Starting phenix.real_space_refine on Wed Jun 25 21:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws9_32751/06_2025/7ws9_32751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws9_32751/06_2025/7ws9_32751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws9_32751/06_2025/7ws9_32751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws9_32751/06_2025/7ws9_32751.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws9_32751/06_2025/7ws9_32751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws9_32751/06_2025/7ws9_32751.cif" } resolution = 2.9 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= 0.052 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 140 5.16 5 C 18989 2.51 5 N 4887 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 2.58s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29710 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "L" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.33, per 1000 atoms: 0.65 Number of scatterers: 29710 At special positions: 0 Unit cell: (134.784, 143.936, 243.776, 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 140 16.00 O 5694 8.00 N 4887 7.00 C 18989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 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 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 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.04 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 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG C1301 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1074 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B1134 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 3.5 seconds 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6946 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 49 sheets defined 32.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.768A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.605A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.590A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.057A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.648A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.321A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.462A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.977A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.623A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.520A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.038A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.005A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.123A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.529A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (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 365 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.638A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.699A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.772A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.531A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 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 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.515A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.544A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.282A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.519A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.503A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.725A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 149 through 154 removed outlier: 3.544A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 154' Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.566A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 221 through 252 removed outlier: 4.380A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.645A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.884A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 331 removed outlier: 3.768A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.522A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.408A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.969A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.348A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.181A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.519A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.769A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.691A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.787A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.006A 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 removed outlier: 3.635A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.998A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.570A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.504A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.574A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.897A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.944A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.905A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.579A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.558A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.620A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.116A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.594A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.678A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.678A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.156A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.687A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 142 removed outlier: 8.086A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.216A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.991A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.578A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.518A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.367A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.095A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.708A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.761A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3585 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: 15.68 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5099 1.32 - 1.45: 8403 1.45 - 1.58: 16727 1.58 - 1.70: 1 1.70 - 1.83: 188 Bond restraints: 30418 Sorted by residual: bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" CA SER C 591 " pdb=" CB SER C 591 " ideal model delta sigma weight residual 1.530 1.480 0.051 1.62e-02 3.81e+03 9.85e+00 bond pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.06e-02 8.90e+03 9.17e+00 bond pdb=" C PRO C 589 " pdb=" O PRO C 589 " ideal model delta sigma weight residual 1.233 1.198 0.035 1.21e-02 6.83e+03 8.27e+00 bond pdb=" CG1 ILE C 742 " pdb=" CD1 ILE C 742 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.11e+00 ... (remaining 30413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 40203 1.58 - 3.16: 1008 3.16 - 4.74: 131 4.74 - 6.32: 23 6.32 - 7.90: 7 Bond angle restraints: 41372 Sorted by residual: angle pdb=" CA PRO D 146 " pdb=" N PRO D 146 " pdb=" CD PRO D 146 " ideal model delta sigma weight residual 112.00 105.46 6.54 1.40e+00 5.10e-01 2.18e+01 angle pdb=" N PHE B 338 " pdb=" CA PHE B 338 " pdb=" C PHE B 338 " ideal model delta sigma weight residual 113.50 108.36 5.14 1.23e+00 6.61e-01 1.75e+01 angle pdb=" CA GLY C 594 " pdb=" C GLY C 594 " pdb=" O GLY C 594 " ideal model delta sigma weight residual 120.94 117.72 3.22 7.80e-01 1.64e+00 1.70e+01 angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 113.55 108.82 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.60 113.96 -5.36 1.46e+00 4.69e-01 1.35e+01 ... (remaining 41367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.51: 17210 19.51 - 39.02: 1181 39.02 - 58.54: 196 58.54 - 78.05: 52 78.05 - 97.56: 22 Dihedral angle restraints: 18661 sinusoidal: 7886 harmonic: 10775 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.76 56.24 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4156 0.070 - 0.140: 571 0.140 - 0.211: 12 0.211 - 0.281: 2 0.281 - 0.351: 1 Chirality restraints: 4742 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 4739 not shown) Planarity restraints: 5322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.023 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP D 461 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PHE A 318 " -0.061 2.00e-02 2.50e+03 pdb=" O PHE A 318 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 319 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.002 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN D 90 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG D 702 " -0.031 2.00e-02 2.50e+03 ... (remaining 5319 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 444 2.66 - 3.22: 27296 3.22 - 3.78: 45741 3.78 - 4.34: 63478 4.34 - 4.90: 104141 Nonbonded interactions: 241100 Sorted by model distance: nonbonded pdb=" OG1 THR C 732 " pdb=" ND2 ASN C 955 " model vdw 2.095 3.120 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.151 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.168 3.040 nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.174 3.040 ... (remaining 241095 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 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 1147 or resid 1301) \ ) selection = (chain 'B' and (resid 14 through 1147 or resid 1301)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.850 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: 0.050 Extract box with map and model: 1.220 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 71.260 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.111 30500 Z= 0.199 Angle : 0.597 8.076 41576 Z= 0.330 Chirality : 0.045 0.351 4742 Planarity : 0.004 0.064 5296 Dihedral : 13.615 97.559 11589 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.31 % Favored : 97.52 % Rotamer: Outliers : 0.03 % Allowed : 0.68 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.14), residues: 3635 helix: 1.64 (0.17), residues: 1019 sheet: 0.34 (0.20), residues: 603 loop : -0.55 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP D 461 HIS 0.004 0.001 HIS C 505 PHE 0.031 0.001 PHE C 429 TYR 0.014 0.001 TYR B 453 ARG 0.007 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 26) link_NAG-ASN : angle 2.12997 ( 78) link_BETA1-4 : bond 0.00355 ( 14) link_BETA1-4 : angle 0.85458 ( 42) hydrogen bonds : bond 0.20903 ( 1244) hydrogen bonds : angle 8.15881 ( 3585) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.15106 ( 84) covalent geometry : bond 0.00378 (30418) covalent geometry : angle 0.58829 (41372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 MET cc_start: 0.7370 (mtp) cc_final: 0.7162 (mtp) REVERT: D 323 MET cc_start: -0.1217 (mtt) cc_final: -0.2688 (pmm) REVERT: D 360 MET cc_start: -0.1345 (mmp) cc_final: -0.1602 (mmp) REVERT: D 383 MET cc_start: 0.6603 (mpp) cc_final: 0.6379 (mpt) REVERT: D 523 PHE cc_start: 0.5535 (m-80) cc_final: 0.4593 (m-80) REVERT: D 579 MET cc_start: -0.0476 (mmt) cc_final: -0.2701 (ppp) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 1.4465 time to fit residues: 396.3724 Evaluate side-chains 151 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 274 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 334 optimal weight: 30.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 901 GLN B 907 ASN C 282 ASN C 417 ASN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 175 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.162672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089996 restraints weight = 54382.426| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.95 r_work: 0.3008 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 30500 Z= 0.342 Angle : 0.704 9.381 41576 Z= 0.362 Chirality : 0.051 0.256 4742 Planarity : 0.005 0.051 5296 Dihedral : 6.869 75.937 4800 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 7.03 % Favored : 91.68 % 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: 0.16 (0.13), residues: 3635 helix: 1.47 (0.16), residues: 1014 sheet: 0.38 (0.19), residues: 697 loop : -0.74 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 461 HIS 0.014 0.002 HIS D 241 PHE 0.024 0.002 PHE A 275 TYR 0.027 0.002 TYR B1067 ARG 0.010 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 26) link_NAG-ASN : angle 2.44042 ( 78) link_BETA1-4 : bond 0.00271 ( 14) link_BETA1-4 : angle 1.13537 ( 42) hydrogen bonds : bond 0.06485 ( 1244) hydrogen bonds : angle 6.12454 ( 3585) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.80101 ( 84) covalent geometry : bond 0.00831 (30418) covalent geometry : angle 0.69164 (41372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7133 (t0) cc_final: 0.6911 (t0) REVERT: A 137 ASN cc_start: 0.8246 (t0) cc_final: 0.8026 (m-40) REVERT: A 170 TYR cc_start: 0.7370 (t80) cc_final: 0.7059 (t80) REVERT: A 237 ARG cc_start: 0.7111 (ptm-80) cc_final: 0.6734 (ttt-90) REVERT: A 592 PHE cc_start: 0.7318 (p90) cc_final: 0.7118 (p90) REVERT: A 1010 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: B 759 PHE cc_start: 0.8041 (m-80) cc_final: 0.7802 (m-80) REVERT: C 309 GLU cc_start: 0.8644 (mp0) cc_final: 0.8073 (pm20) REVERT: C 491 PRO cc_start: 0.7908 (Cg_endo) cc_final: 0.7642 (Cg_exo) REVERT: D 139 GLN cc_start: 0.0810 (pm20) cc_final: 0.0109 (mt0) REVERT: D 225 ASP cc_start: 0.1599 (m-30) cc_final: 0.0875 (m-30) REVERT: D 243 TYR cc_start: 0.4954 (t80) cc_final: 0.4467 (m-80) REVERT: D 323 MET cc_start: 0.0096 (mtt) cc_final: -0.2481 (pmm) REVERT: D 535 HIS cc_start: 0.2317 (OUTLIER) cc_final: 0.1699 (t-90) REVERT: D 579 MET cc_start: 0.0260 (mmt) cc_final: -0.2694 (ppp) outliers start: 42 outliers final: 18 residues processed: 198 average time/residue: 1.2413 time to fit residues: 301.2334 Evaluate side-chains 167 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 74 optimal weight: 0.6980 chunk 280 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 336 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 299 optimal weight: 0.6980 chunk 281 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 314 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.165581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097644 restraints weight = 54579.649| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.19 r_work: 0.3017 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30500 Z= 0.126 Angle : 0.540 8.798 41576 Z= 0.275 Chirality : 0.044 0.279 4742 Planarity : 0.004 0.049 5296 Dihedral : 5.767 54.976 4800 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.39 % Allowed : 9.58 % Favored : 89.03 % 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: 0.50 (0.14), residues: 3635 helix: 1.92 (0.16), residues: 1004 sheet: 0.59 (0.19), residues: 694 loop : -0.62 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 461 HIS 0.010 0.001 HIS D 241 PHE 0.014 0.001 PHE C 106 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 26) link_NAG-ASN : angle 1.87534 ( 78) link_BETA1-4 : bond 0.00336 ( 14) link_BETA1-4 : angle 0.99687 ( 42) hydrogen bonds : bond 0.04862 ( 1244) hydrogen bonds : angle 5.64224 ( 3585) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.12391 ( 84) covalent geometry : bond 0.00279 (30418) covalent geometry : angle 0.53203 (41372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7108 (t0) cc_final: 0.6834 (t0) REVERT: A 137 ASN cc_start: 0.8185 (t0) cc_final: 0.7925 (m-40) REVERT: A 170 TYR cc_start: 0.7261 (t80) cc_final: 0.6916 (t80) REVERT: A 237 ARG cc_start: 0.6887 (ptm-80) cc_final: 0.6516 (ttt-90) REVERT: A 794 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 200 TYR cc_start: 0.8060 (m-80) cc_final: 0.7800 (m-80) REVERT: C 309 GLU cc_start: 0.8454 (mp0) cc_final: 0.7824 (pm20) REVERT: C 491 PRO cc_start: 0.8015 (Cg_endo) cc_final: 0.7801 (Cg_exo) REVERT: C 755 GLN cc_start: 0.9057 (mt0) cc_final: 0.8699 (mp10) REVERT: C 990 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: D 139 GLN cc_start: 0.0763 (pm20) cc_final: 0.0120 (tt0) REVERT: D 225 ASP cc_start: 0.1657 (m-30) cc_final: 0.1003 (m-30) REVERT: D 243 TYR cc_start: 0.5204 (t80) cc_final: 0.4686 (m-80) REVERT: D 297 MET cc_start: -0.1639 (OUTLIER) cc_final: -0.1951 (mmt) REVERT: D 323 MET cc_start: -0.0278 (mtt) cc_final: -0.2345 (pmm) REVERT: D 360 MET cc_start: -0.1554 (mmp) cc_final: -0.1831 (mmp) REVERT: D 376 MET cc_start: 0.4028 (OUTLIER) cc_final: 0.3752 (mtp) REVERT: D 535 HIS cc_start: 0.2355 (OUTLIER) cc_final: 0.1735 (t-90) REVERT: D 579 MET cc_start: 0.0362 (mmt) cc_final: -0.2459 (ppp) outliers start: 45 outliers final: 20 residues processed: 196 average time/residue: 1.2104 time to fit residues: 291.0102 Evaluate side-chains 167 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 196 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 350 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 314 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.164183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095144 restraints weight = 54846.881| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.83 r_work: 0.3010 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30500 Z= 0.168 Angle : 0.550 8.769 41576 Z= 0.280 Chirality : 0.045 0.290 4742 Planarity : 0.004 0.048 5296 Dihedral : 5.141 53.255 4798 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.79 % Allowed : 10.63 % Favored : 87.58 % 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: 0.53 (0.14), residues: 3635 helix: 1.96 (0.16), residues: 1006 sheet: 0.56 (0.19), residues: 700 loop : -0.59 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 461 HIS 0.009 0.001 HIS D 241 PHE 0.019 0.001 PHE A 168 TYR 0.021 0.001 TYR C1067 ARG 0.008 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 26) link_NAG-ASN : angle 1.86066 ( 78) link_BETA1-4 : bond 0.00240 ( 14) link_BETA1-4 : angle 1.05944 ( 42) hydrogen bonds : bond 0.04826 ( 1244) hydrogen bonds : angle 5.43631 ( 3585) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.68993 ( 84) covalent geometry : bond 0.00396 (30418) covalent geometry : angle 0.53942 (41372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7197 (t0) cc_final: 0.6943 (t0) REVERT: A 137 ASN cc_start: 0.8165 (t0) cc_final: 0.7873 (m-40) REVERT: A 237 ARG cc_start: 0.6903 (ptm-80) cc_final: 0.6558 (ttt-90) REVERT: A 794 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8580 (pp) REVERT: B 950 ASP cc_start: 0.8566 (m-30) cc_final: 0.8356 (m-30) REVERT: B 983 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7888 (ttp80) REVERT: C 309 GLU cc_start: 0.8480 (mp0) cc_final: 0.7853 (pm20) REVERT: C 326 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7711 (pt) REVERT: C 755 GLN cc_start: 0.9056 (mt0) cc_final: 0.8720 (mp10) REVERT: D 139 GLN cc_start: 0.0789 (pm20) cc_final: 0.0136 (tt0) REVERT: D 225 ASP cc_start: 0.1679 (m-30) cc_final: 0.1012 (m-30) REVERT: D 243 TYR cc_start: 0.5116 (t80) cc_final: 0.4709 (m-80) REVERT: D 297 MET cc_start: -0.1616 (OUTLIER) cc_final: -0.1968 (mmt) REVERT: D 323 MET cc_start: -0.0140 (mtt) cc_final: -0.2401 (ptm) REVERT: D 360 MET cc_start: -0.1447 (mmp) cc_final: -0.1706 (mmp) REVERT: D 519 THR cc_start: 0.4475 (OUTLIER) cc_final: 0.4080 (p) REVERT: D 523 PHE cc_start: 0.5939 (m-80) cc_final: 0.5325 (m-10) REVERT: D 535 HIS cc_start: 0.2435 (OUTLIER) cc_final: 0.1819 (t-90) REVERT: D 579 MET cc_start: 0.0214 (mmt) cc_final: -0.2377 (ppp) outliers start: 58 outliers final: 26 residues processed: 207 average time/residue: 1.1936 time to fit residues: 300.6090 Evaluate side-chains 175 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 213 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 267 optimal weight: 0.2980 chunk 272 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 334 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 907 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.163882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095597 restraints weight = 55318.277| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.75 r_work: 0.2989 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 30500 Z= 0.237 Angle : 0.597 11.633 41576 Z= 0.302 Chirality : 0.046 0.299 4742 Planarity : 0.004 0.048 5296 Dihedral : 5.105 54.555 4798 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.25 % Allowed : 11.65 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.44 (0.14), residues: 3635 helix: 1.92 (0.17), residues: 999 sheet: 0.47 (0.19), residues: 710 loop : -0.66 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 461 HIS 0.009 0.001 HIS D 241 PHE 0.025 0.002 PHE A 168 TYR 0.022 0.002 TYR C 473 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 26) link_NAG-ASN : angle 1.92585 ( 78) link_BETA1-4 : bond 0.00174 ( 14) link_BETA1-4 : angle 1.09526 ( 42) hydrogen bonds : bond 0.05311 ( 1244) hydrogen bonds : angle 5.45658 ( 3585) SS BOND : bond 0.00424 ( 42) SS BOND : angle 1.82918 ( 84) covalent geometry : bond 0.00573 (30418) covalent geometry : angle 0.58542 (41372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 160 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7275 (t0) cc_final: 0.7003 (t0) REVERT: A 137 ASN cc_start: 0.8133 (t0) cc_final: 0.7858 (m-40) REVERT: A 227 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 239 GLN cc_start: 0.6523 (OUTLIER) cc_final: 0.6268 (mm-40) REVERT: A 347 PHE cc_start: 0.8025 (m-80) cc_final: 0.7766 (m-80) REVERT: A 529 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8016 (mmtm) REVERT: A 794 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8588 (pp) REVERT: B 983 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7816 (ttp80) REVERT: C 309 GLU cc_start: 0.8663 (mp0) cc_final: 0.8038 (pm20) REVERT: C 326 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7816 (pt) REVERT: C 755 GLN cc_start: 0.9171 (mt0) cc_final: 0.8802 (mp10) REVERT: C 990 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: C 1010 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: D 139 GLN cc_start: 0.0701 (pm20) cc_final: 0.0111 (tt0) REVERT: D 225 ASP cc_start: 0.1753 (m-30) cc_final: 0.1126 (m-30) REVERT: D 297 MET cc_start: -0.1653 (OUTLIER) cc_final: -0.2004 (mmt) REVERT: D 360 MET cc_start: -0.1367 (mmp) cc_final: -0.1600 (mmp) REVERT: D 462 MET cc_start: 0.4654 (ttt) cc_final: 0.4077 (mmp) REVERT: D 535 HIS cc_start: 0.2522 (OUTLIER) cc_final: 0.1811 (t-90) REVERT: D 579 MET cc_start: 0.0300 (mmt) cc_final: -0.2335 (ppp) outliers start: 73 outliers final: 29 residues processed: 216 average time/residue: 1.3926 time to fit residues: 368.7951 Evaluate side-chains 186 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 14 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 331 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 153 optimal weight: 0.0060 chunk 49 optimal weight: 0.3980 chunk 146 optimal weight: 20.0000 chunk 295 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 overall best weight: 2.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 314 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.162891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090626 restraints weight = 54765.695| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.98 r_work: 0.3008 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30500 Z= 0.218 Angle : 0.584 9.927 41576 Z= 0.295 Chirality : 0.046 0.288 4742 Planarity : 0.004 0.048 5296 Dihedral : 5.042 55.444 4798 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.91 % Allowed : 13.34 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.39 (0.14), residues: 3635 helix: 1.93 (0.17), residues: 1002 sheet: 0.39 (0.19), residues: 720 loop : -0.70 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 461 HIS 0.009 0.001 HIS D 241 PHE 0.029 0.001 PHE A 168 TYR 0.025 0.001 TYR C 473 ARG 0.003 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 26) link_NAG-ASN : angle 1.82376 ( 78) link_BETA1-4 : bond 0.00226 ( 14) link_BETA1-4 : angle 1.06399 ( 42) hydrogen bonds : bond 0.05092 ( 1244) hydrogen bonds : angle 5.36640 ( 3585) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.64757 ( 84) covalent geometry : bond 0.00526 (30418) covalent geometry : angle 0.57446 (41372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7329 (t0) cc_final: 0.7037 (t0) REVERT: A 137 ASN cc_start: 0.8126 (t0) cc_final: 0.7855 (m-40) REVERT: A 237 ARG cc_start: 0.7119 (ptm-80) cc_final: 0.6911 (ttt-90) REVERT: A 347 PHE cc_start: 0.8042 (m-80) cc_final: 0.7644 (m-80) REVERT: A 355 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7578 (mmm-85) REVERT: A 752 LEU cc_start: 0.9389 (mp) cc_final: 0.9159 (mp) REVERT: A 794 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8625 (pp) REVERT: B 53 ASP cc_start: 0.8553 (t70) cc_final: 0.7943 (t70) REVERT: B 468 ILE cc_start: 0.3469 (OUTLIER) cc_final: 0.3160 (mt) REVERT: B 983 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7952 (ttp80) REVERT: C 309 GLU cc_start: 0.8660 (mp0) cc_final: 0.8040 (pm20) REVERT: C 326 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7824 (pt) REVERT: C 755 GLN cc_start: 0.9178 (mt0) cc_final: 0.8817 (mp10) REVERT: C 990 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: C 1010 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: D 139 GLN cc_start: 0.0777 (pm20) cc_final: 0.0110 (tt0) REVERT: D 225 ASP cc_start: 0.1847 (m-30) cc_final: 0.1240 (m-30) REVERT: D 243 TYR cc_start: 0.5304 (t80) cc_final: 0.4842 (m-80) REVERT: D 297 MET cc_start: -0.1661 (OUTLIER) cc_final: -0.2004 (mmt) REVERT: D 323 MET cc_start: -0.0655 (mtt) cc_final: -0.2789 (ptm) REVERT: D 360 MET cc_start: -0.1504 (mmp) cc_final: -0.1738 (mmp) REVERT: D 462 MET cc_start: 0.4562 (ttt) cc_final: 0.3959 (mmp) REVERT: D 535 HIS cc_start: 0.2315 (OUTLIER) cc_final: 0.1573 (t-90) REVERT: D 579 MET cc_start: 0.0300 (mmt) cc_final: -0.2353 (ppp) outliers start: 62 outliers final: 30 residues processed: 212 average time/residue: 1.1756 time to fit residues: 307.3190 Evaluate side-chains 192 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 264 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.163378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091869 restraints weight = 54858.657| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.95 r_work: 0.3040 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30500 Z= 0.174 Angle : 0.565 10.770 41576 Z= 0.283 Chirality : 0.045 0.281 4742 Planarity : 0.004 0.048 5296 Dihedral : 4.919 57.212 4798 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 13.68 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.45 (0.14), residues: 3635 helix: 1.96 (0.16), residues: 1018 sheet: 0.40 (0.18), residues: 722 loop : -0.67 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.008 0.001 HIS D 241 PHE 0.030 0.001 PHE A 168 TYR 0.027 0.001 TYR A 170 ARG 0.007 0.000 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 26) link_NAG-ASN : angle 1.70665 ( 78) link_BETA1-4 : bond 0.00265 ( 14) link_BETA1-4 : angle 1.02924 ( 42) hydrogen bonds : bond 0.04765 ( 1244) hydrogen bonds : angle 5.27133 ( 3585) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.53348 ( 84) covalent geometry : bond 0.00415 (30418) covalent geometry : angle 0.55618 (41372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 4.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7374 (t0) cc_final: 0.7151 (t0) REVERT: A 137 ASN cc_start: 0.8139 (t0) cc_final: 0.7827 (m-40) REVERT: A 237 ARG cc_start: 0.7148 (ptm-80) cc_final: 0.6866 (ttt-90) REVERT: A 239 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.6182 (mm-40) REVERT: A 347 PHE cc_start: 0.7947 (m-80) cc_final: 0.7579 (m-80) REVERT: A 355 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7625 (mmm-85) REVERT: A 752 LEU cc_start: 0.9391 (mp) cc_final: 0.9174 (mp) REVERT: A 794 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8628 (pp) REVERT: A 811 LYS cc_start: 0.7912 (tptp) cc_final: 0.7412 (tppt) REVERT: B 53 ASP cc_start: 0.8561 (t70) cc_final: 0.7949 (t70) REVERT: B 468 ILE cc_start: 0.3448 (OUTLIER) cc_final: 0.3152 (mt) REVERT: B 983 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8054 (ttp80) REVERT: C 271 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8528 (mt0) REVERT: C 309 GLU cc_start: 0.8618 (mp0) cc_final: 0.7987 (pm20) REVERT: C 326 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7786 (pt) REVERT: C 752 LEU cc_start: 0.9145 (mp) cc_final: 0.8669 (mp) REVERT: C 755 GLN cc_start: 0.9191 (mt0) cc_final: 0.8812 (mp10) REVERT: C 990 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 1010 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: D 225 ASP cc_start: 0.1789 (m-30) cc_final: 0.1207 (m-30) REVERT: D 243 TYR cc_start: 0.5280 (t80) cc_final: 0.4860 (m-80) REVERT: D 297 MET cc_start: -0.1670 (OUTLIER) cc_final: -0.1998 (mmt) REVERT: D 323 MET cc_start: 0.0040 (mtt) cc_final: -0.2318 (ptm) REVERT: D 360 MET cc_start: -0.1420 (mmp) cc_final: -0.1699 (mmp) REVERT: D 462 MET cc_start: 0.4587 (ttt) cc_final: 0.4040 (mmp) REVERT: D 535 HIS cc_start: 0.2443 (OUTLIER) cc_final: 0.1694 (t-90) REVERT: D 579 MET cc_start: 0.0221 (mmt) cc_final: -0.2297 (ppp) outliers start: 66 outliers final: 26 residues processed: 215 average time/residue: 1.5519 time to fit residues: 415.7027 Evaluate side-chains 190 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 66 optimal weight: 2.9990 chunk 341 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 chunk 256 optimal weight: 0.9990 chunk 304 optimal weight: 0.6980 chunk 335 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 350 optimal weight: 30.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.164893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097628 restraints weight = 55482.326| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.93 r_work: 0.3003 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30500 Z= 0.152 Angle : 0.560 11.138 41576 Z= 0.280 Chirality : 0.044 0.296 4742 Planarity : 0.004 0.063 5296 Dihedral : 4.815 59.251 4798 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.69 % Allowed : 14.24 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.53 (0.14), residues: 3635 helix: 2.03 (0.17), residues: 1014 sheet: 0.46 (0.19), residues: 717 loop : -0.62 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.008 0.001 HIS D 241 PHE 0.034 0.001 PHE A 168 TYR 0.027 0.001 TYR A 170 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 26) link_NAG-ASN : angle 1.62481 ( 78) link_BETA1-4 : bond 0.00283 ( 14) link_BETA1-4 : angle 1.00884 ( 42) hydrogen bonds : bond 0.04541 ( 1244) hydrogen bonds : angle 5.18009 ( 3585) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.56733 ( 84) covalent geometry : bond 0.00358 (30418) covalent geometry : angle 0.55105 (41372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7378 (t0) cc_final: 0.7143 (t0) REVERT: A 137 ASN cc_start: 0.8128 (t0) cc_final: 0.7792 (m-40) REVERT: A 239 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6246 (mm-40) REVERT: A 355 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: A 586 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6297 (m-30) REVERT: A 752 LEU cc_start: 0.9369 (mp) cc_final: 0.9162 (mp) REVERT: A 811 LYS cc_start: 0.7873 (tptp) cc_final: 0.7383 (tppt) REVERT: B 53 ASP cc_start: 0.8578 (t70) cc_final: 0.7959 (t70) REVERT: B 468 ILE cc_start: 0.3504 (OUTLIER) cc_final: 0.3228 (mt) REVERT: B 983 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7888 (ttp80) REVERT: C 309 GLU cc_start: 0.8641 (mp0) cc_final: 0.8009 (pm20) REVERT: C 326 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7723 (pt) REVERT: C 752 LEU cc_start: 0.9135 (mp) cc_final: 0.8678 (mp) REVERT: C 755 GLN cc_start: 0.9183 (mt0) cc_final: 0.8796 (mp10) REVERT: C 990 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: C 1010 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: D 243 TYR cc_start: 0.5313 (t80) cc_final: 0.4868 (m-80) REVERT: D 297 MET cc_start: -0.1663 (OUTLIER) cc_final: -0.1972 (mmt) REVERT: D 323 MET cc_start: 0.0075 (mtt) cc_final: -0.2173 (ptm) REVERT: D 360 MET cc_start: -0.1369 (mmp) cc_final: -0.1682 (mmp) REVERT: D 535 HIS cc_start: 0.2534 (OUTLIER) cc_final: 0.1788 (t-90) REVERT: D 579 MET cc_start: 0.0287 (mmt) cc_final: -0.2208 (ppp) outliers start: 55 outliers final: 31 residues processed: 202 average time/residue: 1.2657 time to fit residues: 313.8863 Evaluate side-chains 191 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 239 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 532 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.163586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092239 restraints weight = 54776.124| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.92 r_work: 0.3044 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30500 Z= 0.158 Angle : 0.565 11.969 41576 Z= 0.282 Chirality : 0.044 0.307 4742 Planarity : 0.004 0.061 5296 Dihedral : 4.761 59.784 4798 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 14.67 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.54 (0.14), residues: 3635 helix: 2.04 (0.17), residues: 1017 sheet: 0.43 (0.19), residues: 723 loop : -0.60 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.007 0.001 HIS D 241 PHE 0.014 0.001 PHE B1121 TYR 0.027 0.001 TYR C 489 ARG 0.012 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 26) link_NAG-ASN : angle 1.61215 ( 78) link_BETA1-4 : bond 0.00277 ( 14) link_BETA1-4 : angle 1.00748 ( 42) hydrogen bonds : bond 0.04526 ( 1244) hydrogen bonds : angle 5.13374 ( 3585) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.44977 ( 84) covalent geometry : bond 0.00374 (30418) covalent geometry : angle 0.55737 (41372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 3.236 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7370 (t0) cc_final: 0.7145 (t0) REVERT: A 137 ASN cc_start: 0.8178 (t0) cc_final: 0.7781 (m-40) REVERT: A 239 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6336 (mm-40) REVERT: A 355 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7766 (mmm-85) REVERT: A 586 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6372 (m-30) REVERT: A 811 LYS cc_start: 0.7923 (tptp) cc_final: 0.7452 (tppt) REVERT: B 53 ASP cc_start: 0.8550 (t70) cc_final: 0.7944 (t70) REVERT: B 468 ILE cc_start: 0.3434 (OUTLIER) cc_final: 0.3126 (mt) REVERT: B 740 MET cc_start: 0.8694 (ttm) cc_final: 0.8180 (mtp) REVERT: B 983 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7929 (ttp80) REVERT: C 309 GLU cc_start: 0.8625 (mp0) cc_final: 0.7996 (pm20) REVERT: C 326 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7794 (pt) REVERT: C 752 LEU cc_start: 0.9165 (mp) cc_final: 0.8719 (mp) REVERT: C 755 GLN cc_start: 0.9182 (mt0) cc_final: 0.8769 (mp10) REVERT: C 990 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 1010 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: C 1145 LEU cc_start: 0.8427 (mp) cc_final: 0.8036 (tt) REVERT: D 239 HIS cc_start: 0.4591 (OUTLIER) cc_final: 0.4374 (t-170) REVERT: D 243 TYR cc_start: 0.5320 (t80) cc_final: 0.4919 (m-80) REVERT: D 323 MET cc_start: -0.0083 (mtt) cc_final: -0.2256 (ptm) REVERT: D 360 MET cc_start: -0.1400 (mmp) cc_final: -0.1625 (mmp) REVERT: D 523 PHE cc_start: 0.5373 (m-80) cc_final: 0.4854 (m-10) REVERT: D 535 HIS cc_start: 0.2510 (OUTLIER) cc_final: 0.1773 (t-90) REVERT: D 579 MET cc_start: 0.0202 (mmt) cc_final: -0.2292 (ppp) outliers start: 51 outliers final: 30 residues processed: 202 average time/residue: 1.1402 time to fit residues: 284.5972 Evaluate side-chains 190 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 120 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 360 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 363 optimal weight: 30.0000 chunk 117 optimal weight: 0.0060 chunk 277 optimal weight: 0.7980 chunk 301 optimal weight: 0.4980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.164560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094161 restraints weight = 54716.234| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.29 r_work: 0.3044 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30500 Z= 0.108 Angle : 0.554 13.844 41576 Z= 0.275 Chirality : 0.044 0.324 4742 Planarity : 0.004 0.121 5296 Dihedral : 4.636 58.660 4798 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.05 % Allowed : 15.29 % Favored : 83.67 % 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: 0.67 (0.14), residues: 3635 helix: 2.18 (0.17), residues: 1015 sheet: 0.48 (0.19), residues: 722 loop : -0.51 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.007 0.001 HIS D 241 PHE 0.014 0.001 PHE B 140 TYR 0.024 0.001 TYR C 473 ARG 0.022 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 26) link_NAG-ASN : angle 1.51055 ( 78) link_BETA1-4 : bond 0.00327 ( 14) link_BETA1-4 : angle 0.95780 ( 42) hydrogen bonds : bond 0.04079 ( 1244) hydrogen bonds : angle 5.04153 ( 3585) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.21647 ( 84) covalent geometry : bond 0.00239 (30418) covalent geometry : angle 0.54764 (41372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 7.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7335 (t0) cc_final: 0.7124 (t0) REVERT: A 137 ASN cc_start: 0.8154 (t0) cc_final: 0.7743 (m-40) REVERT: A 355 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: A 586 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6246 (t0) REVERT: A 811 LYS cc_start: 0.7820 (tptp) cc_final: 0.7345 (tppt) REVERT: A 823 PHE cc_start: 0.8676 (t80) cc_final: 0.7894 (m-80) REVERT: A 858 LEU cc_start: 0.4208 (pt) cc_final: 0.3961 (mm) REVERT: B 53 ASP cc_start: 0.8529 (t70) cc_final: 0.7900 (t70) REVERT: B 468 ILE cc_start: 0.3449 (OUTLIER) cc_final: 0.3174 (mt) REVERT: B 740 MET cc_start: 0.8607 (ttm) cc_final: 0.8188 (mtp) REVERT: B 979 ASP cc_start: 0.8324 (t0) cc_final: 0.8080 (t70) REVERT: B 983 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: C 309 GLU cc_start: 0.8592 (mp0) cc_final: 0.8011 (pm20) REVERT: C 752 LEU cc_start: 0.9127 (mp) cc_final: 0.8719 (mp) REVERT: C 755 GLN cc_start: 0.9159 (mt0) cc_final: 0.8741 (mp10) REVERT: C 1145 LEU cc_start: 0.8364 (mp) cc_final: 0.7993 (tt) REVERT: D 239 HIS cc_start: 0.4490 (OUTLIER) cc_final: 0.4232 (t-170) REVERT: D 243 TYR cc_start: 0.5290 (t80) cc_final: 0.4905 (m-80) REVERT: D 323 MET cc_start: 0.0095 (mtt) cc_final: -0.2090 (ptm) REVERT: D 360 MET cc_start: -0.1409 (mmp) cc_final: -0.1725 (mmt) REVERT: D 462 MET cc_start: 0.4784 (ttt) cc_final: 0.4229 (mmt) REVERT: D 523 PHE cc_start: 0.5306 (m-80) cc_final: 0.4790 (m-10) REVERT: D 535 HIS cc_start: 0.2627 (OUTLIER) cc_final: 0.1898 (t-90) REVERT: D 579 MET cc_start: 0.0186 (mmt) cc_final: -0.2299 (ppp) outliers start: 34 outliers final: 22 residues processed: 191 average time/residue: 1.4012 time to fit residues: 331.5390 Evaluate side-chains 178 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 291 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 301 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 439 ASN ** C 474 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 = 0.4338 r_free = 0.4338 target = 0.164536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093625 restraints weight = 54946.923| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.93 r_work: 0.3076 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30500 Z= 0.116 Angle : 0.551 12.233 41576 Z= 0.272 Chirality : 0.044 0.324 4742 Planarity : 0.004 0.112 5296 Dihedral : 4.533 56.183 4798 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.20 % Allowed : 15.38 % Favored : 83.42 % 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: 0.69 (0.14), residues: 3635 helix: 2.17 (0.16), residues: 1027 sheet: 0.49 (0.19), residues: 730 loop : -0.52 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 353 HIS 0.007 0.001 HIS D 241 PHE 0.039 0.001 PHE A 168 TYR 0.036 0.001 TYR A 170 ARG 0.025 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 26) link_NAG-ASN : angle 1.49796 ( 78) link_BETA1-4 : bond 0.00300 ( 14) link_BETA1-4 : angle 0.94992 ( 42) hydrogen bonds : bond 0.04012 ( 1244) hydrogen bonds : angle 4.97518 ( 3585) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.19052 ( 84) covalent geometry : bond 0.00266 (30418) covalent geometry : angle 0.54457 (41372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31734.53 seconds wall clock time: 558 minutes 8.17 seconds (33488.17 seconds total)