Starting phenix.real_space_refine on Fri Mar 6 01:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xcm_22127/03_2026/6xcm_22127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xcm_22127/03_2026/6xcm_22127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xcm_22127/03_2026/6xcm_22127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xcm_22127/03_2026/6xcm_22127.map" model { file = "/net/cci-nas-00/data/ceres_data/6xcm_22127/03_2026/6xcm_22127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xcm_22127/03_2026/6xcm_22127.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.022 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 114 5.16 5 C 17048 2.51 5 N 4375 2.21 5 O 5235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26772 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7393 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 12 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7587 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7735 Chain: "C" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "N" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "K" 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: "M" 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: 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: "P" 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: "Q" 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: "R" 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: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER B 459 " occ=0.40 Time building chain proxies: 8.13, per 1000 atoms: 0.30 Number of scatterers: 26772 At special positions: 0 Unit cell: (132.924, 136.268, 219.868, 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 114 16.00 O 5235 8.00 N 4375 7.00 C 17048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.07 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG F 1 " - " FUC F 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG T 1 " - " FUC T 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG B1303 " - " ASN B 709 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 343 " " NAG B1312 " - " ASN B 603 " " NAG B1313 " - " ASN B 616 " " NAG B1314 " - " ASN B 657 " " NAG B1319 " - " ASN B1074 " " NAG B1320 " - " ASN B1098 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 709 " " NAG C1321 " - " ASN C1098 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG O 1 " - " ASN C 331 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6308 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 66 sheets defined 23.3% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.217A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.181A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.639A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.150A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.445A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.569A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.877A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.855A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.702A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.901A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.552A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.314A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.692A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.598A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.880A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.803A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.981A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.579A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.025A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.233A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.908A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.880A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.483A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'S' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.534A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.833A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.001A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.179A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.629A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.720A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.818A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.525A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.681A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.005A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.822A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.188A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.750A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.640A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.836A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.705A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.510A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.768A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.825A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.689A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.560A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.560A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.571A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.792A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.679A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.069A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.569A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.725A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.163A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 49 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 52 through 55 removed outlier: 4.418A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 104 through 106 removed outlier: 4.005A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.653A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.521A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.556A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.628A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.628A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 539 through 542 Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.308A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 719 removed outlier: 3.562A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AG1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.854A pdb=" N ILE H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.793A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.954A pdb=" N VAL N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET N 82 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU N 80 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.708A pdb=" N THR N 110 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 45 through 47 removed outlier: 3.564A pdb=" N ARG N 38 " --> pdb=" O GLU N 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 49 through 51 removed outlier: 3.619A pdb=" N VAL N 50 " --> pdb=" O TYR N 58 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AH1, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AH2, first strand: chain 'S' and resid 19 through 24 removed outlier: 3.992A pdb=" N THR S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER S 67 " --> pdb=" O THR S 70 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 44 through 49 removed outlier: 6.530A pdb=" N TRP S 35 " --> pdb=" O MET S 47 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR S 49 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER S 90 " --> pdb=" O VAL S 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL S 97 " --> pdb=" O SER S 90 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2388 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: 6.47 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 8460 1.35 - 1.48: 7529 1.48 - 1.62: 11219 1.62 - 1.75: 0 1.75 - 1.89: 144 Bond restraints: 27352 Sorted by residual: bond pdb=" CA LEU A1034 " pdb=" C LEU A1034 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.07e+01 bond pdb=" CA CYS B 291 " pdb=" C CYS B 291 " ideal model delta sigma weight residual 1.523 1.469 0.055 1.34e-02 5.57e+03 1.66e+01 bond pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " ideal model delta sigma weight residual 1.808 1.888 -0.080 3.30e-02 9.18e+02 5.93e+00 bond pdb=" C1 NAG B1313 " pdb=" O5 NAG B1313 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C PHE B1095 " pdb=" N VAL B1096 " ideal model delta sigma weight residual 1.334 1.311 0.023 1.29e-02 6.01e+03 3.28e+00 ... (remaining 27347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 36811 2.81 - 5.61: 409 5.61 - 8.42: 14 8.42 - 11.22: 3 11.22 - 14.03: 1 Bond angle restraints: 37238 Sorted by residual: angle pdb=" CA CYS C 166 " pdb=" CB CYS C 166 " pdb=" SG CYS C 166 " ideal model delta sigma weight residual 114.40 128.43 -14.03 2.30e+00 1.89e-01 3.72e+01 angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 124.71 -10.31 2.30e+00 1.89e-01 2.01e+01 angle pdb=" N CYS C 166 " pdb=" CA CYS C 166 " pdb=" C CYS C 166 " ideal model delta sigma weight residual 108.73 115.14 -6.41 1.63e+00 3.76e-01 1.55e+01 angle pdb=" N ILE C1115 " pdb=" CA ILE C1115 " pdb=" C ILE C1115 " ideal model delta sigma weight residual 106.21 110.23 -4.02 1.07e+00 8.73e-01 1.41e+01 angle pdb=" C ASN B 125 " pdb=" N VAL B 126 " pdb=" CA VAL B 126 " ideal model delta sigma weight residual 120.49 125.40 -4.91 1.38e+00 5.25e-01 1.26e+01 ... (remaining 37233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 15280 21.49 - 42.98: 1314 42.98 - 64.47: 288 64.47 - 85.96: 45 85.96 - 107.45: 21 Dihedral angle restraints: 16948 sinusoidal: 7127 harmonic: 9821 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.54 -87.46 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 1.13 -87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 7.63 85.37 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 16945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3386 0.054 - 0.109: 918 0.109 - 0.163: 115 0.163 - 0.217: 15 0.217 - 0.272: 3 Chirality restraints: 4437 Sorted by residual: chirality pdb=" CA CYS C 166 " pdb=" N CYS C 166 " pdb=" C CYS C 166 " pdb=" CB CYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 4434 not shown) Planarity restraints: 4757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO A 85 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO C 85 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO B 986 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.025 5.00e-02 4.00e+02 ... (remaining 4754 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 647 2.63 - 3.20: 25701 3.20 - 3.77: 40481 3.77 - 4.33: 55343 4.33 - 4.90: 92006 Nonbonded interactions: 214178 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.068 3.040 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.119 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.139 3.040 nonbonded pdb=" O VAL S 51 " pdb=" OG SER S 63 " model vdw 2.155 3.040 ... (remaining 214173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) or \ resid 116 through 124 or (resid 125 and (name N or name CA or name C or name O o \ r name CB )) or resid 126 through 131 or (resid 132 and (name N or name CA or na \ me C or name O or name CB )) or resid 133 or (resid 134 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 66 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB )) or resid 186 through 196 or resid 200 through 211 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 308 or (resid 309 and (name N or name CA or \ name C or name O or name CB )) or resid 310 through 332 or (resid 333 and (name \ N or name CA or name C or name O or name CB )) or resid 334 through 458 or resid \ 460 through 518 or resid 520 through 528 or (resid 529 and (name N or name CA o \ r name C or name O or name CB )) or resid 530 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 through 793 or (re \ sid 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or \ (resid 796 and (name N or name CA or name C or name O or name CB )) or resid 79 \ 7 through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 through 1311)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 166 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 339 or (resid 340 and (name N or name CA or name C or name O or \ name CB )) or resid 341 through 344 or (resid 345 and (name N or name CA or name \ C or name O or name CB )) or resid 346 through 404 or (resid 405 through 406 an \ d (name N or name CA or name C or name O or name CB )) or resid 407 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 419 or (resid 420 and (name N or name CA or name C or name O or name \ CB )) or resid 421 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 through 439 or (resid 440 and (name N or nam \ e CA or name C or name O or name CB )) or resid 441 or (resid 442 and (name N or \ name CA or name C or name O or name CB )) or resid 448 through 457 or (resid 45 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 460 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or re \ sid 466 through 470 or resid 490 through 501 or resid 503 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throug \ h 517 or (resid 518 through 520 and (name N or name CA or name C or name O or na \ me CB )) or resid 521 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 or \ (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 2 through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA o \ r name C or name O or name CB )) or resid 587 through 613 or (resid 614 and (nam \ e N or name CA or name C or name O or name CB )) or resid 615 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 th \ rough 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name \ C or name O or name CB )) or resid 746 through 827 or (resid 855 and (name N or \ name CA or name C or name O or name CB )) or resid 856 through 920 or (resid 921 \ and (name N or name CA or name C or name O or name CB )) or resid 922 through 1 \ 072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or r \ esid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name O \ or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 through 1314)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 166 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 339 or (resid 340 and (name N or name CA or name C or name O or \ name CB )) or resid 341 through 344 or (resid 345 and (name N or name CA or name \ C or name O or name CB )) or resid 346 through 404 or (resid 405 through 406 an \ d (name N or name CA or name C or name O or name CB )) or resid 407 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 419 or (resid 420 and (name N or name CA or name C or name O or name \ CB )) or resid 421 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 through 439 or (resid 440 and (name N or nam \ e CA or name C or name O or name CB )) or resid 441 or (resid 442 and (name N or \ name CA or name C or name O or name CB )) or resid 448 through 457 or (resid 45 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 460 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or re \ sid 466 through 470 or resid 490 through 501 or resid 503 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throug \ h 517 or (resid 518 through 520 and (name N or name CA or name C or name O or na \ me CB )) or resid 521 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 or \ (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 2 through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA o \ r name C or name O or name CB )) or resid 587 through 613 or (resid 614 and (nam \ e N or name CA or name C or name O or name CB )) or resid 615 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 th \ rough 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name \ C or name O or name CB )) or resid 746 through 827 or (resid 855 and (name N or \ name CA or name C or name O or name CB )) or resid 856 through 920 or (resid 921 \ and (name N or name CA or name C or name O or name CB )) or resid 922 through 1 \ 072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or r \ esid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name O \ or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 through 1321)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'N' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) } ncs_group { reference = chain 'L' selection = chain 'S' } 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=0.33 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.440 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 0.080 27453 Z= 0.355 Angle : 0.795 14.027 37495 Z= 0.422 Chirality : 0.049 0.272 4437 Planarity : 0.004 0.073 4714 Dihedral : 16.326 107.448 10520 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.64 % Favored : 88.27 % Rotamer: Outliers : 8.41 % Allowed : 18.80 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.12), residues: 3313 helix: -1.00 (0.17), residues: 679 sheet: -3.34 (0.17), residues: 708 loop : -3.53 (0.11), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.020 0.002 TYR A 265 PHE 0.031 0.002 PHE C 238 TRP 0.011 0.002 TRP H 98 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00805 (27352) covalent geometry : angle 0.77162 (37238) SS BOND : bond 0.00842 ( 40) SS BOND : angle 2.35163 ( 80) hydrogen bonds : bond 0.20125 ( 867) hydrogen bonds : angle 8.93045 ( 2388) Misc. bond : bond 0.00096 ( 2) link_BETA1-4 : bond 0.00506 ( 13) link_BETA1-4 : angle 2.30699 ( 39) link_BETA1-6 : bond 0.00226 ( 3) link_BETA1-6 : angle 2.03005 ( 9) link_NAG-ASN : bond 0.00434 ( 43) link_NAG-ASN : angle 2.51204 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 203 time to evaluate : 0.920 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: A 40 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8222 (p0) REVERT: A 96 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6486 (pt0) REVERT: A 235 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6372 (mt) REVERT: A 984 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7902 (tp) REVERT: B 104 TRP cc_start: 0.7566 (m-90) cc_final: 0.7352 (m-90) REVERT: B 242 LEU cc_start: 0.8003 (mt) cc_final: 0.7795 (tp) REVERT: B 453 TYR cc_start: 0.7567 (p90) cc_final: 0.7322 (p90) REVERT: C 195 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7374 (ptmt) REVERT: C 444 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5601 (tmmt) REVERT: C 457 ARG cc_start: 0.7050 (tpt170) cc_final: 0.6687 (ttp-170) REVERT: C 464 PHE cc_start: 0.7483 (m-80) cc_final: 0.7157 (m-80) REVERT: C 1141 LEU cc_start: 0.8511 (tp) cc_final: 0.7930 (tt) REVERT: H 34 MET cc_start: 0.5596 (tpp) cc_final: 0.5343 (tpp) REVERT: H 66 ARG cc_start: 0.6207 (mtm110) cc_final: 0.5887 (mtp-110) REVERT: N 38 ARG cc_start: 0.5510 (ptp-170) cc_final: 0.5105 (ptm-80) REVERT: N 79 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5994 (t80) REVERT: L 96 VAL cc_start: 0.5697 (p) cc_final: 0.5230 (t) REVERT: S 49 TYR cc_start: 0.4409 (p90) cc_final: 0.4087 (p90) REVERT: S 50 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6884 (mt-10) REVERT: S 95 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7382 (t80) outliers start: 238 outliers final: 174 residues processed: 436 average time/residue: 0.1593 time to fit residues: 113.8599 Evaluate side-chains 332 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 151 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 20.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 437 ASN A 675 GLN A 804 GLN A 901 GLN A 935 GLN A1005 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 196 ASN B 207 HIS B 501 ASN B 675 GLN B 762 GLN B 926 GLN B 955 ASN B1071 GLN C 207 HIS C 422 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C 969 ASN C1071 GLN C1106 GLN H 32 ASN N 32 ASN N 39 GLN N 81 GLN ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.121782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080964 restraints weight = 100785.164| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.49 r_work: 0.3133 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 27453 Z= 0.133 Angle : 0.668 13.884 37495 Z= 0.341 Chirality : 0.047 0.338 4437 Planarity : 0.005 0.070 4714 Dihedral : 10.547 63.242 5108 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 5.02 % Allowed : 21.02 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.13), residues: 3313 helix: 0.85 (0.19), residues: 680 sheet: -2.71 (0.18), residues: 702 loop : -2.76 (0.12), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 38 TYR 0.042 0.002 TYR L 91 PHE 0.029 0.001 PHE A 392 TRP 0.024 0.002 TRP N 103 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00292 (27352) covalent geometry : angle 0.64488 (37238) SS BOND : bond 0.00477 ( 40) SS BOND : angle 2.53986 ( 80) hydrogen bonds : bond 0.04751 ( 867) hydrogen bonds : angle 6.66964 ( 2388) Misc. bond : bond 0.00729 ( 2) link_BETA1-4 : bond 0.00385 ( 13) link_BETA1-4 : angle 1.87823 ( 39) link_BETA1-6 : bond 0.00131 ( 3) link_BETA1-6 : angle 1.53150 ( 9) link_NAG-ASN : bond 0.00409 ( 43) link_NAG-ASN : angle 2.13727 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 175 time to evaluate : 1.330 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 96 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6713 (pt0) REVERT: A 214 ARG cc_start: 0.8898 (tpt170) cc_final: 0.8275 (tpp80) REVERT: A 574 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6235 (t70) REVERT: B 104 TRP cc_start: 0.7291 (m-90) cc_final: 0.7067 (m-90) REVERT: B 188 ASN cc_start: 0.7224 (t0) cc_final: 0.6912 (t0) REVERT: B 332 ILE cc_start: 0.8389 (tp) cc_final: 0.8161 (tt) REVERT: B 451 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.3876 (t80) REVERT: B 501 ASN cc_start: 0.6277 (OUTLIER) cc_final: 0.6059 (t0) REVERT: C 326 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7516 (tt) REVERT: C 456 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: C 457 ARG cc_start: 0.6960 (tpt170) cc_final: 0.6358 (tmm-80) REVERT: C 464 PHE cc_start: 0.7421 (m-80) cc_final: 0.6922 (m-80) REVERT: C 505 TYR cc_start: 0.6750 (m-80) cc_final: 0.6516 (m-80) REVERT: C 1141 LEU cc_start: 0.8225 (tp) cc_final: 0.7746 (tt) REVERT: H 34 MET cc_start: 0.5959 (tpp) cc_final: 0.5707 (tpp) REVERT: H 38 ARG cc_start: 0.5381 (ptm160) cc_final: 0.5151 (ptm160) REVERT: H 98 TRP cc_start: 0.7016 (OUTLIER) cc_final: 0.6776 (p90) REVERT: N 38 ARG cc_start: 0.5274 (ptp-170) cc_final: 0.4925 (ptm-80) REVERT: N 79 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5687 (t80) REVERT: N 86 ASP cc_start: 0.2701 (m-30) cc_final: 0.2437 (m-30) REVERT: L 50 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: L 54 ARG cc_start: 0.5732 (ptp-110) cc_final: 0.5279 (mtp180) REVERT: S 35 TRP cc_start: 0.5768 (OUTLIER) cc_final: 0.5338 (m-10) outliers start: 142 outliers final: 75 residues processed: 304 average time/residue: 0.1656 time to fit residues: 82.0591 Evaluate side-chains 229 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 145 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 TRP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 235 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.118945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080624 restraints weight = 94988.995| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.44 r_work: 0.3088 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 27453 Z= 0.278 Angle : 0.714 12.482 37495 Z= 0.361 Chirality : 0.048 0.326 4437 Planarity : 0.005 0.057 4714 Dihedral : 9.397 59.787 4924 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.80 % Favored : 92.14 % Rotamer: Outliers : 5.37 % Allowed : 21.34 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.13), residues: 3313 helix: 1.00 (0.19), residues: 682 sheet: -2.55 (0.18), residues: 742 loop : -2.60 (0.12), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 38 TYR 0.029 0.002 TYR L 87 PHE 0.025 0.002 PHE C 238 TRP 0.030 0.002 TRP B 436 HIS 0.004 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00658 (27352) covalent geometry : angle 0.69060 (37238) SS BOND : bond 0.00739 ( 40) SS BOND : angle 2.67776 ( 80) hydrogen bonds : bond 0.05088 ( 867) hydrogen bonds : angle 6.48833 ( 2388) Misc. bond : bond 0.00283 ( 2) link_BETA1-4 : bond 0.00299 ( 13) link_BETA1-4 : angle 1.89513 ( 39) link_BETA1-6 : bond 0.00084 ( 3) link_BETA1-6 : angle 1.69269 ( 9) link_NAG-ASN : bond 0.00402 ( 43) link_NAG-ASN : angle 2.15257 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 153 time to evaluate : 0.966 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: A 96 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6617 (pt0) REVERT: A 214 ARG cc_start: 0.8883 (tpt170) cc_final: 0.8292 (tpp80) REVERT: A 525 CYS cc_start: 0.2366 (OUTLIER) cc_final: 0.2082 (m) REVERT: A 574 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6834 (t70) REVERT: B 104 TRP cc_start: 0.7443 (m-90) cc_final: 0.7126 (m-90) REVERT: B 188 ASN cc_start: 0.7412 (t0) cc_final: 0.7157 (t0) REVERT: B 451 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.4031 (t80) REVERT: C 326 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7454 (tt) REVERT: C 346 ARG cc_start: 0.8442 (tpt170) cc_final: 0.7708 (tpm170) REVERT: C 456 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: C 457 ARG cc_start: 0.6957 (tpt170) cc_final: 0.6423 (tmm-80) REVERT: C 464 PHE cc_start: 0.7423 (m-80) cc_final: 0.6908 (m-80) REVERT: C 505 TYR cc_start: 0.6683 (m-80) cc_final: 0.6319 (m-80) REVERT: C 1141 LEU cc_start: 0.8269 (tp) cc_final: 0.7771 (tt) REVERT: H 90 TYR cc_start: 0.4087 (m-10) cc_final: 0.3331 (m-10) REVERT: N 38 ARG cc_start: 0.5189 (ptp-170) cc_final: 0.4872 (ptm-80) REVERT: N 59 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.6104 (t80) REVERT: L 31 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6735 (ptpp) REVERT: L 54 ARG cc_start: 0.5720 (ptp-110) cc_final: 0.5355 (mtp180) REVERT: S 35 TRP cc_start: 0.5557 (OUTLIER) cc_final: 0.5064 (m-10) REVERT: S 47 MET cc_start: 0.2362 (mtt) cc_final: 0.2058 (mtp) outliers start: 152 outliers final: 100 residues processed: 295 average time/residue: 0.1548 time to fit residues: 75.8104 Evaluate side-chains 251 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 143 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 74 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 297 optimal weight: 30.0000 chunk 159 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 0.0670 chunk 96 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 289 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 501 ASN C 394 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.121623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080225 restraints weight = 98215.192| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.26 r_work: 0.3143 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 27453 Z= 0.143 Angle : 0.619 10.121 37495 Z= 0.311 Chirality : 0.045 0.312 4437 Planarity : 0.004 0.049 4714 Dihedral : 8.655 59.839 4913 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 5.12 % Allowed : 21.52 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3313 helix: 1.56 (0.20), residues: 671 sheet: -2.31 (0.18), residues: 719 loop : -2.32 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 38 TYR 0.021 0.001 TYR L 91 PHE 0.019 0.001 PHE A 392 TRP 0.029 0.002 TRP H 98 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00326 (27352) covalent geometry : angle 0.59910 (37238) SS BOND : bond 0.00631 ( 40) SS BOND : angle 2.07852 ( 80) hydrogen bonds : bond 0.04316 ( 867) hydrogen bonds : angle 6.09512 ( 2388) Misc. bond : bond 0.00205 ( 2) link_BETA1-4 : bond 0.00461 ( 13) link_BETA1-4 : angle 1.80455 ( 39) link_BETA1-6 : bond 0.00199 ( 3) link_BETA1-6 : angle 1.47793 ( 9) link_NAG-ASN : bond 0.00336 ( 43) link_NAG-ASN : angle 1.96835 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 160 time to evaluate : 0.964 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 96 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6654 (pt0) REVERT: A 214 ARG cc_start: 0.8864 (tpt170) cc_final: 0.8306 (tpp80) REVERT: A 525 CYS cc_start: 0.2054 (OUTLIER) cc_final: 0.1787 (m) REVERT: A 574 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6570 (t70) REVERT: B 104 TRP cc_start: 0.7340 (m-90) cc_final: 0.7097 (m-90) REVERT: B 188 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.7136 (t0) REVERT: B 200 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.3935 (p90) REVERT: B 242 LEU cc_start: 0.8100 (mt) cc_final: 0.7135 (mp) REVERT: B 451 TYR cc_start: 0.5633 (OUTLIER) cc_final: 0.4086 (t80) REVERT: B 517 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7840 (pt) REVERT: B 752 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9067 (tt) REVERT: B 762 GLN cc_start: 0.8876 (tt0) cc_final: 0.8453 (tp40) REVERT: C 346 ARG cc_start: 0.8483 (tpt170) cc_final: 0.8160 (tpp80) REVERT: C 456 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: C 457 ARG cc_start: 0.6852 (tpt170) cc_final: 0.6118 (tmm-80) REVERT: C 464 PHE cc_start: 0.7414 (m-80) cc_final: 0.6905 (m-80) REVERT: C 1141 LEU cc_start: 0.8288 (tp) cc_final: 0.7804 (tt) REVERT: H 6 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: H 99 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8528 (mm-30) REVERT: N 38 ARG cc_start: 0.5190 (ptp-170) cc_final: 0.4846 (ptm-80) REVERT: N 59 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.6136 (t80) REVERT: N 79 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.5407 (t80) REVERT: L 30 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.4089 (p90) REVERT: L 54 ARG cc_start: 0.5768 (ptp-110) cc_final: 0.5265 (mtp180) REVERT: L 91 TYR cc_start: 0.5273 (t80) cc_final: 0.4841 (t80) REVERT: S 35 TRP cc_start: 0.5919 (m-10) cc_final: 0.5494 (m-10) outliers start: 145 outliers final: 93 residues processed: 294 average time/residue: 0.1625 time to fit residues: 78.3094 Evaluate side-chains 247 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 142 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 205 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 303 optimal weight: 50.0000 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 293 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077827 restraints weight = 110329.264| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.55 r_work: 0.3087 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 27453 Z= 0.240 Angle : 0.667 11.503 37495 Z= 0.335 Chirality : 0.046 0.264 4437 Planarity : 0.004 0.051 4714 Dihedral : 8.411 59.961 4907 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.29 % Favored : 92.68 % Rotamer: Outliers : 5.23 % Allowed : 22.33 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.14), residues: 3313 helix: 1.54 (0.20), residues: 662 sheet: -2.15 (0.18), residues: 718 loop : -2.26 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 190 TYR 0.023 0.002 TYR L 32 PHE 0.022 0.002 PHE C 238 TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00569 (27352) covalent geometry : angle 0.64328 (37238) SS BOND : bond 0.00784 ( 40) SS BOND : angle 2.75327 ( 80) hydrogen bonds : bond 0.04578 ( 867) hydrogen bonds : angle 6.11449 ( 2388) Misc. bond : bond 0.00156 ( 2) link_BETA1-4 : bond 0.00351 ( 13) link_BETA1-4 : angle 1.79981 ( 39) link_BETA1-6 : bond 0.00055 ( 3) link_BETA1-6 : angle 1.62212 ( 9) link_NAG-ASN : bond 0.00345 ( 43) link_NAG-ASN : angle 2.00918 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 143 time to evaluate : 1.021 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 96 GLU cc_start: 0.7758 (mm-30) cc_final: 0.6640 (pt0) REVERT: A 168 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8050 (t80) REVERT: A 214 ARG cc_start: 0.8900 (tpt170) cc_final: 0.8320 (tpp80) REVERT: A 525 CYS cc_start: 0.2151 (OUTLIER) cc_final: 0.1867 (m) REVERT: A 574 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6792 (t70) REVERT: B 104 TRP cc_start: 0.7456 (m-90) cc_final: 0.7181 (m-90) REVERT: B 188 ASN cc_start: 0.7312 (t0) cc_final: 0.6990 (t0) REVERT: B 200 TYR cc_start: 0.5157 (OUTLIER) cc_final: 0.3900 (p90) REVERT: B 242 LEU cc_start: 0.8217 (mt) cc_final: 0.7222 (mp) REVERT: B 451 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.4224 (t80) REVERT: B 762 GLN cc_start: 0.8979 (tt0) cc_final: 0.8561 (tp40) REVERT: C 449 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7565 (t80) REVERT: C 457 ARG cc_start: 0.6844 (tpt170) cc_final: 0.6114 (tmm-80) REVERT: C 464 PHE cc_start: 0.7438 (m-80) cc_final: 0.6917 (m-80) REVERT: C 1141 LEU cc_start: 0.8267 (tp) cc_final: 0.7770 (tt) REVERT: H 99 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8495 (mm-30) REVERT: N 38 ARG cc_start: 0.5129 (ptp-170) cc_final: 0.4758 (ptm-80) REVERT: N 59 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6175 (t80) REVERT: N 79 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5368 (t80) REVERT: L 54 ARG cc_start: 0.5793 (ptp-110) cc_final: 0.5313 (mtp180) REVERT: L 61 ARG cc_start: 0.6831 (mtm180) cc_final: 0.6508 (mtt180) REVERT: S 35 TRP cc_start: 0.5863 (m-10) cc_final: 0.5296 (m-10) outliers start: 148 outliers final: 115 residues processed: 279 average time/residue: 0.1542 time to fit residues: 71.2603 Evaluate side-chains 254 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 131 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 303 optimal weight: 50.0000 chunk 113 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 51 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 290 optimal weight: 0.5980 chunk 270 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 324 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.118258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075686 restraints weight = 104930.708| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.67 r_work: 0.3009 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27453 Z= 0.119 Angle : 0.621 22.780 37495 Z= 0.306 Chirality : 0.047 1.024 4437 Planarity : 0.004 0.045 4714 Dihedral : 7.983 59.423 4906 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 4.38 % Allowed : 23.18 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.14), residues: 3313 helix: 1.81 (0.20), residues: 663 sheet: -2.04 (0.19), residues: 700 loop : -2.04 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.039 0.001 TYR L 30 PHE 0.023 0.001 PHE A 392 TRP 0.017 0.001 TRP B 436 HIS 0.015 0.001 HIS S 39 Details of bonding type rmsd covalent geometry : bond 0.00265 (27352) covalent geometry : angle 0.58511 (37238) SS BOND : bond 0.00652 ( 40) SS BOND : angle 2.43303 ( 80) hydrogen bonds : bond 0.04036 ( 867) hydrogen bonds : angle 5.80673 ( 2388) Misc. bond : bond 0.00157 ( 2) link_BETA1-4 : bond 0.00405 ( 13) link_BETA1-4 : angle 1.67986 ( 39) link_BETA1-6 : bond 0.00192 ( 3) link_BETA1-6 : angle 1.43599 ( 9) link_NAG-ASN : bond 0.00494 ( 43) link_NAG-ASN : angle 2.95888 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 146 time to evaluate : 1.439 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: A 96 GLU cc_start: 0.7825 (mm-30) cc_final: 0.6557 (pt0) REVERT: A 133 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.4443 (m-80) REVERT: A 168 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (t80) REVERT: A 214 ARG cc_start: 0.8994 (tpt170) cc_final: 0.8248 (tpp80) REVERT: A 525 CYS cc_start: 0.1878 (OUTLIER) cc_final: 0.1662 (m) REVERT: A 574 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6224 (t70) REVERT: A 902 MET cc_start: 0.9362 (tpt) cc_final: 0.9011 (tpt) REVERT: B 104 TRP cc_start: 0.7388 (m-90) cc_final: 0.7103 (m-90) REVERT: B 188 ASN cc_start: 0.7312 (t0) cc_final: 0.7002 (t0) REVERT: B 200 TYR cc_start: 0.5275 (OUTLIER) cc_final: 0.4021 (p90) REVERT: B 242 LEU cc_start: 0.8144 (mt) cc_final: 0.7268 (mp) REVERT: B 451 TYR cc_start: 0.5489 (OUTLIER) cc_final: 0.4245 (t80) REVERT: B 762 GLN cc_start: 0.8846 (tt0) cc_final: 0.8311 (tp40) REVERT: C 346 ARG cc_start: 0.8491 (tpt170) cc_final: 0.8149 (tpp80) REVERT: C 449 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7616 (t80) REVERT: C 457 ARG cc_start: 0.6869 (tpt170) cc_final: 0.6153 (tmm-80) REVERT: C 464 PHE cc_start: 0.7437 (m-80) cc_final: 0.6891 (m-80) REVERT: C 563 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8695 (mt0) REVERT: C 1141 LEU cc_start: 0.8172 (tp) cc_final: 0.7699 (tt) REVERT: N 59 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6330 (t80) REVERT: N 79 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5122 (t80) REVERT: L 6 GLN cc_start: 0.5222 (OUTLIER) cc_final: 0.4717 (mp10) REVERT: L 31 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.5818 (pttp) REVERT: L 54 ARG cc_start: 0.5751 (ptp-110) cc_final: 0.5295 (mtp180) REVERT: L 61 ARG cc_start: 0.6765 (mtm180) cc_final: 0.6484 (mtt180) REVERT: S 35 TRP cc_start: 0.6131 (m-10) cc_final: 0.5609 (m-10) REVERT: S 36 TYR cc_start: 0.5244 (m-80) cc_final: 0.4968 (m-80) outliers start: 124 outliers final: 91 residues processed: 261 average time/residue: 0.1529 time to fit residues: 66.2840 Evaluate side-chains 243 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 140 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 262 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 205 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.117826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078727 restraints weight = 112358.219| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.98 r_work: 0.2997 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27453 Z= 0.135 Angle : 0.602 17.574 37495 Z= 0.298 Chirality : 0.046 0.753 4437 Planarity : 0.004 0.044 4714 Dihedral : 7.671 59.991 4896 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 4.35 % Allowed : 23.07 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3313 helix: 1.84 (0.20), residues: 672 sheet: -1.91 (0.19), residues: 716 loop : -1.94 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.030 0.001 TYR L 30 PHE 0.022 0.001 PHE A 392 TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00314 (27352) covalent geometry : angle 0.56904 (37238) SS BOND : bond 0.00543 ( 40) SS BOND : angle 2.64336 ( 80) hydrogen bonds : bond 0.03950 ( 867) hydrogen bonds : angle 5.67075 ( 2388) Misc. bond : bond 0.00122 ( 2) link_BETA1-4 : bond 0.00416 ( 13) link_BETA1-4 : angle 1.66710 ( 39) link_BETA1-6 : bond 0.00171 ( 3) link_BETA1-6 : angle 1.46687 ( 9) link_NAG-ASN : bond 0.00378 ( 43) link_NAG-ASN : angle 2.54884 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 154 time to evaluate : 0.909 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 96 GLU cc_start: 0.7790 (mm-30) cc_final: 0.6534 (pt0) REVERT: A 214 ARG cc_start: 0.8994 (tpt170) cc_final: 0.8292 (tpp80) REVERT: A 525 CYS cc_start: 0.2134 (OUTLIER) cc_final: 0.1855 (m) REVERT: A 574 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6364 (t70) REVERT: A 902 MET cc_start: 0.9363 (tpt) cc_final: 0.9063 (tpt) REVERT: B 104 TRP cc_start: 0.7380 (m-90) cc_final: 0.7090 (m-90) REVERT: B 188 ASN cc_start: 0.7406 (t0) cc_final: 0.7167 (t0) REVERT: B 200 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.4020 (p90) REVERT: B 242 LEU cc_start: 0.8196 (mt) cc_final: 0.7340 (mp) REVERT: B 451 TYR cc_start: 0.5482 (OUTLIER) cc_final: 0.4368 (t80) REVERT: B 762 GLN cc_start: 0.8812 (tt0) cc_final: 0.8318 (tp40) REVERT: B 1029 MET cc_start: 0.8938 (tpp) cc_final: 0.8631 (ttm) REVERT: C 346 ARG cc_start: 0.8529 (tpt170) cc_final: 0.8203 (tpp80) REVERT: C 449 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7567 (t80) REVERT: C 457 ARG cc_start: 0.6803 (tpt170) cc_final: 0.6086 (tmm-80) REVERT: C 464 PHE cc_start: 0.7451 (m-80) cc_final: 0.7114 (m-80) REVERT: C 563 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8693 (mt0) REVERT: C 1141 LEU cc_start: 0.8176 (tp) cc_final: 0.7710 (tt) REVERT: N 59 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6391 (t80) REVERT: L 6 GLN cc_start: 0.5074 (OUTLIER) cc_final: 0.4496 (mp10) REVERT: L 31 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.5801 (pttp) REVERT: L 61 ARG cc_start: 0.6664 (mtm180) cc_final: 0.6428 (mtt180) REVERT: S 36 TYR cc_start: 0.5330 (m-80) cc_final: 0.5057 (m-80) REVERT: S 50 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6525 (mp0) outliers start: 123 outliers final: 96 residues processed: 265 average time/residue: 0.1567 time to fit residues: 68.4499 Evaluate side-chains 248 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 143 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 259 optimal weight: 0.0470 chunk 50 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075848 restraints weight = 106131.461| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.65 r_work: 0.3013 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27453 Z= 0.130 Angle : 0.604 15.832 37495 Z= 0.298 Chirality : 0.045 0.659 4437 Planarity : 0.004 0.042 4714 Dihedral : 7.494 59.909 4891 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 4.10 % Allowed : 23.25 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3313 helix: 1.88 (0.20), residues: 672 sheet: -1.79 (0.19), residues: 728 loop : -1.84 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 66 TYR 0.031 0.001 TYR C 423 PHE 0.036 0.001 PHE B 497 TRP 0.027 0.001 TRP S 35 HIS 0.008 0.001 HIS S 39 Details of bonding type rmsd covalent geometry : bond 0.00302 (27352) covalent geometry : angle 0.57414 (37238) SS BOND : bond 0.00509 ( 40) SS BOND : angle 2.57132 ( 80) hydrogen bonds : bond 0.03880 ( 867) hydrogen bonds : angle 5.57827 ( 2388) Misc. bond : bond 0.00124 ( 2) link_BETA1-4 : bond 0.00378 ( 13) link_BETA1-4 : angle 1.62171 ( 39) link_BETA1-6 : bond 0.00170 ( 3) link_BETA1-6 : angle 1.45204 ( 9) link_NAG-ASN : bond 0.00370 ( 43) link_NAG-ASN : angle 2.39968 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 147 time to evaluate : 0.970 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 96 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6445 (pt0) REVERT: A 214 ARG cc_start: 0.8971 (tpt170) cc_final: 0.8295 (tpp80) REVERT: A 574 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6297 (t70) REVERT: A 902 MET cc_start: 0.9366 (tpt) cc_final: 0.8986 (tpt) REVERT: A 983 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8806 (mtp85) REVERT: B 104 TRP cc_start: 0.7358 (m-90) cc_final: 0.7105 (m-90) REVERT: B 188 ASN cc_start: 0.7407 (t0) cc_final: 0.7162 (t0) REVERT: B 200 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.4137 (p90) REVERT: B 242 LEU cc_start: 0.8212 (mt) cc_final: 0.7370 (mp) REVERT: B 451 TYR cc_start: 0.5429 (OUTLIER) cc_final: 0.4495 (t80) REVERT: B 762 GLN cc_start: 0.8759 (tt0) cc_final: 0.8296 (tp40) REVERT: B 1029 MET cc_start: 0.8933 (tpp) cc_final: 0.8629 (ttm) REVERT: C 346 ARG cc_start: 0.8533 (tpt170) cc_final: 0.8201 (tpp80) REVERT: C 449 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 456 PHE cc_start: 0.8167 (m-80) cc_final: 0.7585 (m-80) REVERT: C 457 ARG cc_start: 0.6773 (tpt170) cc_final: 0.6102 (tmm-80) REVERT: C 464 PHE cc_start: 0.7496 (m-80) cc_final: 0.6934 (m-80) REVERT: C 563 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8693 (mt0) REVERT: C 1141 LEU cc_start: 0.8173 (tp) cc_final: 0.7709 (tt) REVERT: N 59 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6515 (t80) REVERT: L 6 GLN cc_start: 0.5320 (OUTLIER) cc_final: 0.4858 (mp10) REVERT: L 31 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5714 (pttp) REVERT: L 54 ARG cc_start: 0.5905 (ptp-110) cc_final: 0.5375 (ttm170) REVERT: L 61 ARG cc_start: 0.6646 (mtm180) cc_final: 0.6273 (mtt180) REVERT: S 35 TRP cc_start: 0.5879 (m-10) cc_final: 0.5644 (m-10) REVERT: S 36 TYR cc_start: 0.5204 (m-80) cc_final: 0.4981 (m-10) REVERT: S 50 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6485 (mp0) outliers start: 116 outliers final: 96 residues processed: 255 average time/residue: 0.1569 time to fit residues: 65.4468 Evaluate side-chains 242 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 137 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 176 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 317 optimal weight: 30.0000 chunk 26 optimal weight: 0.0370 chunk 133 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 306 optimal weight: 40.0000 chunk 246 optimal weight: 0.5980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1088 HIS C 437 ASN ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.121506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079629 restraints weight = 91302.053| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.80 r_work: 0.2996 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 27453 Z= 0.106 Angle : 0.582 14.414 37495 Z= 0.288 Chirality : 0.045 0.578 4437 Planarity : 0.004 0.041 4714 Dihedral : 7.253 59.589 4888 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 4.03 % Allowed : 23.50 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3313 helix: 1.85 (0.20), residues: 691 sheet: -1.62 (0.19), residues: 733 loop : -1.74 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.029 0.001 TYR B 369 PHE 0.057 0.001 PHE B 497 TRP 0.027 0.001 TRP S 35 HIS 0.020 0.001 HIS S 39 Details of bonding type rmsd covalent geometry : bond 0.00234 (27352) covalent geometry : angle 0.55907 (37238) SS BOND : bond 0.00477 ( 40) SS BOND : angle 1.95910 ( 80) hydrogen bonds : bond 0.03676 ( 867) hydrogen bonds : angle 5.45252 ( 2388) Misc. bond : bond 0.00123 ( 2) link_BETA1-4 : bond 0.00423 ( 13) link_BETA1-4 : angle 1.58722 ( 39) link_BETA1-6 : bond 0.00251 ( 3) link_BETA1-6 : angle 1.38192 ( 9) link_NAG-ASN : bond 0.00384 ( 43) link_NAG-ASN : angle 2.24073 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 142 time to evaluate : 1.017 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: A 96 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6391 (pt0) REVERT: A 214 ARG cc_start: 0.8988 (tpt170) cc_final: 0.8256 (tpp80) REVERT: A 574 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5834 (t70) REVERT: A 983 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8848 (mtp85) REVERT: B 104 TRP cc_start: 0.7262 (m-90) cc_final: 0.6955 (m-90) REVERT: B 188 ASN cc_start: 0.7292 (t0) cc_final: 0.7008 (t0) REVERT: B 200 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.4199 (p90) REVERT: B 242 LEU cc_start: 0.8257 (mt) cc_final: 0.7505 (mp) REVERT: B 451 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.4860 (t80) REVERT: B 1029 MET cc_start: 0.8736 (tpp) cc_final: 0.8431 (ttm) REVERT: C 346 ARG cc_start: 0.8546 (tpt170) cc_final: 0.8206 (tpp80) REVERT: C 449 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7668 (t80) REVERT: C 457 ARG cc_start: 0.6725 (tpt170) cc_final: 0.6053 (tmm-80) REVERT: C 464 PHE cc_start: 0.7462 (m-80) cc_final: 0.6876 (m-80) REVERT: C 563 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: C 1141 LEU cc_start: 0.8125 (tp) cc_final: 0.7683 (tt) REVERT: N 59 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6460 (t80) REVERT: L 6 GLN cc_start: 0.5291 (OUTLIER) cc_final: 0.5030 (mp10) REVERT: L 31 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5625 (pttp) REVERT: L 61 ARG cc_start: 0.6560 (mtm180) cc_final: 0.6310 (mtm180) REVERT: L 98 PHE cc_start: 0.6144 (t80) cc_final: 0.5742 (t80) REVERT: S 50 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6516 (mp0) outliers start: 114 outliers final: 87 residues processed: 247 average time/residue: 0.1577 time to fit residues: 64.2505 Evaluate side-chains 223 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 127 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 95 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 32 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN C 188 ASN ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078304 restraints weight = 92803.110| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.99 r_work: 0.3112 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 27453 Z= 0.234 Angle : 0.664 14.051 37495 Z= 0.329 Chirality : 0.046 0.570 4437 Planarity : 0.004 0.046 4714 Dihedral : 7.453 58.900 4883 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 3.67 % Allowed : 23.89 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3313 helix: 1.67 (0.20), residues: 681 sheet: -1.72 (0.19), residues: 739 loop : -1.80 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.031 0.002 TYR S 36 PHE 0.047 0.002 PHE B 497 TRP 0.043 0.002 TRP S 35 HIS 0.004 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00556 (27352) covalent geometry : angle 0.63821 (37238) SS BOND : bond 0.00626 ( 40) SS BOND : angle 2.58765 ( 80) hydrogen bonds : bond 0.04277 ( 867) hydrogen bonds : angle 5.67391 ( 2388) Misc. bond : bond 0.00016 ( 2) link_BETA1-4 : bond 0.00279 ( 13) link_BETA1-4 : angle 1.65391 ( 39) link_BETA1-6 : bond 0.00039 ( 3) link_BETA1-6 : angle 1.59656 ( 9) link_NAG-ASN : bond 0.00385 ( 43) link_NAG-ASN : angle 2.32614 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 135 time to evaluate : 0.911 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 96 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6477 (pt0) REVERT: A 214 ARG cc_start: 0.8788 (tpt170) cc_final: 0.8222 (tpp80) REVERT: A 574 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6942 (t70) REVERT: A 585 LEU cc_start: 0.5043 (OUTLIER) cc_final: 0.4638 (pp) REVERT: A 983 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8879 (mtp85) REVERT: B 104 TRP cc_start: 0.7386 (m-90) cc_final: 0.7108 (m-90) REVERT: B 200 TYR cc_start: 0.5286 (OUTLIER) cc_final: 0.4092 (p90) REVERT: B 242 LEU cc_start: 0.8195 (mt) cc_final: 0.7286 (mp) REVERT: B 451 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.4891 (t80) REVERT: B 762 GLN cc_start: 0.8727 (tt0) cc_final: 0.8430 (tp40) REVERT: B 1029 MET cc_start: 0.9005 (tpp) cc_final: 0.8729 (ttm) REVERT: C 449 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7413 (t80) REVERT: C 457 ARG cc_start: 0.6823 (tpt170) cc_final: 0.6080 (tmm-80) REVERT: C 464 PHE cc_start: 0.7480 (m-80) cc_final: 0.6904 (m-80) REVERT: C 563 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8773 (mt0) REVERT: C 1141 LEU cc_start: 0.8234 (tp) cc_final: 0.7733 (tt) REVERT: N 59 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6473 (t80) REVERT: L 6 GLN cc_start: 0.4896 (OUTLIER) cc_final: 0.4486 (mp10) outliers start: 104 outliers final: 88 residues processed: 231 average time/residue: 0.1542 time to fit residues: 59.5273 Evaluate side-chains 229 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 132 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 79 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 220 optimal weight: 0.0970 chunk 133 optimal weight: 0.0020 chunk 1 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** L 39 HIS ** 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 = 0.3998 r_free = 0.3998 target = 0.118522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076721 restraints weight = 77064.312| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.84 r_work: 0.3054 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27453 Z= 0.126 Angle : 0.600 13.349 37495 Z= 0.297 Chirality : 0.045 0.524 4437 Planarity : 0.004 0.041 4714 Dihedral : 7.285 58.982 4883 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 3.60 % Allowed : 23.99 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3313 helix: 1.84 (0.20), residues: 683 sheet: -1.60 (0.19), residues: 741 loop : -1.72 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 66 TYR 0.032 0.001 TYR B 369 PHE 0.044 0.001 PHE B 497 TRP 0.072 0.002 TRP S 35 HIS 0.016 0.001 HIS S 39 Details of bonding type rmsd covalent geometry : bond 0.00292 (27352) covalent geometry : angle 0.57784 (37238) SS BOND : bond 0.00541 ( 40) SS BOND : angle 2.01031 ( 80) hydrogen bonds : bond 0.03866 ( 867) hydrogen bonds : angle 5.53301 ( 2388) Misc. bond : bond 0.00190 ( 2) link_BETA1-4 : bond 0.00413 ( 13) link_BETA1-4 : angle 1.56755 ( 39) link_BETA1-6 : bond 0.00212 ( 3) link_BETA1-6 : angle 1.41141 ( 9) link_NAG-ASN : bond 0.00375 ( 43) link_NAG-ASN : angle 2.19922 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7947.53 seconds wall clock time: 136 minutes 20.03 seconds (8180.03 seconds total)