Starting phenix.real_space_refine on Fri Jun 27 21:46:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csj_26964/06_2025/8csj_26964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csj_26964/06_2025/8csj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8csj_26964/06_2025/8csj_26964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csj_26964/06_2025/8csj_26964.map" model { file = "/net/cci-nas-00/data/ceres_data/8csj_26964/06_2025/8csj_26964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csj_26964/06_2025/8csj_26964.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 1.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.62, per 1000 atoms: 0.58 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: 6.57 Conformation dependent library (CDL) restraints added in 3.9 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: 5.27 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: 15.27 Time building geometry restraints manager: 7.90 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 1147 or resid 1301 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 1147 or resid 1201 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: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 74.170 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.240 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.920 ------------------------------------------------------------------------------- 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 : 4.36 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.001 TRP D 50 HIS 0.004 0.001 HIS C 625 PHE 0.027 0.001 PHE E 62 TYR 0.033 0.001 TYR H 27 ARG 0.007 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 38) link_NAG-ASN : angle 2.69711 ( 114) link_BETA1-4 : bond 0.01297 ( 5) link_BETA1-4 : angle 7.20295 ( 15) hydrogen bonds : bond 0.22073 ( 955) hydrogen bonds : angle 8.57732 ( 2631) SS BOND : bond 0.00207 ( 44) SS BOND : angle 0.88896 ( 88) covalent geometry : bond 0.00358 (32669) covalent geometry : angle 0.67862 (44474) Misc. bond : bond 0.00053 ( 1) *********************** 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 : 3.606 Fit side-chains 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: 0.5002 time to fit residues: 118.6664 Evaluate side-chains 130 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 3.798 ------------------------------------------------------------------------------- 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 339 optimal weight: 0.7980 chunk 304 optimal weight: 0.0670 chunk 169 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 365 optimal weight: 7.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- 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 625 HIS A 644 GLN A 901 GLN A1011 GLN B 317 ASN B 474 GLN B 544 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.050757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.033746 restraints weight = 234556.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.034891 restraints weight = 117297.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035655 restraints weight = 77455.745| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32757 Z= 0.245 Angle : 0.658 14.435 44691 Z= 0.328 Chirality : 0.045 0.506 5135 Planarity : 0.005 0.103 5703 Dihedral : 6.930 59.461 5287 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 13.60 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3997 helix: 1.68 (0.21), residues: 664 sheet: 0.37 (0.16), residues: 1015 loop : -0.88 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 436 HIS 0.007 0.001 HIS C1083 PHE 0.029 0.002 PHE C 562 TYR 0.028 0.001 TYR B 508 ARG 0.004 0.001 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 38) link_NAG-ASN : angle 2.42170 ( 114) link_BETA1-4 : bond 0.00981 ( 5) link_BETA1-4 : angle 4.68254 ( 15) hydrogen bonds : bond 0.04337 ( 955) hydrogen bonds : angle 5.92302 ( 2631) SS BOND : bond 0.00343 ( 44) SS BOND : angle 1.11431 ( 88) covalent geometry : bond 0.00505 (32669) covalent geometry : angle 0.64053 (44474) Misc. bond : bond 0.00077 ( 1) *********************** 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 200 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8927 (m) REVERT: A 52 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8490 (tp40) REVERT: A 309 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8929 (mp0) REVERT: A 740 MET cc_start: 0.9432 (tpp) cc_final: 0.9081 (tpp) REVERT: A 869 MET cc_start: 0.8811 (pmm) cc_final: 0.8593 (pmm) REVERT: H 23 LYS cc_start: 0.9501 (tppt) cc_final: 0.9299 (tppt) REVERT: B 429 PHE cc_start: 0.7312 (t80) cc_final: 0.7014 (t80) REVERT: B 900 MET cc_start: 0.9286 (mmt) cc_final: 0.9007 (mmt) REVERT: C 22 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7853 (p) REVERT: C 900 MET cc_start: 0.9303 (mmm) cc_final: 0.8983 (mtt) REVERT: C 906 PHE cc_start: 0.9694 (OUTLIER) cc_final: 0.9472 (m-10) REVERT: G 95 LEU cc_start: 0.9202 (mp) cc_final: 0.8904 (pp) outliers start: 71 outliers final: 42 residues processed: 184 average time/residue: 0.4132 time to fit residues: 130.0072 Evaluate side-chains 160 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 GLN 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 608 VAL Chi-restraints excluded: chain A residue 697 MET 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 598 ILE 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 991 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 83 LYS 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 107 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- 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 901 GLN C 613 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.049808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032707 restraints weight = 214417.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.033852 restraints weight = 110081.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.034594 restraints weight = 72479.560| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32757 Z= 0.126 Angle : 0.528 11.905 44691 Z= 0.262 Chirality : 0.043 0.427 5135 Planarity : 0.004 0.085 5703 Dihedral : 6.362 59.754 5283 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 1.67 % Allowed : 14.67 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 3997 helix: 2.29 (0.21), residues: 650 sheet: 0.37 (0.16), residues: 1013 loop : -0.77 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 50 HIS 0.003 0.001 HIS B 655 PHE 0.031 0.001 PHE A 490 TYR 0.013 0.001 TYR B 904 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 38) link_NAG-ASN : angle 2.09425 ( 114) link_BETA1-4 : bond 0.00813 ( 5) link_BETA1-4 : angle 4.56469 ( 15) hydrogen bonds : bond 0.03962 ( 955) hydrogen bonds : angle 5.43591 ( 2631) SS BOND : bond 0.00213 ( 44) SS BOND : angle 0.79225 ( 88) covalent geometry : bond 0.00269 (32669) covalent geometry : angle 0.51040 (44474) Misc. bond : bond 0.00039 ( 1) *********************** 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 184 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9455 (tpp) cc_final: 0.9066 (tpp) REVERT: A 869 MET cc_start: 0.8795 (pmm) cc_final: 0.8375 (pmm) REVERT: B 429 PHE cc_start: 0.7477 (t80) cc_final: 0.7210 (t80) REVERT: B 508 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8923 (t80) REVERT: B 900 MET cc_start: 0.9292 (mmt) cc_final: 0.9000 (mmt) REVERT: C 22 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7853 (p) REVERT: C 198 ASP cc_start: 0.9441 (m-30) cc_final: 0.9019 (t0) REVERT: G 18 ARG cc_start: 0.9385 (tpt-90) cc_final: 0.9083 (tmt-80) REVERT: G 95 LEU cc_start: 0.9218 (mp) cc_final: 0.8940 (pp) outliers start: 58 outliers final: 38 residues processed: 170 average time/residue: 0.4181 time to fit residues: 120.6830 Evaluate side-chains 158 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 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 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 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 456 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 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 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 486 PHE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 170 optimal weight: 9.9990 chunk 110 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 386 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 300 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN C 563 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.048964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032040 restraints weight = 216175.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033134 restraints weight = 109691.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033860 restraints weight = 72062.801| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32757 Z= 0.130 Angle : 0.526 11.936 44691 Z= 0.261 Chirality : 0.043 0.405 5135 Planarity : 0.004 0.073 5703 Dihedral : 6.040 58.946 5283 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 2.33 % Allowed : 14.29 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 3997 helix: 2.52 (0.21), residues: 644 sheet: 0.43 (0.16), residues: 1016 loop : -0.72 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 47 HIS 0.003 0.001 HIS B 655 PHE 0.023 0.001 PHE A 562 TYR 0.023 0.001 TYR D 27 ARG 0.003 0.000 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 38) link_NAG-ASN : angle 2.04014 ( 114) link_BETA1-4 : bond 0.00610 ( 5) link_BETA1-4 : angle 4.45480 ( 15) hydrogen bonds : bond 0.03496 ( 955) hydrogen bonds : angle 5.13779 ( 2631) SS BOND : bond 0.00231 ( 44) SS BOND : angle 0.79476 ( 88) covalent geometry : bond 0.00279 (32669) covalent geometry : angle 0.50924 (44474) Misc. bond : bond 0.00041 ( 1) *********************** 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 198 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 117 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8974 (pmm) cc_final: 0.8508 (pmm) REVERT: L 60 ASP cc_start: 0.9336 (m-30) cc_final: 0.9097 (t0) REVERT: B 177 MET cc_start: 0.5666 (pmm) cc_final: 0.5081 (pmm) REVERT: B 508 TYR cc_start: 0.9371 (OUTLIER) cc_final: 0.8976 (t80) REVERT: B 900 MET cc_start: 0.9295 (mmt) cc_final: 0.8963 (mmt) REVERT: B 1083 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8100 (t-90) REVERT: C 22 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7724 (p) REVERT: C 198 ASP cc_start: 0.9488 (m-30) cc_final: 0.9074 (t0) REVERT: D 34 MET cc_start: 0.8766 (tpt) cc_final: 0.8432 (tpt) REVERT: E 37 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8699 (tp40) REVERT: G 95 LEU cc_start: 0.9265 (mp) cc_final: 0.9014 (pp) outliers start: 81 outliers final: 60 residues processed: 185 average time/residue: 0.5472 time to fit residues: 175.7290 Evaluate side-chains 177 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 114 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 632 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 751 ASN 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 456 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL 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 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 B residue 1142 GLN 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 486 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS 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 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 33 VAL 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 55 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 44 optimal weight: 0.0030 chunk 231 optimal weight: 0.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- 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** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.048484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.031813 restraints weight = 216640.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.032966 restraints weight = 109662.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.033704 restraints weight = 71080.289| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32757 Z= 0.111 Angle : 0.511 12.207 44691 Z= 0.253 Chirality : 0.043 0.393 5135 Planarity : 0.003 0.066 5703 Dihedral : 5.906 59.592 5283 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 1.93 % Allowed : 14.84 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3997 helix: 2.58 (0.21), residues: 647 sheet: 0.37 (0.16), residues: 1032 loop : -0.63 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 152 HIS 0.002 0.001 HIS A 146 PHE 0.025 0.001 PHE A 562 TYR 0.014 0.001 TYR D 27 ARG 0.001 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 38) link_NAG-ASN : angle 2.00299 ( 114) link_BETA1-4 : bond 0.00758 ( 5) link_BETA1-4 : angle 4.38164 ( 15) hydrogen bonds : bond 0.03392 ( 955) hydrogen bonds : angle 4.98589 ( 2631) SS BOND : bond 0.00212 ( 44) SS BOND : angle 0.93908 ( 88) covalent geometry : bond 0.00239 (32669) covalent geometry : angle 0.49422 (44474) Misc. bond : bond 0.00044 ( 1) *********************** 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 191 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 124 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8421 (tp40) REVERT: A 298 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8514 (tm-30) REVERT: A 382 VAL cc_start: 0.9204 (t) cc_final: 0.8863 (p) REVERT: A 869 MET cc_start: 0.9050 (pmm) cc_final: 0.8760 (pmm) REVERT: B 177 MET cc_start: 0.5727 (pmm) cc_final: 0.5128 (pmm) REVERT: B 564 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.5765 (mm110) REVERT: B 697 MET cc_start: 0.8440 (mmm) cc_final: 0.8087 (mtp) REVERT: B 900 MET cc_start: 0.9257 (mmt) cc_final: 0.8910 (mmt) REVERT: B 1083 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8136 (t-90) REVERT: C 22 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7712 (p) REVERT: C 198 ASP cc_start: 0.9483 (m-30) cc_final: 0.9078 (t0) REVERT: C 697 MET cc_start: 0.8870 (mmm) cc_final: 0.8336 (tpt) REVERT: E 37 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8369 (tp-100) REVERT: G 95 LEU cc_start: 0.9295 (mp) cc_final: 0.9038 (pp) outliers start: 67 outliers final: 55 residues processed: 180 average time/residue: 0.4106 time to fit residues: 127.1247 Evaluate side-chains 175 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 3.282 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU 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 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 21 ILE Chi-restraints excluded: chain L residue 46 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 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU 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 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 433 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS 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 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 33 VAL 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 16 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 372 optimal weight: 0.0020 chunk 78 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 259 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- 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 644 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** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.046036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.029497 restraints weight = 224132.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.030612 restraints weight = 112644.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.031316 restraints weight = 73023.225| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 32757 Z= 0.243 Angle : 0.633 13.003 44691 Z= 0.316 Chirality : 0.044 0.388 5135 Planarity : 0.004 0.095 5703 Dihedral : 6.091 59.156 5283 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 2.65 % Allowed : 14.52 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3997 helix: 2.40 (0.21), residues: 662 sheet: 0.29 (0.16), residues: 1010 loop : -0.63 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.004 0.001 HIS C1083 PHE 0.031 0.001 PHE C 562 TYR 0.025 0.001 TYR A 489 ARG 0.011 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 38) link_NAG-ASN : angle 2.11399 ( 114) link_BETA1-4 : bond 0.00628 ( 5) link_BETA1-4 : angle 4.33376 ( 15) hydrogen bonds : bond 0.03857 ( 955) hydrogen bonds : angle 5.23870 ( 2631) SS BOND : bond 0.00562 ( 44) SS BOND : angle 1.17980 ( 88) covalent geometry : bond 0.00513 (32669) covalent geometry : angle 0.61817 (44474) Misc. bond : bond 0.00095 ( 1) *********************** 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 217 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 125 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: A 52 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8384 (tp40) REVERT: A 490 PHE cc_start: 0.9464 (t80) cc_final: 0.9224 (t80) REVERT: A 869 MET cc_start: 0.9135 (pmm) cc_final: 0.8595 (pmm) REVERT: H 3 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8709 (mm-40) REVERT: B 177 MET cc_start: 0.6383 (pmm) cc_final: 0.5746 (pmm) REVERT: B 564 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7053 (mm110) REVERT: B 584 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8640 (tp) REVERT: B 900 MET cc_start: 0.9342 (mmt) cc_final: 0.8924 (mmt) REVERT: B 1083 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.8191 (t-90) REVERT: C 198 ASP cc_start: 0.9562 (m-30) cc_final: 0.9051 (t0) REVERT: C 629 LEU cc_start: -0.0635 (OUTLIER) cc_final: -0.0864 (tt) REVERT: E 37 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8641 (tp40) REVERT: G 95 LEU cc_start: 0.9334 (mp) cc_final: 0.9134 (pp) outliers start: 92 outliers final: 70 residues processed: 204 average time/residue: 0.4051 time to fit residues: 141.9079 Evaluate side-chains 188 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 112 time to evaluate : 3.575 ------------------------------------------------------------------------------- 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 131 CYS 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 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 697 MET 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 1104 VAL Chi-restraints excluded: chain H residue 11 LEU 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 456 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 GLN 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 708 SER 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 486 PHE 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 629 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 734 THR 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 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 76 SER 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 175 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 316 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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** C 239 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.046657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.030106 restraints weight = 219000.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031237 restraints weight = 108473.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.031964 restraints weight = 69752.040| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32757 Z= 0.115 Angle : 0.541 13.387 44691 Z= 0.268 Chirality : 0.043 0.388 5135 Planarity : 0.003 0.062 5703 Dihedral : 5.962 58.160 5283 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 2.16 % Allowed : 15.07 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3997 helix: 2.62 (0.21), residues: 653 sheet: 0.34 (0.16), residues: 1010 loop : -0.59 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 152 HIS 0.002 0.000 HIS B1083 PHE 0.013 0.001 PHE C 562 TYR 0.016 0.001 TYR D 27 ARG 0.005 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 38) link_NAG-ASN : angle 1.92918 ( 114) link_BETA1-4 : bond 0.00887 ( 5) link_BETA1-4 : angle 4.25453 ( 15) hydrogen bonds : bond 0.03508 ( 955) hydrogen bonds : angle 4.98735 ( 2631) SS BOND : bond 0.00226 ( 44) SS BOND : angle 1.03901 ( 88) covalent geometry : bond 0.00250 (32669) covalent geometry : angle 0.52562 (44474) Misc. bond : bond 0.00044 ( 1) *********************** 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 191 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 116 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7937 (pp30) REVERT: A 52 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8406 (tp40) REVERT: A 298 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: A 869 MET cc_start: 0.9152 (pmm) cc_final: 0.8601 (pmm) REVERT: H 3 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8641 (mm-40) REVERT: B 177 MET cc_start: 0.6412 (pmm) cc_final: 0.5807 (pmm) REVERT: B 584 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8597 (tp) REVERT: B 900 MET cc_start: 0.9244 (mmt) cc_final: 0.8789 (mmt) REVERT: B 1083 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.8192 (t-90) REVERT: C 198 ASP cc_start: 0.9550 (m-30) cc_final: 0.9051 (t0) REVERT: C 697 MET cc_start: 0.8837 (tpt) cc_final: 0.8542 (tpt) REVERT: C 759 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8774 (t80) REVERT: E 37 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8509 (tp-100) REVERT: G 95 LEU cc_start: 0.9370 (mp) cc_final: 0.9166 (pp) outliers start: 75 outliers final: 56 residues processed: 181 average time/residue: 0.4505 time to fit residues: 143.1822 Evaluate side-chains 174 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 3.396 ------------------------------------------------------------------------------- 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 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 312 ILE 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 608 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 11 LEU 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 508 TYR 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 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 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 325 SER 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 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 33 VAL 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 256 optimal weight: 5.9990 chunk 347 optimal weight: 0.0970 chunk 248 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 179 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 330 optimal weight: 4.9990 overall best weight: 3.2382 ------------------------------------------------------------------------------- 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** A1088 HIS ** 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 239 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 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 = 0.3293 r_free = 0.3293 target = 0.044883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.028628 restraints weight = 224619.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029706 restraints weight = 110384.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.030255 restraints weight = 71185.593| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32757 Z= 0.235 Angle : 0.629 13.702 44691 Z= 0.312 Chirality : 0.044 0.384 5135 Planarity : 0.004 0.050 5703 Dihedral : 6.126 59.709 5283 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 2.19 % Allowed : 15.10 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3997 helix: 2.25 (0.21), residues: 676 sheet: 0.19 (0.16), residues: 1030 loop : -0.63 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.007 0.001 HIS C1083 PHE 0.028 0.001 PHE C 562 TYR 0.014 0.001 TYR D 27 ARG 0.007 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 38) link_NAG-ASN : angle 2.13003 ( 114) link_BETA1-4 : bond 0.00844 ( 5) link_BETA1-4 : angle 4.22382 ( 15) hydrogen bonds : bond 0.03879 ( 955) hydrogen bonds : angle 5.20857 ( 2631) SS BOND : bond 0.00336 ( 44) SS BOND : angle 1.10041 ( 88) covalent geometry : bond 0.00505 (32669) covalent geometry : angle 0.61393 (44474) Misc. bond : bond 0.00099 ( 1) *********************** 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 191 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 115 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8161 (pp30) REVERT: A 52 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: A 869 MET cc_start: 0.9192 (pmm) cc_final: 0.8607 (pmm) REVERT: H 3 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8645 (mm-40) REVERT: H 23 LYS cc_start: 0.9598 (tppt) cc_final: 0.9339 (tppp) REVERT: B 177 MET cc_start: 0.7017 (pmm) cc_final: 0.6413 (pmm) REVERT: B 275 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9019 (m-80) REVERT: B 584 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8690 (tp) REVERT: B 900 MET cc_start: 0.9326 (mmt) cc_final: 0.8897 (mmt) REVERT: B 1083 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.8293 (t-90) REVERT: C 198 ASP cc_start: 0.9595 (m-30) cc_final: 0.9032 (t0) REVERT: C 759 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8868 (t80) REVERT: E 37 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8202 (tp-100) REVERT: F 34 MET cc_start: 0.9083 (tpp) cc_final: 0.8685 (tpp) outliers start: 76 outliers final: 62 residues processed: 183 average time/residue: 0.3843 time to fit residues: 122.0384 Evaluate side-chains 174 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 106 time to evaluate : 3.441 ------------------------------------------------------------------------------- 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 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 312 ILE 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 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 1104 VAL Chi-restraints excluded: chain H residue 11 LEU 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 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 512 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 708 SER 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 303 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU 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 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 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain E residue 33 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 232 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 362 optimal weight: 9.9990 chunk 105 optimal weight: 0.0020 chunk 28 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 398 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 901 GLN C 239 GLN ** D 43 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 = 0.3326 r_free = 0.3326 target = 0.045788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.029530 restraints weight = 216392.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.030616 restraints weight = 105018.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.031334 restraints weight = 67728.425| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32757 Z= 0.098 Angle : 0.553 13.982 44691 Z= 0.272 Chirality : 0.044 0.387 5135 Planarity : 0.003 0.046 5703 Dihedral : 5.949 57.783 5283 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 1.73 % Allowed : 15.79 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3997 helix: 2.46 (0.21), residues: 665 sheet: 0.25 (0.16), residues: 1011 loop : -0.60 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 633 HIS 0.002 0.000 HIS B1083 PHE 0.028 0.001 PHE A 490 TYR 0.016 0.001 TYR A 495 ARG 0.005 0.000 ARG B 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 38) link_NAG-ASN : angle 1.87295 ( 114) link_BETA1-4 : bond 0.00871 ( 5) link_BETA1-4 : angle 4.19187 ( 15) hydrogen bonds : bond 0.03499 ( 955) hydrogen bonds : angle 4.91708 ( 2631) SS BOND : bond 0.00208 ( 44) SS BOND : angle 0.77362 ( 88) covalent geometry : bond 0.00213 (32669) covalent geometry : angle 0.54004 (44474) Misc. bond : bond 0.00038 ( 1) *********************** 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 181 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 121 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8013 (pp30) REVERT: A 52 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8391 (tp40) REVERT: A 536 ASN cc_start: 0.8181 (p0) cc_final: 0.7923 (m110) REVERT: A 612 TYR cc_start: 0.8956 (m-80) cc_final: 0.8578 (m-80) REVERT: A 869 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8589 (pmm) REVERT: H 3 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8593 (mm-40) REVERT: H 23 LYS cc_start: 0.9607 (tppt) cc_final: 0.9340 (tppp) REVERT: B 177 MET cc_start: 0.6812 (pmm) cc_final: 0.6202 (pmm) REVERT: B 275 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9062 (m-80) REVERT: B 584 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8525 (tp) REVERT: B 900 MET cc_start: 0.9211 (mmt) cc_final: 0.8827 (mmt) REVERT: C 177 MET cc_start: 0.8785 (pmm) cc_final: 0.8578 (pmm) REVERT: C 198 ASP cc_start: 0.9572 (m-30) cc_final: 0.8974 (t0) REVERT: C 759 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8765 (t80) REVERT: D 100 PHE cc_start: 0.8507 (m-80) cc_final: 0.8110 (t80) outliers start: 60 outliers final: 47 residues processed: 175 average time/residue: 0.4094 time to fit residues: 122.6861 Evaluate side-chains 169 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 3.547 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 131 CYS 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 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL 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 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 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER 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 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 455 LEU 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 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 98 PHE 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 304 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 379 optimal weight: 10.0000 chunk 292 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 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** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.044793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028714 restraints weight = 222477.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.029779 restraints weight = 108088.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030450 restraints weight = 69560.789| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32757 Z= 0.195 Angle : 0.601 13.732 44691 Z= 0.296 Chirality : 0.043 0.379 5135 Planarity : 0.004 0.045 5703 Dihedral : 5.976 59.823 5283 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 1.75 % Allowed : 15.88 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3997 helix: 2.36 (0.21), residues: 676 sheet: 0.24 (0.16), residues: 1022 loop : -0.59 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.012 0.001 HIS B1083 PHE 0.022 0.001 PHE C 562 TYR 0.016 0.001 TYR D 27 ARG 0.006 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 38) link_NAG-ASN : angle 1.99287 ( 114) link_BETA1-4 : bond 0.00827 ( 5) link_BETA1-4 : angle 4.15048 ( 15) hydrogen bonds : bond 0.03619 ( 955) hydrogen bonds : angle 5.02330 ( 2631) SS BOND : bond 0.00314 ( 44) SS BOND : angle 0.93576 ( 88) covalent geometry : bond 0.00421 (32669) covalent geometry : angle 0.58781 (44474) Misc. bond : bond 0.00084 ( 1) ********************** 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 173 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8121 (pp30) REVERT: A 52 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8386 (tp40) REVERT: A 298 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: A 536 ASN cc_start: 0.8162 (p0) cc_final: 0.7802 (p0) REVERT: A 697 MET cc_start: 0.9126 (ttm) cc_final: 0.8823 (mtp) REVERT: A 869 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8606 (pmm) REVERT: H 3 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8631 (mm-40) REVERT: H 23 LYS cc_start: 0.9610 (tppt) cc_final: 0.9353 (tppp) REVERT: B 177 MET cc_start: 0.7024 (pmm) cc_final: 0.6396 (pmm) REVERT: B 275 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9132 (m-80) REVERT: B 584 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8529 (tp) REVERT: B 900 MET cc_start: 0.9294 (mmt) cc_final: 0.8815 (mmt) REVERT: C 177 MET cc_start: 0.8773 (pmm) cc_final: 0.8571 (pmm) REVERT: C 198 ASP cc_start: 0.9580 (m-30) cc_final: 0.9010 (t0) REVERT: C 557 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8555 (tmtt) REVERT: F 34 MET cc_start: 0.9101 (tpp) cc_final: 0.8735 (tpp) outliers start: 61 outliers final: 50 residues processed: 169 average time/residue: 0.3911 time to fit residues: 113.7109 Evaluate side-chains 166 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 3.453 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 298 GLU 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 569 ILE Chi-restraints excluded: chain A residue 590 CYS 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 869 MET Chi-restraints excluded: chain H residue 11 LEU 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 584 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER 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 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 557 LYS 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 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 98 PHE 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 202 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 335 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 392 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 334 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 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 = 0.3247 r_free = 0.3247 target = 0.043378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027361 restraints weight = 226509.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.028389 restraints weight = 111602.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029081 restraints weight = 72789.595| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32757 Z= 0.299 Angle : 0.708 14.098 44691 Z= 0.352 Chirality : 0.045 0.370 5135 Planarity : 0.004 0.052 5703 Dihedral : 6.425 59.478 5283 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 1.90 % Allowed : 15.88 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3997 helix: 2.13 (0.21), residues: 672 sheet: -0.02 (0.17), residues: 975 loop : -0.76 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 50 HIS 0.008 0.001 HIS C1083 PHE 0.036 0.002 PHE D 67 TYR 0.016 0.002 TYR C 170 ARG 0.007 0.001 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 38) link_NAG-ASN : angle 2.22907 ( 114) link_BETA1-4 : bond 0.00733 ( 5) link_BETA1-4 : angle 4.18806 ( 15) hydrogen bonds : bond 0.04126 ( 955) hydrogen bonds : angle 5.44795 ( 2631) SS BOND : bond 0.00528 ( 44) SS BOND : angle 1.38158 ( 88) covalent geometry : bond 0.00637 (32669) covalent geometry : angle 0.69399 (44474) Misc. bond : bond 0.00148 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9972.51 seconds wall clock time: 175 minutes 45.37 seconds (10545.37 seconds total)