Starting phenix.real_space_refine on Fri Mar 6 15:46:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csj_26964/03_2026/8csj_26964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csj_26964/03_2026/8csj_26964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8csj_26964/03_2026/8csj_26964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csj_26964/03_2026/8csj_26964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8csj_26964/03_2026/8csj_26964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csj_26964/03_2026/8csj_26964.map" } resolution = 3.53 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= -0.001 sd= 0.031 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 137 5.16 5 C 20271 2.51 5 N 5269 2.21 5 O 6257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 31934 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8740 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 3 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 802 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 8740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8740 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 3 Chain: "C" Number of atoms: 8583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8583 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1043} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 802 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 802 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" 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: "C" 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 Time building chain proxies: 6.97, per 1000 atoms: 0.22 Number of scatterers: 31934 At special positions: 0 Unit cell: (173.34, 180.83, 176.55, 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 137 16.00 O 6257 8.00 N 5269 7.00 C 20271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 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 B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM31398 O3 NAG M 1 69.362 139.196 96.127 1.00250.57 O !!! !!! HETATM31411 N2 NAG M 2 68.449 139.472 95.075 1.00265.55 N !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No carbon atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 149 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 74 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN B 234 " " NAG B1201 " - " ASN B 603 " " NAG B1202 " - " ASN B 616 " " NAG B1203 " - " ASN B 657 " " NAG B1204 " - " ASN B 709 " " NAG B1205 " - " ASN B1074 " " NAG B1206 " - " ASN B 149 " " NAG B1207 " - " ASN B 282 " " NAG B1208 " - " ASN B 74 " " NAG B1209 " - " ASN B 61 " " NAG B1210 " - " ASN B 17 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 343 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C1074 " " NAG C1207 " - " ASN C 149 " " NAG C1208 " - " ASN C 74 " " NAG C1209 " - " ASN C 61 " " NAG C1210 " - " ASN C 234 " " NAG J 1 " - " ASN A 17 " " NAG K 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 282 " " NAG N 1 " - " ASN C 122 " " NAG O 1 " - " ASN C 17 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 55 sheets defined 20.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.751A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.802A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.616A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 737 through 743 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 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.535A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.639A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.868A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.122A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 removed outlier: 3.553A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.100A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.103A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.624A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.992A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.710A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.623A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 4.082A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.773A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 628 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.717A pdb=" N ARG B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.626A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.695A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.903A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 940 removed outlier: 4.272A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.504A 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 984 removed outlier: 3.724A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.233A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.730A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.717A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 635 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 760 through 783 removed outlier: 3.553A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.765A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 940 removed outlier: 4.133A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 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: 6.057A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.977A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.501A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.512A pdb=" N THR F 87 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.543A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 30 current: chain 'A' and resid 77 through 79 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 77 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 3.612A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.601A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 122 removed outlier: 3.947A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.999A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.800A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.532A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.311A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.841A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1077 Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.730A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.817A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.607A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.693A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 77 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 3.766A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.259A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 160 removed outlier: 5.632A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.982A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 508 through 516 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.895A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.947A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.545A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.408A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 30 current: chain 'C' and resid 77 through 79 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 77 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 3.675A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 222 through 227 current: chain 'C' and resid 285 through 290 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 117 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 154 through 160 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.234A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.513A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 551 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.714A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.778A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.467A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.250A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.620A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLU D 10 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 110 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 9 through 13 current: chain 'E' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 48 current: chain 'E' and resid 96 through 98 No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 18 through 24 Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.613A pdb=" N SER F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.543A pdb=" N THR F 110 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 9 through 13 current: chain 'G' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 96 through 98 No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'G' and resid 18 through 23 955 hydrogen bonds defined for protein. 2631 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: 7.06 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10219 1.34 - 1.47: 8178 1.47 - 1.59: 14097 1.59 - 1.71: 2 1.71 - 1.83: 173 Bond restraints: 32669 Sorted by residual: bond pdb=" CA ASP D 100E" pdb=" CB ASP D 100E" ideal model delta sigma weight residual 1.526 1.665 -0.139 1.76e-02 3.23e+03 6.23e+01 bond pdb=" C GLN B 271 " pdb=" O GLN B 271 " ideal model delta sigma weight residual 1.237 1.294 -0.057 1.38e-02 5.25e+03 1.69e+01 bond pdb=" C LEU B 270 " pdb=" N GLN B 271 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.46e-02 4.69e+03 1.07e+01 bond pdb=" CB PRO A 589 " pdb=" CG PRO A 589 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.81e+00 bond pdb=" N GLN C 853 " pdb=" CA GLN C 853 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.74e+00 ... (remaining 32664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 44275 3.63 - 7.26: 155 7.26 - 10.89: 36 10.89 - 14.52: 7 14.52 - 18.15: 1 Bond angle restraints: 44474 Sorted by residual: angle pdb=" CA PRO A 589 " pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 112.00 99.30 12.70 1.40e+00 5.10e-01 8.23e+01 angle pdb=" O GLN B 271 " pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 121.72 113.74 7.98 9.80e-01 1.04e+00 6.63e+01 angle pdb=" CA GLN B 271 " pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 117.93 127.67 -9.74 1.42e+00 4.96e-01 4.70e+01 angle pdb=" CA LYS E 45 " pdb=" CB LYS E 45 " pdb=" CG LYS E 45 " ideal model delta sigma weight residual 114.10 125.38 -11.28 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CA LEU A 560 " pdb=" CB LEU A 560 " pdb=" CG LEU A 560 " ideal model delta sigma weight residual 116.30 134.45 -18.15 3.50e+00 8.16e-02 2.69e+01 ... (remaining 44469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 17850 18.09 - 36.17: 1572 36.17 - 54.26: 401 54.26 - 72.35: 63 72.35 - 90.44: 54 Dihedral angle restraints: 19940 sinusoidal: 8263 harmonic: 11677 Sorted by residual: dihedral pdb=" CA LEU A 560 " pdb=" C LEU A 560 " pdb=" N PRO A 561 " pdb=" CA PRO A 561 " ideal model delta harmonic sigma weight residual -180.00 -127.71 -52.29 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -176.56 -90.44 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -175.60 89.60 1 1.00e+01 1.00e-02 9.53e+01 ... (remaining 19937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 5102 0.144 - 0.287: 31 0.287 - 0.431: 1 0.431 - 0.574: 0 0.574 - 0.718: 1 Chirality restraints: 5135 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG B1206 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1206 " pdb=" O5 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 5132 not shown) Planarity restraints: 5741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.110 5.00e-02 4.00e+02 1.55e-01 3.86e+01 pdb=" N PRO A 589 " -0.268 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " -0.087 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A 561 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 271 " 0.027 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C GLN B 271 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN B 271 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO B 272 " 0.030 2.00e-02 2.50e+03 ... (remaining 5738 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 3 2.00 - 2.72: 1514 2.72 - 3.45: 44208 3.45 - 4.17: 76245 4.17 - 4.90: 132176 Nonbonded interactions: 254146 Sorted by model distance: nonbonded pdb=" O ILE C 850 " pdb=" NZ LYS C 854 " model vdw 1.270 3.120 nonbonded pdb=" O3 NAG M 1 " pdb=" N2 NAG M 2 " model vdw 1.420 3.120 nonbonded pdb=" O3 NAG M 1 " pdb=" C2 NAG M 2 " model vdw 1.456 3.470 nonbonded pdb=" OE2 GLU A 298 " pdb=" OG1 THR A 315 " model vdw 2.245 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.253 3.040 ... (remaining 254141 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 14 through 828 or (resid 850 and (name N or name CA or nam \ e C or name O or name CB )) or resid 851 through 1310)) selection = (chain 'B' and (resid 14 through 828 or (resid 850 and (name N or name CA or nam \ e C or name O or name CB )) or resid 851 through 1210)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.210 Find NCS groups from input model: 0.810 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.004 0.148 32757 Z= 0.176 Angle : 0.704 18.145 44691 Z= 0.353 Chirality : 0.048 0.718 5135 Planarity : 0.005 0.155 5703 Dihedral : 14.995 89.862 12332 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.67 % Rotamer: Outliers : 0.29 % Allowed : 16.13 % Favored : 83.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 3997 helix: 0.00 (0.18), residues: 661 sheet: 0.56 (0.17), residues: 986 loop : -1.11 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 634 TYR 0.033 0.001 TYR H 27 PHE 0.027 0.001 PHE E 62 TRP 0.016 0.001 TRP D 50 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00358 (32669) covalent geometry : angle 0.67862 (44474) SS BOND : bond 0.00207 ( 44) SS BOND : angle 0.88896 ( 88) hydrogen bonds : bond 0.22073 ( 955) hydrogen bonds : angle 8.57732 ( 2631) Misc. bond : bond 0.00053 ( 1) link_BETA1-4 : bond 0.01297 ( 5) link_BETA1-4 : angle 7.20295 ( 15) link_NAG-ASN : bond 0.00570 ( 38) link_NAG-ASN : angle 2.69711 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 PHE cc_start: 0.8763 (p90) cc_final: 0.8515 (p90) REVERT: A 740 MET cc_start: 0.9218 (tpp) cc_final: 0.8958 (tpp) REVERT: E 37 GLN cc_start: 0.8980 (tp40) cc_final: 0.8349 (tp40) REVERT: F 48 MET cc_start: 0.8753 (pmm) cc_final: 0.8470 (pmm) REVERT: G 95 LEU cc_start: 0.9058 (mp) cc_final: 0.8768 (pp) outliers start: 10 outliers final: 3 residues processed: 140 average time/residue: 0.1802 time to fit residues: 42.6091 Evaluate side-chains 129 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 901 GLN A1011 GLN B 474 GLN B 901 GLN C 115 GLN C 613 GLN C 901 GLN E 37 GLN F 56 ASN G 17 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.051915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034886 restraints weight = 235165.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036133 restraints weight = 117077.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.036845 restraints weight = 75491.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037323 restraints weight = 57658.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.037611 restraints weight = 48763.215| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.004 0.051 32757 Z= 0.190 Angle : 0.607 13.960 44691 Z= 0.303 Chirality : 0.044 0.524 5135 Planarity : 0.004 0.102 5703 Dihedral : 6.861 59.428 5287 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 1.90 % Allowed : 13.55 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 3997 helix: 1.69 (0.21), residues: 664 sheet: 0.43 (0.16), residues: 1015 loop : -0.89 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.023 0.001 TYR B 508 PHE 0.021 0.001 PHE C 562 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00404 (32669) covalent geometry : angle 0.58911 (44474) SS BOND : bond 0.00283 ( 44) SS BOND : angle 1.01151 ( 88) hydrogen bonds : bond 0.04286 ( 955) hydrogen bonds : angle 5.92701 ( 2631) Misc. bond : bond 0.00062 ( 1) link_BETA1-4 : bond 0.00503 ( 5) link_BETA1-4 : angle 4.67980 ( 15) link_NAG-ASN : bond 0.00389 ( 38) link_NAG-ASN : angle 2.31088 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 132 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8840 (mp0) REVERT: A 490 PHE cc_start: 0.9449 (t80) cc_final: 0.9205 (t80) REVERT: A 563 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.8989 (tm-30) REVERT: A 740 MET cc_start: 0.9419 (tpp) cc_final: 0.9071 (tpp) REVERT: H 23 LYS cc_start: 0.9473 (tppt) cc_final: 0.9263 (tppt) REVERT: B 508 TYR cc_start: 0.9036 (m-80) cc_final: 0.8457 (t80) REVERT: C 22 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8014 (p) REVERT: C 900 MET cc_start: 0.9300 (mmm) cc_final: 0.8722 (mmt) REVERT: C 906 PHE cc_start: 0.9663 (OUTLIER) cc_final: 0.9446 (m-10) REVERT: G 95 LEU cc_start: 0.9160 (mp) cc_final: 0.8854 (pp) outliers start: 66 outliers final: 38 residues processed: 185 average time/residue: 0.1892 time to fit residues: 59.5548 Evaluate side-chains 157 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 54 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 146 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 331 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN B 544 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN D 43 GLN D 81 GLN E 37 GLN E 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032637 restraints weight = 234250.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033766 restraints weight = 116551.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.034425 restraints weight = 76494.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.034953 restraints weight = 59601.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.035254 restraints weight = 50129.519| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32757 Z= 0.186 Angle : 0.580 13.759 44691 Z= 0.292 Chirality : 0.044 0.405 5135 Planarity : 0.004 0.061 5703 Dihedral : 6.318 59.138 5283 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 1.93 % Allowed : 14.12 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.13), residues: 3997 helix: 2.31 (0.21), residues: 649 sheet: 0.33 (0.16), residues: 1004 loop : -0.77 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 18 TYR 0.024 0.001 TYR D 79 PHE 0.023 0.001 PHE C 562 TRP 0.007 0.001 TRP F 50 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00396 (32669) covalent geometry : angle 0.56383 (44474) SS BOND : bond 0.00292 ( 44) SS BOND : angle 0.95345 ( 88) hydrogen bonds : bond 0.04404 ( 955) hydrogen bonds : angle 5.42553 ( 2631) Misc. bond : bond 0.00083 ( 1) link_BETA1-4 : bond 0.00737 ( 5) link_BETA1-4 : angle 4.64636 ( 15) link_NAG-ASN : bond 0.00360 ( 38) link_NAG-ASN : angle 2.12880 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 127 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (tp40) REVERT: A 382 VAL cc_start: 0.9267 (t) cc_final: 0.8919 (p) REVERT: A 490 PHE cc_start: 0.9486 (t80) cc_final: 0.9199 (t80) REVERT: A 869 MET cc_start: 0.8854 (pmm) cc_final: 0.8517 (pmm) REVERT: C 22 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7697 (p) REVERT: C 198 ASP cc_start: 0.9479 (m-30) cc_final: 0.9097 (t0) REVERT: D 34 MET cc_start: 0.8982 (tpt) cc_final: 0.8645 (tpt) REVERT: E 37 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8795 (tp40) REVERT: F 34 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: G 95 LEU cc_start: 0.9244 (mp) cc_final: 0.8986 (pp) outliers start: 67 outliers final: 45 residues processed: 182 average time/residue: 0.1840 time to fit residues: 57.4628 Evaluate side-chains 164 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 276 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 389 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 487 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A1088 HIS H 81 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS D 43 GLN F 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.045019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.028745 restraints weight = 225814.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.029768 restraints weight = 112494.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.030464 restraints weight = 73098.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.030924 restraints weight = 55773.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031194 restraints weight = 46669.088| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 32757 Z= 0.340 Angle : 0.763 13.503 44691 Z= 0.386 Chirality : 0.046 0.423 5135 Planarity : 0.005 0.108 5703 Dihedral : 6.782 59.834 5283 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 3.19 % Allowed : 14.38 % Favored : 82.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3997 helix: 1.71 (0.21), residues: 681 sheet: -0.01 (0.16), residues: 976 loop : -0.87 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 18 TYR 0.019 0.002 TYR B 660 PHE 0.034 0.002 PHE C 562 TRP 0.018 0.002 TRP A 436 HIS 0.008 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00722 (32669) covalent geometry : angle 0.74640 (44474) SS BOND : bond 0.00548 ( 44) SS BOND : angle 1.25181 ( 88) hydrogen bonds : bond 0.04589 ( 955) hydrogen bonds : angle 5.82841 ( 2631) Misc. bond : bond 0.00138 ( 1) link_BETA1-4 : bond 0.00786 ( 5) link_BETA1-4 : angle 4.54412 ( 15) link_NAG-ASN : bond 0.00621 ( 38) link_NAG-ASN : angle 2.59513 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 121 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8401 (tp40) REVERT: A 490 PHE cc_start: 0.9570 (t80) cc_final: 0.9300 (t80) REVERT: B 177 MET cc_start: 0.6559 (pmm) cc_final: 0.6167 (pmm) REVERT: B 584 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8597 (tp) REVERT: B 1083 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8190 (t-90) REVERT: C 583 GLU cc_start: 0.6422 (pt0) cc_final: 0.5906 (tm-30) REVERT: C 759 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8912 (t80) REVERT: D 82 ILE cc_start: 0.5858 (mm) cc_final: 0.5544 (mm) REVERT: E 37 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8313 (tp-100) REVERT: E 86 TYR cc_start: 0.8285 (m-80) cc_final: 0.7887 (m-80) REVERT: F 34 MET cc_start: 0.9383 (tpt) cc_final: 0.9072 (tpt) REVERT: G 95 LEU cc_start: 0.9353 (mp) cc_final: 0.9150 (pp) outliers start: 111 outliers final: 75 residues processed: 217 average time/residue: 0.1802 time to fit residues: 67.8693 Evaluate side-chains 185 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 106 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 230 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 159 optimal weight: 40.0000 chunk 94 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 chunk 328 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 955 ASN B 641 ASN C 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029291 restraints weight = 219768.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.030390 restraints weight = 108715.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031118 restraints weight = 70108.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.031570 restraints weight = 53086.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031860 restraints weight = 44438.507| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32757 Z= 0.143 Angle : 0.566 14.060 44691 Z= 0.284 Chirality : 0.044 0.402 5135 Planarity : 0.004 0.071 5703 Dihedral : 6.380 58.670 5283 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 1.98 % Allowed : 15.67 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 3997 helix: 2.18 (0.21), residues: 674 sheet: 0.08 (0.16), residues: 966 loop : -0.80 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 18 TYR 0.023 0.001 TYR A 495 PHE 0.016 0.001 PHE C 562 TRP 0.018 0.001 TRP C 633 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00308 (32669) covalent geometry : angle 0.54736 (44474) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.30804 ( 88) hydrogen bonds : bond 0.03910 ( 955) hydrogen bonds : angle 5.34796 ( 2631) Misc. bond : bond 0.00055 ( 1) link_BETA1-4 : bond 0.00864 ( 5) link_BETA1-4 : angle 4.41156 ( 15) link_NAG-ASN : bond 0.00362 ( 38) link_NAG-ASN : angle 2.14969 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 115 time to evaluate : 1.255 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 52 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8426 (tp40) REVERT: A 490 PHE cc_start: 0.9568 (t80) cc_final: 0.9287 (t80) REVERT: H 3 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8621 (mm-40) REVERT: B 177 MET cc_start: 0.6531 (pmm) cc_final: 0.6164 (pmm) REVERT: B 1083 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8200 (t-90) REVERT: C 177 MET cc_start: 0.8719 (pmm) cc_final: 0.8447 (pmm) REVERT: D 100 PHE cc_start: 0.8474 (m-80) cc_final: 0.8058 (t80) REVERT: E 37 GLN cc_start: 0.9239 (tp-100) cc_final: 0.8607 (tp40) REVERT: F 34 MET cc_start: 0.9275 (tpt) cc_final: 0.9005 (tpt) REVERT: G 95 LEU cc_start: 0.9366 (mp) cc_final: 0.9156 (pp) outliers start: 69 outliers final: 49 residues processed: 176 average time/residue: 0.1840 time to fit residues: 55.7731 Evaluate side-chains 163 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 321 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 395 optimal weight: 20.0000 chunk 252 optimal weight: 7.9990 chunk 366 optimal weight: 20.0000 chunk 358 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 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 14 GLN A 487 ASN A 563 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.044403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028315 restraints weight = 225691.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.029343 restraints weight = 111420.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.030011 restraints weight = 71590.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.030324 restraints weight = 54951.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.030666 restraints weight = 47867.674| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 32757 Z= 0.259 Angle : 0.640 14.538 44691 Z= 0.321 Chirality : 0.044 0.399 5135 Planarity : 0.004 0.068 5703 Dihedral : 6.393 57.871 5283 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer: Outliers : 2.73 % Allowed : 15.19 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3997 helix: 2.01 (0.21), residues: 679 sheet: -0.07 (0.16), residues: 1003 loop : -0.78 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 18 TYR 0.015 0.001 TYR C 269 PHE 0.027 0.001 PHE C 562 TRP 0.013 0.001 TRP C 152 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00555 (32669) covalent geometry : angle 0.62370 (44474) SS BOND : bond 0.00407 ( 44) SS BOND : angle 1.13051 ( 88) hydrogen bonds : bond 0.04039 ( 955) hydrogen bonds : angle 5.46226 ( 2631) Misc. bond : bond 0.00111 ( 1) link_BETA1-4 : bond 0.00743 ( 5) link_BETA1-4 : angle 4.39088 ( 15) link_NAG-ASN : bond 0.00438 ( 38) link_NAG-ASN : angle 2.29760 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 113 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: A 490 PHE cc_start: 0.9624 (t80) cc_final: 0.9346 (t80) REVERT: A 820 ASP cc_start: 0.9613 (OUTLIER) cc_final: 0.9202 (m-30) REVERT: H 3 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8654 (mm-40) REVERT: H 23 LYS cc_start: 0.9609 (tppt) cc_final: 0.9349 (tppp) REVERT: B 177 MET cc_start: 0.6913 (pmm) cc_final: 0.6592 (pmm) REVERT: B 584 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8636 (tp) REVERT: B 1083 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8308 (t-90) REVERT: C 177 MET cc_start: 0.8808 (pmm) cc_final: 0.8603 (pmm) REVERT: C 759 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8892 (t80) REVERT: D 100 PHE cc_start: 0.8499 (m-80) cc_final: 0.8109 (t80) REVERT: E 37 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8525 (tp-100) outliers start: 95 outliers final: 75 residues processed: 198 average time/residue: 0.1803 time to fit residues: 60.9718 Evaluate side-chains 185 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 105 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 259 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN B 66 HIS B 321 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** 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 = 0.3287 r_free = 0.3287 target = 0.044700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.028536 restraints weight = 222171.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029632 restraints weight = 108801.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030328 restraints weight = 70095.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.030753 restraints weight = 52975.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031046 restraints weight = 44593.095| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32757 Z= 0.160 Angle : 0.573 14.803 44691 Z= 0.286 Chirality : 0.043 0.394 5135 Planarity : 0.004 0.063 5703 Dihedral : 6.261 57.080 5283 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.42 % Allowed : 15.73 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3997 helix: 2.19 (0.21), residues: 679 sheet: 0.02 (0.16), residues: 970 loop : -0.77 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 18 TYR 0.015 0.001 TYR C 423 PHE 0.030 0.001 PHE A 515 TRP 0.009 0.001 TRP C 633 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00346 (32669) covalent geometry : angle 0.55678 (44474) SS BOND : bond 0.00299 ( 44) SS BOND : angle 0.90825 ( 88) hydrogen bonds : bond 0.03761 ( 955) hydrogen bonds : angle 5.24530 ( 2631) Misc. bond : bond 0.00063 ( 1) link_BETA1-4 : bond 0.00804 ( 5) link_BETA1-4 : angle 4.36076 ( 15) link_NAG-ASN : bond 0.00347 ( 38) link_NAG-ASN : angle 2.11701 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 116 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8728 (t) REVERT: A 52 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8406 (tp40) REVERT: A 298 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8548 (tm-30) REVERT: A 346 ARG cc_start: 0.9247 (mmm160) cc_final: 0.9010 (mmm160) REVERT: A 490 PHE cc_start: 0.9613 (t80) cc_final: 0.9331 (t80) REVERT: H 3 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8602 (mm-40) REVERT: H 23 LYS cc_start: 0.9617 (tppt) cc_final: 0.9334 (tppp) REVERT: B 177 MET cc_start: 0.6844 (pmm) cc_final: 0.6525 (pmm) REVERT: B 275 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.9141 (m-10) REVERT: B 584 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8537 (tp) REVERT: B 900 MET cc_start: 0.9470 (mmt) cc_final: 0.8857 (mmt) REVERT: B 1083 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.8295 (t-90) REVERT: C 177 MET cc_start: 0.8827 (pmm) cc_final: 0.8627 (pmm) REVERT: C 759 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8878 (t80) REVERT: D 100 PHE cc_start: 0.8566 (m-80) cc_final: 0.8152 (t80) REVERT: E 37 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8600 (tp-100) outliers start: 84 outliers final: 59 residues processed: 192 average time/residue: 0.1890 time to fit residues: 61.4847 Evaluate side-chains 179 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 113 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 226 optimal weight: 9.9990 chunk 392 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 357 optimal weight: 40.0000 chunk 239 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 236 optimal weight: 0.6980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 487 ASN B1135 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.044462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028419 restraints weight = 223605.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.029492 restraints weight = 109342.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.030175 restraints weight = 70299.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030618 restraints weight = 53201.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.030892 restraints weight = 44586.583| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32757 Z= 0.175 Angle : 0.581 14.716 44691 Z= 0.288 Chirality : 0.043 0.391 5135 Planarity : 0.004 0.055 5703 Dihedral : 6.158 57.297 5283 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 2.36 % Allowed : 15.73 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3997 helix: 2.23 (0.21), residues: 678 sheet: -0.03 (0.16), residues: 975 loop : -0.72 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 18 TYR 0.011 0.001 TYR A 369 PHE 0.025 0.001 PHE A 515 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00378 (32669) covalent geometry : angle 0.56615 (44474) SS BOND : bond 0.00327 ( 44) SS BOND : angle 0.90266 ( 88) hydrogen bonds : bond 0.03705 ( 955) hydrogen bonds : angle 5.17389 ( 2631) Misc. bond : bond 0.00071 ( 1) link_BETA1-4 : bond 0.00805 ( 5) link_BETA1-4 : angle 4.31086 ( 15) link_NAG-ASN : bond 0.00343 ( 38) link_NAG-ASN : angle 2.07571 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 113 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8742 (t) REVERT: A 52 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8411 (tp40) REVERT: A 298 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8533 (tm-30) REVERT: A 490 PHE cc_start: 0.9627 (t80) cc_final: 0.9359 (t80) REVERT: A 612 TYR cc_start: 0.9192 (m-80) cc_final: 0.8700 (m-80) REVERT: H 3 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8603 (mm-40) REVERT: H 23 LYS cc_start: 0.9616 (tppt) cc_final: 0.9352 (tppp) REVERT: B 177 MET cc_start: 0.6927 (pmm) cc_final: 0.6601 (pmm) REVERT: B 275 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.9067 (m-10) REVERT: B 584 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8527 (tp) REVERT: B 900 MET cc_start: 0.9492 (mmt) cc_final: 0.8872 (mmt) REVERT: B 1083 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8343 (t-90) REVERT: C 177 MET cc_start: 0.8779 (pmm) cc_final: 0.8566 (pmm) REVERT: D 100 PHE cc_start: 0.8595 (m-80) cc_final: 0.8170 (t80) REVERT: E 37 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8353 (tp-100) REVERT: F 34 MET cc_start: 0.9220 (tpp) cc_final: 0.8883 (tpp) outliers start: 82 outliers final: 64 residues processed: 187 average time/residue: 0.1873 time to fit residues: 60.0671 Evaluate side-chains 181 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 111 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 179 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 174 optimal weight: 0.3980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 487 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.044631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.028484 restraints weight = 221360.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.029530 restraints weight = 108886.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.030241 restraints weight = 69509.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030676 restraints weight = 52418.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.030903 restraints weight = 44161.492| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32757 Z= 0.141 Angle : 0.568 14.602 44691 Z= 0.280 Chirality : 0.043 0.389 5135 Planarity : 0.004 0.049 5703 Dihedral : 6.098 56.430 5283 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 2.30 % Allowed : 15.79 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3997 helix: 2.29 (0.21), residues: 675 sheet: -0.03 (0.16), residues: 992 loop : -0.69 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 18 TYR 0.012 0.001 TYR A 369 PHE 0.023 0.001 PHE H 67 TRP 0.008 0.001 TRP C 633 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00308 (32669) covalent geometry : angle 0.55306 (44474) SS BOND : bond 0.00274 ( 44) SS BOND : angle 0.82696 ( 88) hydrogen bonds : bond 0.03584 ( 955) hydrogen bonds : angle 5.06084 ( 2631) Misc. bond : bond 0.00061 ( 1) link_BETA1-4 : bond 0.00875 ( 5) link_BETA1-4 : angle 4.28394 ( 15) link_NAG-ASN : bond 0.00346 ( 38) link_NAG-ASN : angle 2.05687 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 114 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8777 (t) REVERT: A 52 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8451 (tp40) REVERT: A 298 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: A 490 PHE cc_start: 0.9644 (t80) cc_final: 0.9381 (t80) REVERT: A 612 TYR cc_start: 0.9203 (m-80) cc_final: 0.8616 (m-80) REVERT: A 697 MET cc_start: 0.9028 (mtp) cc_final: 0.8334 (tpp) REVERT: H 3 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8587 (mm-40) REVERT: H 23 LYS cc_start: 0.9615 (tppt) cc_final: 0.9347 (tppp) REVERT: B 177 MET cc_start: 0.6940 (pmm) cc_final: 0.6611 (pmm) REVERT: B 275 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8958 (m-80) REVERT: B 434 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7422 (mm) REVERT: B 584 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8535 (tp) REVERT: B 900 MET cc_start: 0.9468 (mmt) cc_final: 0.8815 (mmt) REVERT: C 177 MET cc_start: 0.8785 (pmm) cc_final: 0.8584 (pmm) REVERT: E 37 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8611 (tp-100) REVERT: F 32 TYR cc_start: 0.8375 (m-10) cc_final: 0.8135 (m-10) REVERT: F 34 MET cc_start: 0.9249 (tpp) cc_final: 0.8919 (tpp) outliers start: 80 outliers final: 67 residues processed: 187 average time/residue: 0.1887 time to fit residues: 60.1905 Evaluate side-chains 183 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 110 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 180 optimal weight: 30.0000 chunk 373 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 376 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 368 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 257 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 487 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.043978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.027875 restraints weight = 225625.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.028925 restraints weight = 111651.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.029596 restraints weight = 72654.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.030040 restraints weight = 55504.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030262 restraints weight = 46838.616| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32757 Z= 0.213 Angle : 0.614 14.256 44691 Z= 0.304 Chirality : 0.044 0.382 5135 Planarity : 0.004 0.054 5703 Dihedral : 6.049 57.013 5280 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 2.24 % Allowed : 15.82 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3997 helix: 2.33 (0.21), residues: 672 sheet: 0.04 (0.16), residues: 971 loop : -0.73 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 18 TYR 0.011 0.001 TYR C 170 PHE 0.023 0.001 PHE C 562 TRP 0.009 0.001 TRP A 258 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00459 (32669) covalent geometry : angle 0.59939 (44474) SS BOND : bond 0.00338 ( 44) SS BOND : angle 1.01237 ( 88) hydrogen bonds : bond 0.03725 ( 955) hydrogen bonds : angle 5.14803 ( 2631) Misc. bond : bond 0.00094 ( 1) link_BETA1-4 : bond 0.01005 ( 5) link_BETA1-4 : angle 4.24113 ( 15) link_NAG-ASN : bond 0.00370 ( 38) link_NAG-ASN : angle 2.08624 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 110 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8794 (t) REVERT: A 52 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8382 (tp40) REVERT: A 298 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: A 490 PHE cc_start: 0.9658 (t80) cc_final: 0.9417 (t80) REVERT: A 697 MET cc_start: 0.8966 (mtp) cc_final: 0.8140 (tpp) REVERT: H 3 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8605 (mm-40) REVERT: H 23 LYS cc_start: 0.9610 (tppt) cc_final: 0.9358 (tppp) REVERT: L 103 LYS cc_start: 0.9518 (tppt) cc_final: 0.9252 (tptp) REVERT: B 177 MET cc_start: 0.7209 (pmm) cc_final: 0.6864 (pmm) REVERT: B 275 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: B 434 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7637 (mm) REVERT: B 584 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 900 MET cc_start: 0.9493 (mmt) cc_final: 0.8818 (mmt) REVERT: C 697 MET cc_start: 0.8822 (mmm) cc_final: 0.8312 (tpt) REVERT: D 100 PHE cc_start: 0.8512 (m-80) cc_final: 0.8171 (t80) REVERT: E 37 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8747 (tp-100) REVERT: F 34 MET cc_start: 0.9238 (tpp) cc_final: 0.8933 (tpp) outliers start: 78 outliers final: 67 residues processed: 182 average time/residue: 0.1891 time to fit residues: 59.0559 Evaluate side-chains 179 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 106 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 4 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 385 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 364 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN L 37 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.043627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027636 restraints weight = 226116.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.028651 restraints weight = 113745.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.029335 restraints weight = 72837.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029656 restraints weight = 54995.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.029974 restraints weight = 47712.223| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32757 Z= 0.230 Angle : 0.627 14.428 44691 Z= 0.311 Chirality : 0.044 0.382 5135 Planarity : 0.004 0.054 5703 Dihedral : 6.143 58.122 5280 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 2.16 % Allowed : 15.96 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3997 helix: 2.25 (0.21), residues: 676 sheet: -0.03 (0.16), residues: 964 loop : -0.74 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 408 TYR 0.010 0.001 TYR A 369 PHE 0.024 0.001 PHE C 562 TRP 0.010 0.001 TRP F 50 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00493 (32669) covalent geometry : angle 0.61272 (44474) SS BOND : bond 0.00572 ( 44) SS BOND : angle 1.19349 ( 88) hydrogen bonds : bond 0.03781 ( 955) hydrogen bonds : angle 5.23341 ( 2631) Misc. bond : bond 0.00106 ( 1) link_BETA1-4 : bond 0.00868 ( 5) link_BETA1-4 : angle 4.24731 ( 15) link_NAG-ASN : bond 0.00365 ( 38) link_NAG-ASN : angle 2.10341 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.52 seconds wall clock time: 99 minutes 30.82 seconds (5970.82 seconds total)