp20) cc_final: 0.8563 (tm-30) REVERT: C 375 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7969 (mtmm) REVERT: C 381 LYS cc_start: 0.7723 (mttp) cc_final: 0.7264 (mmtt) REVERT: C 387 PHE cc_start: 0.7482 (m-80) cc_final: 0.7235 (m-80) REVERT: C 488 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8608 (mtmm) REVERT: C 515 LEU cc_start: 0.8826 (mp) cc_final: 0.8611 (mp) REVERT: C 530 LEU cc_start: 0.8389 (tt) cc_final: 0.8126 (tt) REVERT: C 595 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6951 (mt-10) REVERT: C 621 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8609 (mm-30) REVERT: C 639 ASN cc_start: 0.8589 (t0) cc_final: 0.8237 (t0) REVERT: C 693 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8197 (mm-30) REVERT: C 723 ASP cc_start: 0.8264 (t0) cc_final: 0.7989 (t70) REVERT: C 774 GLN cc_start: 0.8358 (tp40) cc_final: 0.7936 (tp40) REVERT: C 807 ASP cc_start: 0.9263 (m-30) cc_final: 0.9038 (m-30) REVERT: C 845 ASN cc_start: 0.8068 (m110) cc_final: 0.7566 (m-40) REVERT: C 867 ASP cc_start: 0.8674 (m-30) cc_final: 0.8310 (m-30) REVERT: C 877 GLN cc_start: 0.8629 (tt0) cc_final: 0.8307 (tt0) REVERT: C 908 GLN cc_start: 0.9035 (tp40) cc_final: 0.8833 (tp-100) REVERT: C 911 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8597 (tm-30) REVERT: C 920 SER cc_start: 0.8959 (m) cc_final: 0.8401 (p) REVERT: C 978 GLN cc_start: 0.8239 (pm20) cc_final: 0.7938 (pm20) outliers start: 109 outliers final: 81 residues processed: 663 average time/residue: 0.3503 time to fit residues: 354.5759 Evaluate side-chains 625 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 537 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 268 SER Chi-restraints excluded: chain A residue 270 ASP 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 331 ASN 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 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 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 958 LYS 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 213 ASN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 741 ASP 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 176 ASN 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 270 ASP 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 380 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 453 ASP 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 143 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 731 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 GLN C 980 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 22977 Z= 0.404 Angle : 0.824 11.377 30939 Z= 0.416 Chirality : 0.055 0.581 3393 Planarity : 0.005 0.051 4020 Dihedral : 13.448 115.887 5101 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.48 % Favored : 93.31 % Rotamer: Outliers : 6.34 % Allowed : 18.02 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 2853 helix: 0.05 (0.19), residues: 660 sheet: -0.86 (0.20), residues: 621 loop : -2.14 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 360 HIS 0.007 0.002 HIS A 297 PHE 0.041 0.002 PHE C 219 TYR 0.043 0.002 TYR C 96 ARG 0.007 0.001 ARG C 197 *********************** 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 657 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 519 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8132 (tt0) cc_final: 0.7809 (tt0) REVERT: A 371 PHE cc_start: 0.8879 (p90) cc_final: 0.8561 (p90) REVERT: A 375 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 381 LYS cc_start: 0.8085 (mttp) cc_final: 0.7657 (mmtt) REVERT: A 439 MET cc_start: 0.7330 (tpp) cc_final: 0.6941 (mmt) REVERT: A 445 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8760 (mmmt) REVERT: A 507 GLN cc_start: 0.8795 (tp40) cc_final: 0.8011 (mp10) REVERT: A 631 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8401 (tttm) REVERT: A 635 ASP cc_start: 0.8471 (t0) cc_final: 0.8234 (t0) REVERT: A 723 ASP cc_start: 0.8289 (t0) cc_final: 0.8007 (t0) REVERT: A 728 GLN cc_start: 0.8524 (mt0) cc_final: 0.8260 (mt0) REVERT: A 782 LEU cc_start: 0.8115 (mp) cc_final: 0.7725 (tp) REVERT: A 789 GLU cc_start: 0.8775 (pp20) cc_final: 0.8208 (pp20) REVERT: A 840 GLN cc_start: 0.9136 (tp40) cc_final: 0.8862 (tp40) REVERT: A 845 ASN cc_start: 0.8065 (m110) cc_final: 0.7528 (m-40) REVERT: A 856 GLN cc_start: 0.9162 (tp40) cc_final: 0.8738 (mm-40) REVERT: A 867 ASP cc_start: 0.8237 (m-30) cc_final: 0.7986 (m-30) REVERT: A 880 ARG cc_start: 0.8720 (ptm160) cc_final: 0.8318 (ptm160) REVERT: A 908 GLN cc_start: 0.8938 (tp40) cc_final: 0.8400 (tm-30) REVERT: A 911 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8843 (tp-100) REVERT: A 958 LYS cc_start: 0.8229 (tppt) cc_final: 0.8027 (tttp) REVERT: A 985 LYS cc_start: 0.9062 (tttt) cc_final: 0.8851 (tttt) REVERT: A 986 GLU cc_start: 0.8703 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 1018 PHE cc_start: 0.7551 (m-10) cc_final: 0.7280 (m-80) REVERT: B 74 PHE cc_start: 0.8744 (m-80) cc_final: 0.8440 (m-80) REVERT: B 265 ASP cc_start: 0.8600 (t0) cc_final: 0.8344 (m-30) REVERT: B 381 LYS cc_start: 0.7994 (mttp) cc_final: 0.7708 (mmtt) REVERT: B 529 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 530 LEU cc_start: 0.8007 (tp) cc_final: 0.7772 (tt) REVERT: B 647 ASP cc_start: 0.8817 (t0) cc_final: 0.8551 (t0) REVERT: B 717 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9126 (mmmm) REVERT: B 723 ASP cc_start: 0.8284 (t0) cc_final: 0.7734 (p0) REVERT: B 745 MET cc_start: 0.8812 (tpp) cc_final: 0.8600 (tpt) REVERT: B 807 ASP cc_start: 0.8855 (m-30) cc_final: 0.8459 (m-30) REVERT: B 840 GLN cc_start: 0.9346 (tp40) cc_final: 0.9001 (tm-30) REVERT: B 856 GLN cc_start: 0.9261 (tp-100) cc_final: 0.9027 (mm110) REVERT: B 859 SER cc_start: 0.8995 (t) cc_final: 0.8548 (p) REVERT: B 868 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8493 (mtp85) REVERT: B 876 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8816 (tm-30) REVERT: B 908 GLN cc_start: 0.8989 (tp40) cc_final: 0.8558 (tm-30) REVERT: B 911 GLN cc_start: 0.8766 (tt0) cc_final: 0.8505 (tp-100) REVERT: B 916 GLU cc_start: 0.7713 (tp30) cc_final: 0.7254 (tp30) REVERT: B 985 LYS cc_start: 0.8905 (tttt) cc_final: 0.8566 (tttm) REVERT: C 74 PHE cc_start: 0.9097 (m-80) cc_final: 0.8613 (m-80) REVERT: C 79 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5053 (pt) REVERT: C 135 LYS cc_start: 0.7724 (tttm) cc_final: 0.7055 (tptp) REVERT: C 215 GLU cc_start: 0.6826 (tt0) cc_final: 0.6341 (tt0) REVERT: C 285 GLU cc_start: 0.8936 (pp20) cc_final: 0.8499 (tm-30) REVERT: C 371 PHE cc_start: 0.8240 (p90) cc_final: 0.8036 (p90) REVERT: C 381 LYS cc_start: 0.7969 (mttp) cc_final: 0.7446 (mmtt) REVERT: C 515 LEU cc_start: 0.8966 (mp) cc_final: 0.8736 (mp) REVERT: C 571 TYR cc_start: 0.8401 (p90) cc_final: 0.8033 (p90) REVERT: C 595 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7018 (mt-10) REVERT: C 624 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9071 (tptp) REVERT: C 639 ASN cc_start: 0.8813 (t0) cc_final: 0.8435 (t0) REVERT: C 807 ASP cc_start: 0.9284 (m-30) cc_final: 0.9019 (m-30) REVERT: C 845 ASN cc_start: 0.8229 (m110) cc_final: 0.7699 (m110) REVERT: C 867 ASP cc_start: 0.8820 (m-30) cc_final: 0.8616 (m-30) REVERT: C 876 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8202 (tm-30) outliers start: 138 outliers final: 110 residues processed: 611 average time/residue: 0.3267 time to fit residues: 308.6219 Evaluate side-chains 592 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 479 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN 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 270 ASP 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 400 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 LYS 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 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 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 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 270 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 304 LEU 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 384 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 SER 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 595 GLU 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 78 LEU 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 176 ASN 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 333 ASN 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 380 VAL 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 453 ASP Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 875 ASP Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 976 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.9990 chunk 194 optimal weight: 0.0370 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 260 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 728 GLN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 297 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22977 Z= 0.181 Angle : 0.677 8.124 30939 Z= 0.338 Chirality : 0.051 0.521 3393 Planarity : 0.004 0.048 4020 Dihedral : 12.052 113.164 5081 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.73 % Favored : 95.06 % Rotamer: Outliers : 5.75 % Allowed : 20.55 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 2853 helix: 0.57 (0.20), residues: 660 sheet: -0.46 (0.21), residues: 576 loop : -2.09 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 360 HIS 0.004 0.001 HIS B 297 PHE 0.040 0.002 PHE A 219 TYR 0.034 0.001 TYR B 96 ARG 0.005 0.000 ARG C 461 *********************** 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 654 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 529 time to evaluate : 2.530 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 74 PHE cc_start: 0.8612 (m-80) cc_final: 0.8326 (m-80) REVERT: A 192 GLU cc_start: 0.8134 (tt0) cc_final: 0.7689 (tt0) REVERT: A 371 PHE cc_start: 0.8826 (p90) cc_final: 0.8498 (p90) REVERT: A 439 MET cc_start: 0.7283 (tpp) cc_final: 0.7039 (mmp) REVERT: A 445 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8696 (mmmt) REVERT: A 507 GLN cc_start: 0.8844 (tp40) cc_final: 0.8070 (mp10) REVERT: A 517 GLU cc_start: 0.8644 (tp30) cc_final: 0.8355 (tp30) REVERT: A 631 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8254 (tttm) REVERT: A 635 ASP cc_start: 0.8387 (t0) cc_final: 0.8095 (t0) REVERT: A 644 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8768 (tm-30) REVERT: A 840 GLN cc_start: 0.9097 (tp40) cc_final: 0.8817 (tp40) REVERT: A 845 ASN cc_start: 0.8285 (m110) cc_final: 0.7737 (m-40) REVERT: A 856 GLN cc_start: 0.9157 (tp40) cc_final: 0.8572 (mm110) REVERT: A 867 ASP cc_start: 0.8263 (m-30) cc_final: 0.8007 (m-30) REVERT: A 880 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8226 (ptm160) REVERT: A 908 GLN cc_start: 0.8902 (tp40) cc_final: 0.8462 (tm-30) REVERT: A 911 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8613 (tp-100) REVERT: A 958 LYS cc_start: 0.8301 (tppt) cc_final: 0.8097 (tttp) REVERT: A 959 ASP cc_start: 0.8628 (p0) cc_final: 0.8402 (p0) REVERT: A 985 LYS cc_start: 0.9033 (tttt) cc_final: 0.8797 (tttt) REVERT: A 986 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 74 PHE cc_start: 0.8611 (m-80) cc_final: 0.8309 (m-80) REVERT: B 390 LYS cc_start: 0.7034 (mtpp) cc_final: 0.6639 (ttpp) REVERT: B 507 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8293 (mm-40) REVERT: B 514 MET cc_start: 0.8624 (mtt) cc_final: 0.8385 (mmm) REVERT: B 529 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 647 ASP cc_start: 0.8879 (t0) cc_final: 0.8605 (t0) REVERT: B 656 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8460 (tppt) REVERT: B 723 ASP cc_start: 0.8202 (t0) cc_final: 0.7661 (p0) REVERT: B 736 LEU cc_start: 0.9124 (mt) cc_final: 0.8860 (mt) REVERT: B 807 ASP cc_start: 0.8880 (m-30) cc_final: 0.8473 (m-30) REVERT: B 840 GLN cc_start: 0.9368 (tp40) cc_final: 0.8899 (tm-30) REVERT: B 856 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8932 (mm110) REVERT: B 868 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8464 (mtp85) REVERT: B 876 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8834 (tm-30) REVERT: B 908 GLN cc_start: 0.8959 (tp40) cc_final: 0.8615 (tm-30) REVERT: B 916 GLU cc_start: 0.7689 (tp30) cc_final: 0.7193 (tp30) REVERT: B 923 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8739 (mmmt) REVERT: B 985 LYS cc_start: 0.8916 (tttt) cc_final: 0.8564 (tttm) REVERT: C 74 PHE cc_start: 0.9021 (m-80) cc_final: 0.8486 (m-80) REVERT: C 79 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5062 (pt) REVERT: C 135 LYS cc_start: 0.7408 (tttm) cc_final: 0.6803 (tptp) REVERT: C 215 GLU cc_start: 0.6582 (tt0) cc_final: 0.6273 (tt0) REVERT: C 285 GLU cc_start: 0.8947 (pp20) cc_final: 0.8479 (tm-30) REVERT: C 381 LYS cc_start: 0.8047 (mttp) cc_final: 0.7744 (mmtt) REVERT: C 515 LEU cc_start: 0.8832 (mp) cc_final: 0.8620 (mp) REVERT: C 571 TYR cc_start: 0.8458 (p90) cc_final: 0.8110 (p90) REVERT: C 595 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7005 (mt-10) REVERT: C 624 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8780 (tptp) REVERT: C 647 ASP cc_start: 0.8860 (t0) cc_final: 0.8587 (t0) REVERT: C 774 GLN cc_start: 0.8408 (tp40) cc_final: 0.8037 (tp40) REVERT: C 807 ASP cc_start: 0.9258 (m-30) cc_final: 0.8975 (m-30) REVERT: C 832 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8619 (mttm) REVERT: C 845 ASN cc_start: 0.8202 (m110) cc_final: 0.7774 (m110) REVERT: C 867 ASP cc_start: 0.8731 (m-30) cc_final: 0.8453 (m-30) REVERT: C 876 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 920 SER cc_start: 0.9080 (m) cc_final: 0.8613 (p) REVERT: C 986 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8306 (tt0) outliers start: 125 outliers final: 99 residues processed: 612 average time/residue: 0.3304 time to fit residues: 313.2457 Evaluate side-chains 593 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 491 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 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 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 453 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 193 PHE 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 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 396 CYS Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 595 GLU 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 LEU 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 176 ASN 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 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 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 453 ASP Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 624 LYS 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 880 ARG Chi-restraints excluded: chain C residue 928 CYS 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 229 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 chunk 205 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 140 optimal weight: 0.0570 chunk 247 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 728 GLN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 331 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 873 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 508 GLN C 565 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22977 Z= 0.179 Angle : 0.655 10.926 30939 Z= 0.327 Chirality : 0.050 0.519 3393 Planarity : 0.004 0.049 4020 Dihedral : 11.186 111.474 5065 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.47 % Favored : 94.32 % Rotamer: Outliers : 5.98 % Allowed : 20.78 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2853 helix: 0.79 (0.20), residues: 663 sheet: -0.40 (0.21), residues: 576 loop : -2.02 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 419 HIS 0.003 0.001 HIS B 299 PHE 0.042 0.001 PHE B 219 TYR 0.038 0.001 TYR A 96 ARG 0.008 0.000 ARG C 868 *********************** 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 642 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 512 time to evaluate : 2.452 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 74 PHE cc_start: 0.8624 (m-80) cc_final: 0.8343 (m-80) REVERT: A 192 GLU cc_start: 0.8128 (tt0) cc_final: 0.7649 (tt0) REVERT: A 371 PHE cc_start: 0.8787 (p90) cc_final: 0.8463 (p90) REVERT: A 439 MET cc_start: 0.7492 (tpp) cc_final: 0.7281 (mmp) REVERT: A 445 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8705 (mmmt) REVERT: A 507 GLN cc_start: 0.8850 (tp40) cc_final: 0.8061 (mp10) REVERT: A 517 GLU cc_start: 0.8715 (tp30) cc_final: 0.8391 (tp30) REVERT: A 623 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 631 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7856 (tttp) REVERT: A 723 ASP cc_start: 0.8047 (t0) cc_final: 0.7700 (t0) REVERT: A 728 GLN cc_start: 0.8452 (mt0) cc_final: 0.8225 (mt0) REVERT: A 840 GLN cc_start: 0.9088 (tp40) cc_final: 0.8815 (tp40) REVERT: A 845 ASN cc_start: 0.8258 (m110) cc_final: 0.7671 (m-40) REVERT: A 856 GLN cc_start: 0.9165 (tp40) cc_final: 0.8533 (mm110) REVERT: A 867 ASP cc_start: 0.8304 (m-30) cc_final: 0.8018 (m-30) REVERT: A 880 ARG cc_start: 0.8660 (ptm160) cc_final: 0.8267 (ptm160) REVERT: A 908 GLN cc_start: 0.8890 (tp40) cc_final: 0.8522 (tm-30) REVERT: A 911 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8683 (tp-100) REVERT: A 958 LYS cc_start: 0.8287 (tppt) cc_final: 0.8083 (tttp) REVERT: A 959 ASP cc_start: 0.8631 (p0) cc_final: 0.8397 (p0) REVERT: A 986 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 74 PHE cc_start: 0.8590 (m-80) cc_final: 0.8156 (m-80) REVERT: B 219 PHE cc_start: 0.8863 (t80) cc_final: 0.8631 (t80) REVERT: B 507 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8284 (mm-40) REVERT: B 514 MET cc_start: 0.8622 (mtt) cc_final: 0.8377 (mmm) REVERT: B 529 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 530 LEU cc_start: 0.8135 (tp) cc_final: 0.7869 (tt) REVERT: B 621 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8540 (mm-30) REVERT: B 624 LYS cc_start: 0.9059 (tptp) cc_final: 0.8846 (mmmm) REVERT: B 647 ASP cc_start: 0.8827 (t0) cc_final: 0.8615 (t0) REVERT: B 807 ASP cc_start: 0.8869 (m-30) cc_final: 0.8451 (m-30) REVERT: B 840 GLN cc_start: 0.9403 (tp40) cc_final: 0.8825 (tm-30) REVERT: B 856 GLN cc_start: 0.9233 (tp-100) cc_final: 0.9000 (mm110) REVERT: B 868 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8454 (mtp85) REVERT: B 876 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8760 (tm-30) REVERT: B 908 GLN cc_start: 0.8916 (tp40) cc_final: 0.8542 (tm-30) REVERT: B 916 GLU cc_start: 0.7725 (tp30) cc_final: 0.7186 (tp30) REVERT: B 985 LYS cc_start: 0.8898 (tttt) cc_final: 0.8564 (tttm) REVERT: C 74 PHE cc_start: 0.8975 (m-80) cc_final: 0.8511 (m-80) REVERT: C 135 LYS cc_start: 0.7325 (tttm) cc_final: 0.6782 (tptp) REVERT: C 215 GLU cc_start: 0.6613 (tt0) cc_final: 0.6257 (tt0) REVERT: C 285 GLU cc_start: 0.8943 (pp20) cc_final: 0.8450 (tm-30) REVERT: C 381 LYS cc_start: 0.8309 (mttp) cc_final: 0.8007 (mmtt) REVERT: C 515 LEU cc_start: 0.8800 (mp) cc_final: 0.8486 (mp) REVERT: C 571 TYR cc_start: 0.8471 (p90) cc_final: 0.8144 (p90) REVERT: C 595 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 624 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8773 (tptp) REVERT: C 774 GLN cc_start: 0.8650 (tp40) cc_final: 0.8127 (tp40) REVERT: C 807 ASP cc_start: 0.9249 (m-30) cc_final: 0.8954 (m-30) REVERT: C 823 LEU cc_start: 0.8183 (mm) cc_final: 0.7444 (pp) REVERT: C 832 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8648 (mttm) REVERT: C 845 ASN cc_start: 0.8172 (m110) cc_final: 0.7683 (m110) REVERT: C 867 ASP cc_start: 0.8796 (m-30) cc_final: 0.8515 (m-30) REVERT: C 876 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 902 GLU cc_start: 0.8608 (pp20) cc_final: 0.7938 (tm-30) REVERT: C 920 SER cc_start: 0.9091 (m) cc_final: 0.8768 (p) REVERT: C 997 MET cc_start: 0.8115 (mtt) cc_final: 0.7887 (mtt) outliers start: 130 outliers final: 103 residues processed: 592 average time/residue: 0.3174 time to fit residues: 293.5031 Evaluate side-chains 596 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 490 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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 268 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 MET 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 934 ILE Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 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 176 ASN 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 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 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 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 453 ASP Chi-restraints excluded: chain C residue 565 GLN Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 624 LYS 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 880 ARG Chi-restraints excluded: chain C residue 928 CYS 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 92 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22977 Z= 0.247 Angle : 0.673 8.558 30939 Z= 0.339 Chirality : 0.051 0.538 3393 Planarity : 0.004 0.049 4020 Dihedral : 10.911 109.172 5057 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.10 % Favored : 93.69 % Rotamer: Outliers : 5.93 % Allowed : 21.29 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 2853 helix: 0.84 (0.21), residues: 663 sheet: -0.58 (0.21), residues: 555 loop : -2.02 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 419 HIS 0.004 0.001 HIS A 200 PHE 0.036 0.002 PHE A 219 TYR 0.035 0.002 TYR A 96 ARG 0.006 0.001 ARG C 868 *********************** 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 630 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 501 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8704 (m-80) cc_final: 0.8433 (m-80) REVERT: A 192 GLU cc_start: 0.8097 (tt0) cc_final: 0.7675 (tt0) REVERT: A 317 CYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6589 (m) REVERT: A 371 PHE cc_start: 0.8651 (p90) cc_final: 0.8428 (p90) REVERT: A 439 MET cc_start: 0.7496 (tpp) cc_final: 0.7280 (mmp) REVERT: A 507 GLN cc_start: 0.8903 (tp40) cc_final: 0.8125 (mp10) REVERT: A 517 GLU cc_start: 0.8740 (tp30) cc_final: 0.8383 (tp30) REVERT: A 623 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 724 LEU cc_start: 0.8687 (mt) cc_final: 0.8365 (tp) REVERT: A 728 GLN cc_start: 0.8488 (mt0) cc_final: 0.8067 (mt0) REVERT: A 802 MET cc_start: 0.9157 (mmm) cc_final: 0.8903 (mmm) REVERT: A 840 GLN cc_start: 0.9096 (tp40) cc_final: 0.8830 (tp40) REVERT: A 845 ASN cc_start: 0.8348 (m110) cc_final: 0.7811 (m110) REVERT: A 856 GLN cc_start: 0.9189 (tp40) cc_final: 0.8711 (mm110) REVERT: A 880 ARG cc_start: 0.8724 (ptm160) cc_final: 0.8460 (ptm160) REVERT: A 908 GLN cc_start: 0.8894 (tp40) cc_final: 0.8545 (tm-30) REVERT: A 958 LYS cc_start: 0.8268 (tppt) cc_final: 0.8063 (tttp) REVERT: A 959 ASP cc_start: 0.8657 (p0) cc_final: 0.8420 (p0) REVERT: B 74 PHE cc_start: 0.8713 (m-80) cc_final: 0.8384 (m-80) REVERT: B 219 PHE cc_start: 0.8810 (t80) cc_final: 0.8606 (t80) REVERT: B 375 LYS cc_start: 0.7871 (mmtp) cc_final: 0.7368 (mmmm) REVERT: B 386 CYS cc_start: 0.7984 (m) cc_final: 0.7410 (t) REVERT: B 507 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8306 (mm-40) REVERT: B 514 MET cc_start: 0.8688 (mtt) cc_final: 0.8375 (mmm) REVERT: B 807 ASP cc_start: 0.8816 (m-30) cc_final: 0.8418 (m-30) REVERT: B 840 GLN cc_start: 0.9404 (tp40) cc_final: 0.8838 (tm-30) REVERT: B 856 GLN cc_start: 0.9314 (tp-100) cc_final: 0.9070 (mm110) REVERT: B 868 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8458 (mtp85) REVERT: B 876 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 908 GLN cc_start: 0.8929 (tp40) cc_final: 0.8596 (tm-30) REVERT: B 916 GLU cc_start: 0.7793 (tp30) cc_final: 0.7256 (tp30) REVERT: B 985 LYS cc_start: 0.8866 (tttt) cc_final: 0.8530 (tttm) REVERT: B 1014 CYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (t) REVERT: C 74 PHE cc_start: 0.9033 (m-80) cc_final: 0.8591 (m-80) REVERT: C 135 LYS cc_start: 0.7291 (tttm) cc_final: 0.6648 (tptp) REVERT: C 215 GLU cc_start: 0.6689 (tt0) cc_final: 0.6265 (tt0) REVERT: C 285 GLU cc_start: 0.8934 (pp20) cc_final: 0.8483 (pp20) REVERT: C 450 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7879 (t0) REVERT: C 515 LEU cc_start: 0.8828 (mp) cc_final: 0.8391 (mp) REVERT: C 571 TYR cc_start: 0.8448 (p90) cc_final: 0.8034 (p90) REVERT: C 595 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7029 (mt-10) REVERT: C 774 GLN cc_start: 0.8693 (tp40) cc_final: 0.8081 (tp40) REVERT: C 807 ASP cc_start: 0.9227 (m-30) cc_final: 0.8941 (m-30) REVERT: C 823 LEU cc_start: 0.8007 (mm) cc_final: 0.7425 (pp) REVERT: C 832 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8677 (mttm) REVERT: C 845 ASN cc_start: 0.8198 (m110) cc_final: 0.7758 (m110) REVERT: C 867 ASP cc_start: 0.8856 (m-30) cc_final: 0.8587 (m-30) REVERT: C 868 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8294 (ttm-80) REVERT: C 876 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 902 GLU cc_start: 0.8610 (pp20) cc_final: 0.7954 (tm-30) REVERT: C 908 GLN cc_start: 0.9053 (tp40) cc_final: 0.8573 (tm-30) REVERT: C 920 SER cc_start: 0.9200 (m) cc_final: 0.8808 (p) outliers start: 129 outliers final: 111 residues processed: 579 average time/residue: 0.3263 time to fit residues: 295.9697 Evaluate side-chains 599 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 484 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 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 268 SER Chi-restraints excluded: chain A residue 270 ASP 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 317 CYS 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 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 980 ASN 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 186 LEU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 332 PHE 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 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 820 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 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 176 ASN 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 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 380 VAL Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 875 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 265 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 157 optimal weight: 0.3980 chunk 201 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 297 HIS ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 GLN ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 0.030 22977 Z= 0.171 Angle : 0.638 9.012 30939 Z= 0.321 Chirality : 0.050 0.514 3393 Planarity : 0.004 0.076 4020 Dihedral : 10.452 107.937 5052 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.68 % Favored : 94.11 % Rotamer: Outliers : 5.61 % Allowed : 22.16 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2853 helix: 0.96 (0.21), residues: 678 sheet: -0.63 (0.21), residues: 579 loop : -2.00 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 419 HIS 0.011 0.001 HIS B 297 PHE 0.032 0.001 PHE B 219 TYR 0.031 0.001 TYR A 96 ARG 0.005 0.000 ARG C 868 *********************** 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 628 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 506 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8083 (tt0) cc_final: 0.7629 (tt0) REVERT: A 317 CYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6911 (m) REVERT: A 371 PHE cc_start: 0.8574 (p90) cc_final: 0.8262 (p90) REVERT: A 410 TYR cc_start: 0.7061 (t80) cc_final: 0.6641 (t80) REVERT: A 439 MET cc_start: 0.7466 (tpp) cc_final: 0.7251 (mmp) REVERT: A 445 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8686 (mmmt) REVERT: A 507 GLN cc_start: 0.8904 (tp40) cc_final: 0.8121 (mp10) REVERT: A 517 GLU cc_start: 0.8744 (tp30) cc_final: 0.8381 (tp30) REVERT: A 623 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 635 ASP cc_start: 0.8384 (t0) cc_final: 0.8064 (t0) REVERT: A 728 GLN cc_start: 0.8366 (mt0) cc_final: 0.8106 (mt0) REVERT: A 840 GLN cc_start: 0.9084 (tp40) cc_final: 0.8801 (tp40) REVERT: A 845 ASN cc_start: 0.8289 (m110) cc_final: 0.7720 (m110) REVERT: A 856 GLN cc_start: 0.9177 (tp40) cc_final: 0.8701 (mm110) REVERT: A 880 ARG cc_start: 0.8686 (ptm160) cc_final: 0.8421 (ptm160) REVERT: A 908 GLN cc_start: 0.8882 (tp40) cc_final: 0.8589 (tm-30) REVERT: A 958 LYS cc_start: 0.8294 (tppt) cc_final: 0.8092 (tttp) REVERT: A 959 ASP cc_start: 0.8642 (p0) cc_final: 0.8401 (p0) REVERT: A 986 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 74 PHE cc_start: 0.8641 (m-80) cc_final: 0.8198 (m-80) REVERT: B 370 PRO cc_start: 0.9024 (Cg_exo) cc_final: 0.8778 (Cg_endo) REVERT: B 375 LYS cc_start: 0.7818 (mmtp) cc_final: 0.7314 (mmmm) REVERT: B 507 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8298 (mm-40) REVERT: B 514 MET cc_start: 0.8675 (mtt) cc_final: 0.8405 (mmt) REVERT: B 693 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7971 (mt-10) REVERT: B 719 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8008 (pt) REVERT: B 807 ASP cc_start: 0.8820 (m-30) cc_final: 0.8412 (m-30) REVERT: B 840 GLN cc_start: 0.9395 (tp40) cc_final: 0.9168 (tp-100) REVERT: B 856 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8995 (mm110) REVERT: B 868 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8399 (mtp85) REVERT: B 876 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8736 (tm-30) REVERT: B 908 GLN cc_start: 0.8886 (tp40) cc_final: 0.8594 (tm-30) REVERT: B 916 GLU cc_start: 0.7886 (tp30) cc_final: 0.7392 (tp30) REVERT: B 985 LYS cc_start: 0.8818 (tttt) cc_final: 0.8475 (tttm) REVERT: C 72 ARG cc_start: 0.7645 (ptm160) cc_final: 0.7407 (ptm160) REVERT: C 74 PHE cc_start: 0.9002 (m-80) cc_final: 0.8551 (m-80) REVERT: C 135 LYS cc_start: 0.7455 (tttm) cc_final: 0.6795 (tptp) REVERT: C 215 GLU cc_start: 0.6623 (tt0) cc_final: 0.6220 (tt0) REVERT: C 285 GLU cc_start: 0.8915 (pp20) cc_final: 0.8461 (pp20) REVERT: C 515 LEU cc_start: 0.8765 (mp) cc_final: 0.8531 (mp) REVERT: C 565 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: C 571 TYR cc_start: 0.8446 (p90) cc_final: 0.8113 (p90) REVERT: C 595 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7094 (mt-10) REVERT: C 624 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8648 (tptp) REVERT: C 723 ASP cc_start: 0.8256 (t0) cc_final: 0.7975 (t70) REVERT: C 774 GLN cc_start: 0.8718 (tp40) cc_final: 0.8267 (tp40) REVERT: C 807 ASP cc_start: 0.9230 (m-30) cc_final: 0.8923 (m-30) REVERT: C 823 LEU cc_start: 0.7982 (mm) cc_final: 0.7454 (pp) REVERT: C 832 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8685 (mttm) REVERT: C 845 ASN cc_start: 0.8195 (m110) cc_final: 0.7775 (m110) REVERT: C 867 ASP cc_start: 0.8824 (m-30) cc_final: 0.8569 (m-30) REVERT: C 876 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 908 GLN cc_start: 0.9031 (tp40) cc_final: 0.8544 (tm-30) REVERT: C 920 SER cc_start: 0.9169 (m) cc_final: 0.8850 (p) REVERT: C 986 GLU cc_start: 0.8396 (tt0) cc_final: 0.8177 (tt0) outliers start: 122 outliers final: 99 residues processed: 584 average time/residue: 0.3200 time to fit residues: 293.2744 Evaluate side-chains 599 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 495 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 ARG 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 270 ASP 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 317 CYS 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 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 453 ASP Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 692 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 B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 251 ASN 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 363 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 719 LEU 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 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 176 ASN 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 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 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 327 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL 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 453 ASP Chi-restraints excluded: chain C residue 565 GLN Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 331 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 856 GLN ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 731 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22977 Z= 0.383 Angle : 0.767 12.306 30939 Z= 0.388 Chirality : 0.053 0.566 3393 Planarity : 0.004 0.075 4020 Dihedral : 10.682 105.447 5048 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 6.16 % Allowed : 22.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 2853 helix: 0.73 (0.20), residues: 663 sheet: -0.80 (0.19), residues: 648 loop : -2.19 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 83 HIS 0.005 0.001 HIS A 200 PHE 0.037 0.002 PHE A 219 TYR 0.036 0.002 TYR C 96 ARG 0.021 0.001 ARG C 567 *********************** 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 599 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 465 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8059 (tt0) cc_final: 0.7649 (tt0) REVERT: A 371 PHE cc_start: 0.8543 (p90) cc_final: 0.8265 (p90) REVERT: A 410 TYR cc_start: 0.7365 (t80) cc_final: 0.7063 (t80) REVERT: A 439 MET cc_start: 0.7265 (tpp) cc_final: 0.7037 (mmp) REVERT: A 445 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8737 (mmmt) REVERT: A 507 GLN cc_start: 0.8872 (tp40) cc_final: 0.8089 (mp10) REVERT: A 517 GLU cc_start: 0.8792 (tp30) cc_final: 0.8386 (tp30) REVERT: A 623 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (tt) REVERT: A 635 ASP cc_start: 0.8396 (t0) cc_final: 0.8073 (t0) REVERT: A 728 GLN cc_start: 0.8448 (mt0) cc_final: 0.8223 (mt0) REVERT: A 802 MET cc_start: 0.9166 (mmm) cc_final: 0.8936 (mmm) REVERT: A 840 GLN cc_start: 0.9109 (tp40) cc_final: 0.8846 (tp40) REVERT: A 856 GLN cc_start: 0.9256 (tp40) cc_final: 0.8752 (mm110) REVERT: A 880 ARG cc_start: 0.8768 (ptm160) cc_final: 0.8519 (ptm160) REVERT: A 908 GLN cc_start: 0.8911 (tp40) cc_final: 0.8589 (tm-30) REVERT: A 959 ASP cc_start: 0.8723 (p0) cc_final: 0.8423 (p0) REVERT: A 985 LYS cc_start: 0.9008 (tttt) cc_final: 0.8803 (tttt) REVERT: B 74 PHE cc_start: 0.8794 (m-80) cc_final: 0.8462 (m-80) REVERT: B 118 ARG cc_start: 0.7877 (ttt180) cc_final: 0.6772 (ttt180) REVERT: B 514 MET cc_start: 0.8661 (mtt) cc_final: 0.8424 (mmt) REVERT: B 719 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7981 (pt) REVERT: B 807 ASP cc_start: 0.8788 (m-30) cc_final: 0.8412 (m-30) REVERT: B 840 GLN cc_start: 0.9406 (tp40) cc_final: 0.8860 (tm-30) REVERT: B 868 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8429 (mtp85) REVERT: B 908 GLN cc_start: 0.8923 (tp40) cc_final: 0.8515 (tm-30) REVERT: B 912 GLN cc_start: 0.8902 (tt0) cc_final: 0.8701 (tt0) REVERT: B 916 GLU cc_start: 0.8043 (tp30) cc_final: 0.7491 (tp30) REVERT: B 985 LYS cc_start: 0.8795 (tttt) cc_final: 0.8390 (tttm) REVERT: B 1014 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7723 (t) REVERT: C 74 PHE cc_start: 0.9139 (m-80) cc_final: 0.8645 (m-80) REVERT: C 285 GLU cc_start: 0.8876 (pp20) cc_final: 0.8434 (pp20) REVERT: C 515 LEU cc_start: 0.8843 (mp) cc_final: 0.8596 (mp) REVERT: C 595 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7188 (mt-10) REVERT: C 807 ASP cc_start: 0.9230 (m-30) cc_final: 0.8973 (m-30) REVERT: C 845 ASN cc_start: 0.8208 (m110) cc_final: 0.7768 (m110) REVERT: C 867 ASP cc_start: 0.8893 (m-30) cc_final: 0.8619 (m-30) REVERT: C 876 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 908 GLN cc_start: 0.8968 (tp40) cc_final: 0.8473 (tm-30) REVERT: C 986 GLU cc_start: 0.8466 (tt0) cc_final: 0.8261 (tt0) outliers start: 134 outliers final: 115 residues processed: 554 average time/residue: 0.3036 time to fit residues: 264.2822 Evaluate side-chains 571 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 453 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 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 268 SER Chi-restraints excluded: chain A residue 270 ASP 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 327 ILE 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 453 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 992 ILE 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 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 251 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 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 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 928 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 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 176 ASN 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 230 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 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 453 ASP Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 856 GLN ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 731 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22977 Z= 0.271 Angle : 0.715 11.284 30939 Z= 0.360 Chirality : 0.052 0.520 3393 Planarity : 0.004 0.076 4020 Dihedral : 10.426 104.414 5046 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 5.93 % Allowed : 22.71 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2853 helix: 0.88 (0.21), residues: 660 sheet: -0.66 (0.22), residues: 522 loop : -2.13 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.003 TRP C 360 HIS 0.004 0.001 HIS B 297 PHE 0.020 0.002 PHE B 209 TYR 0.032 0.002 TYR C 96 ARG 0.006 0.001 ARG B 72 *********************** 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 603 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 474 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8074 (tt0) cc_final: 0.7633 (tt0) REVERT: A 371 PHE cc_start: 0.8611 (p90) cc_final: 0.8314 (p90) REVERT: A 410 TYR cc_start: 0.7087 (t80) cc_final: 0.6795 (t80) REVERT: A 439 MET cc_start: 0.7233 (tpp) cc_final: 0.6975 (mmp) REVERT: A 445 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8726 (mmmt) REVERT: A 517 GLU cc_start: 0.8834 (tp30) cc_final: 0.8448 (tp30) REVERT: A 623 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 635 ASP cc_start: 0.8410 (t0) cc_final: 0.8074 (t0) REVERT: A 728 GLN cc_start: 0.8406 (mt0) cc_final: 0.8179 (mt0) REVERT: A 802 MET cc_start: 0.9181 (mmm) cc_final: 0.8939 (mmm) REVERT: A 840 GLN cc_start: 0.9087 (tp40) cc_final: 0.8817 (tp40) REVERT: A 856 GLN cc_start: 0.9250 (tp40) cc_final: 0.8752 (mm110) REVERT: A 869 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7108 (mm) REVERT: A 880 ARG cc_start: 0.8743 (ptm160) cc_final: 0.8510 (ptm160) REVERT: A 908 GLN cc_start: 0.8870 (tp40) cc_final: 0.8534 (tm-30) REVERT: A 959 ASP cc_start: 0.8648 (p0) cc_final: 0.8363 (p0) REVERT: A 985 LYS cc_start: 0.9011 (tttt) cc_final: 0.8801 (tttt) REVERT: B 74 PHE cc_start: 0.8689 (m-80) cc_final: 0.8248 (m-80) REVERT: B 507 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8353 (mm-40) REVERT: B 514 MET cc_start: 0.8644 (mtt) cc_final: 0.8350 (mmt) REVERT: B 719 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7911 (pt) REVERT: B 807 ASP cc_start: 0.8755 (m-30) cc_final: 0.8390 (m-30) REVERT: B 840 GLN cc_start: 0.9396 (tp40) cc_final: 0.8842 (tm-30) REVERT: B 856 GLN cc_start: 0.9281 (tp-100) cc_final: 0.9041 (mm110) REVERT: B 868 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8440 (mtp85) REVERT: B 908 GLN cc_start: 0.8861 (tp40) cc_final: 0.8482 (tm-30) REVERT: B 916 GLU cc_start: 0.8075 (tp30) cc_final: 0.7542 (tp30) REVERT: B 923 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8626 (mmmt) REVERT: B 985 LYS cc_start: 0.8878 (tttt) cc_final: 0.8439 (tttm) REVERT: B 1014 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7882 (t) REVERT: C 74 PHE cc_start: 0.9111 (m-80) cc_final: 0.8625 (m-80) REVERT: C 285 GLU cc_start: 0.8888 (pp20) cc_final: 0.8439 (pp20) REVERT: C 515 LEU cc_start: 0.8822 (mp) cc_final: 0.8568 (mp) REVERT: C 595 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7181 (mt-10) REVERT: C 774 GLN cc_start: 0.8719 (tp40) cc_final: 0.7991 (tp40) REVERT: C 807 ASP cc_start: 0.9209 (m-30) cc_final: 0.8946 (m-30) REVERT: C 845 ASN cc_start: 0.8213 (m110) cc_final: 0.7754 (m110) REVERT: C 876 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 908 GLN cc_start: 0.8898 (tp40) cc_final: 0.8414 (tm-30) outliers start: 129 outliers final: 113 residues processed: 559 average time/residue: 0.3243 time to fit residues: 286.5136 Evaluate side-chains 585 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 468 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 264 CYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 270 ASP 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 376 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 479 ASN 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 572 ASP 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 724 LEU Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 928 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE 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 208 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 251 ASN 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 363 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 820 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1014 CYS 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 78 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 176 ASN 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 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 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 453 ASP Chi-restraints excluded: chain C residue 565 GLN Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.0060 chunk 128 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 174 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.1718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 863 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22977 Z= 0.205 Angle : 0.691 12.977 30939 Z= 0.345 Chirality : 0.051 0.502 3393 Planarity : 0.004 0.076 4020 Dihedral : 10.109 104.264 5042 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.13 % Favored : 93.66 % Rotamer: Outliers : 5.33 % Allowed : 23.54 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2853 helix: 1.03 (0.21), residues: 660 sheet: -0.60 (0.23), residues: 522 loop : -2.09 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP C 360 HIS 0.003 0.001 HIS A 200 PHE 0.038 0.002 PHE A 219 TYR 0.029 0.001 TYR C 96 ARG 0.014 0.001 ARG C 261 ********************** 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 608 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 492 time to evaluate : 2.532 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: A 192 GLU cc_start: 0.8035 (tt0) cc_final: 0.7604 (tt0) REVERT: A 371 PHE cc_start: 0.8605 (p90) cc_final: 0.8281 (p90) REVERT: A 410 TYR cc_start: 0.7123 (t80) cc_final: 0.6830 (t80) REVERT: A 439 MET cc_start: 0.7243 (tpp) cc_final: 0.6967 (mmp) REVERT: A 445 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8738 (mmmt) REVERT: A 517 GLU cc_start: 0.8868 (tp30) cc_final: 0.8450 (tp30) REVERT: A 623 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 635 ASP cc_start: 0.8381 (t0) cc_final: 0.8044 (t0) REVERT: A 728 GLN cc_start: 0.8300 (mt0) cc_final: 0.8055 (mt0) REVERT: A 802 MET cc_start: 0.9173 (mmm) cc_final: 0.8924 (mmm) REVERT: A 840 GLN cc_start: 0.9084 (tp40) cc_final: 0.8801 (tp40) REVERT: A 856 GLN cc_start: 0.9232 (tp40) cc_final: 0.8733 (mm110) REVERT: A 869 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7007 (mm) REVERT: A 880 ARG cc_start: 0.8699 (ptm160) cc_final: 0.8457 (ptm160) REVERT: A 908 GLN cc_start: 0.8872 (tp40) cc_final: 0.8570 (tm-30) REVERT: A 959 ASP cc_start: 0.8757 (p0) cc_final: 0.8383 (p0) REVERT: A 985 LYS cc_start: 0.9011 (tttt) cc_final: 0.8805 (tttt) REVERT: B 74 PHE cc_start: 0.8635 (m-80) cc_final: 0.8223 (m-80) REVERT: B 507 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 514 MET cc_start: 0.8650 (mtt) cc_final: 0.8345 (mmt) REVERT: B 618 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8530 (mmm-85) REVERT: B 719 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (pt) REVERT: B 798 PHE cc_start: 0.9058 (t80) cc_final: 0.8769 (t80) REVERT: B 807 ASP cc_start: 0.8771 (m-30) cc_final: 0.8408 (m-30) REVERT: B 840 GLN cc_start: 0.9386 (tp40) cc_final: 0.9156 (tp-100) REVERT: B 856 GLN cc_start: 0.9257 (tp-100) cc_final: 0.9023 (mm110) REVERT: B 868 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8514 (mtp85) REVERT: B 908 GLN cc_start: 0.8851 (tp40) cc_final: 0.8469 (tm-30) REVERT: B 911 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8598 (tp-100) REVERT: B 916 GLU cc_start: 0.8051 (tp30) cc_final: 0.7575 (tp30) REVERT: B 923 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8646 (mmmt) REVERT: B 985 LYS cc_start: 0.8874 (tttt) cc_final: 0.8453 (tttm) REVERT: B 1014 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7882 (t) REVERT: C 74 PHE cc_start: 0.9075 (m-80) cc_final: 0.8595 (m-80) REVERT: C 285 GLU cc_start: 0.8901 (pp20) cc_final: 0.8451 (pp20) REVERT: C 515 LEU cc_start: 0.8802 (mp) cc_final: 0.8552 (mp) REVERT: C 595 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7137 (mt-10) REVERT: C 774 GLN cc_start: 0.8737 (tp40) cc_final: 0.8236 (tp40) REVERT: C 807 ASP cc_start: 0.9191 (m-30) cc_final: 0.8899 (m-30) REVERT: C 845 ASN cc_start: 0.8216 (m110) cc_final: 0.7753 (m-40) REVERT: C 876 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 908 GLN cc_start: 0.8899 (tp40) cc_final: 0.8434 (tm-30) outliers start: 116 outliers final: 105 residues processed: 566 average time/residue: 0.3203 time to fit residues: 283.9886 Evaluate side-chains 590 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 481 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 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 268 SER Chi-restraints excluded: chain A residue 270 ASP 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 331 ASN Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 479 ASN 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 572 ASP 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 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 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 251 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 820 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 959 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 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 176 ASN Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 211 LEU 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 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 453 ASP Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 62 optimal weight: 0.2980 chunk 226 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 731 ASN ** 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 = 0.3688 r_free = 0.3688 target = 0.120998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101685 restraints weight = 47616.728| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.87 r_work: 0.3300 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 22977 Z= 0.378 Angle : 0.868 59.189 30939 Z= 0.476 Chirality : 0.052 0.522 3393 Planarity : 0.004 0.112 4020 Dihedral : 10.106 104.288 5040 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.17 % Favored : 93.62 % Rotamer: Outliers : 5.43 % Allowed : 24.00 % Favored : 70.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2853 helix: 1.03 (0.21), residues: 660 sheet: -0.60 (0.23), residues: 522 loop : -2.09 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP C 360 HIS 0.003 0.001 HIS A 200 PHE 0.023 0.002 PHE B 209 TYR 0.043 0.002 TYR B 208 ARG 0.010 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5691.88 seconds wall clock time: 103 minutes 6.71 seconds (6186.71 seconds total)