Starting phenix.real_space_refine on Fri Jun 20 10:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elp_48158/06_2025/9elp_48158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elp_48158/06_2025/9elp_48158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elp_48158/06_2025/9elp_48158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elp_48158/06_2025/9elp_48158.map" model { file = "/net/cci-nas-00/data/ceres_data/9elp_48158/06_2025/9elp_48158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elp_48158/06_2025/9elp_48158.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 15002 2.51 5 N 3826 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23543 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8137 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Chain: "B" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7889 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 48, 'TRANS': 957} Chain breaks: 9 Chain: "C" Number of atoms: 6782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6782 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 44, 'TRANS': 827} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.54, per 1000 atoms: 0.66 Number of scatterers: 23543 At special positions: 0 Unit cell: (128.522, 143.6, 180.936, 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 101 16.00 O 4614 8.00 N 3826 7.00 C 15002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 165 " distance=2.06 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.04 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.04 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.02 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.02 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 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 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=2.04 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=2.02 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 354 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 614 " " NAG B1302 " - " ASN B 715 " " NAG B1303 " - " ASN B1072 " " NAG B1304 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 282 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 707 " " NAG I 1 " - " ASN B1096 " " NAG J 1 " - " ASN B1132 " " NAG K 1 " - " ASN B 280 " " NAG L 1 " - " ASN B 329 " " NAG M 1 " - " ASN B 799 " " NAG N 1 " - " ASN B 232 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C 717 " Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.7 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 39 sheets defined 27.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 71 through 79 removed outlier: 6.767A pdb=" N THR A 76 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 78 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.714A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.396A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.710A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.245A pdb=" N GLY A 889 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.999A 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 removed outlier: 3.660A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.300A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1146 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 342 removed outlier: 3.542A pdb=" N VAL B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 4.197A pdb=" N ALA B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.947A pdb=" N SER B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 Processing helix chain 'B' and resid 735 through 742 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 864 through 883 Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.577A pdb=" N GLY B 887 " --> pdb=" O TRP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 907 Processing helix chain 'B' and resid 911 through 917 Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.571A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.587A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.619A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.578A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.996A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.884A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.531A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1139 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.549A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.531A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 65 removed outlier: 6.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.822A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.162A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.716A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 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 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.539A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.434A pdb=" N ALA A 701 " --> pdb=" O ILE B 786 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS B 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN A 703 " --> pdb=" O LYS B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.823A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.823A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.426A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.526A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.980A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.384A pdb=" N THR B 272 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP B 288 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 274 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA B 286 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS B 276 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AC3, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.053A pdb=" N SER B 204 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.346A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 323 through 326 removed outlier: 5.259A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 573 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 396 through 401 Processing sheet with id=AC7, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.189A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 699 through 702 removed outlier: 6.023A pdb=" N ALA B 699 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS C 790 " --> pdb=" O ALA B 699 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASN B 701 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.873A pdb=" N GLN B1069 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE B 716 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE B 718 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B1065 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 720 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1063 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B 722 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B1061 " --> pdb=" O THR B 722 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 724 " --> pdb=" O VAL B1059 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B1059 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY B1057 " --> pdb=" O PRO B 726 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.873A pdb=" N GLN B1069 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE B 716 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE B 718 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B1065 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 720 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1063 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B 722 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B1061 " --> pdb=" O THR B 722 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 724 " --> pdb=" O VAL B1059 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B1059 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY B1057 " --> pdb=" O PRO B 726 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.698A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.899A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.596A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.783A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.766A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.904A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.324A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.426A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.812A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 969 hydrogen bonds defined for protein. 2709 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: 12.47 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7429 1.35 - 1.50: 6833 1.50 - 1.64: 9673 1.64 - 1.78: 10 1.78 - 1.92: 117 Bond restraints: 24062 Sorted by residual: bond pdb=" CA PHE A 888 " pdb=" C PHE A 888 " ideal model delta sigma weight residual 1.522 1.461 0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.29e-02 6.01e+03 1.63e+01 bond pdb=" CA TYR C1138 " pdb=" C TYR C1138 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.28e-02 6.10e+03 1.62e+01 bond pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " ideal model delta sigma weight residual 1.808 1.924 -0.116 3.30e-02 9.18e+02 1.24e+01 bond pdb=" CA SER A 27 " pdb=" CB SER A 27 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.66e-02 3.63e+03 1.11e+01 ... (remaining 24057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 32133 3.78 - 7.55: 574 7.55 - 11.33: 14 11.33 - 15.11: 2 15.11 - 18.88: 3 Bond angle restraints: 32726 Sorted by residual: angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 123.55 -9.75 1.00e+00 1.00e+00 9.51e+01 angle pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 112.00 101.33 10.67 1.40e+00 5.10e-01 5.81e+01 angle pdb=" N PHE A 888 " pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " ideal model delta sigma weight residual 110.33 120.78 -10.45 1.50e+00 4.44e-01 4.85e+01 angle pdb=" N ASP A1146 " pdb=" CA ASP A1146 " pdb=" C ASP A1146 " ideal model delta sigma weight residual 113.02 104.76 8.26 1.20e+00 6.94e-01 4.74e+01 angle pdb=" CA PRO A 230 " pdb=" N PRO A 230 " pdb=" CD PRO A 230 " ideal model delta sigma weight residual 112.00 103.07 8.93 1.40e+00 5.10e-01 4.07e+01 ... (remaining 32721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 14218 21.39 - 42.78: 540 42.78 - 64.16: 154 64.16 - 85.55: 67 85.55 - 106.94: 38 Dihedral angle restraints: 15017 sinusoidal: 6544 harmonic: 8473 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -4.04 -81.96 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 130 " pdb=" SG CYS B 130 " pdb=" SG CYS B 165 " pdb=" CB CYS B 165 " ideal model delta sinusoidal sigma weight residual 93.00 152.07 -59.07 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -132.55 46.55 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 15014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 3814 0.168 - 0.336: 69 0.336 - 0.504: 2 0.504 - 0.672: 2 0.672 - 0.840: 1 Chirality restraints: 3888 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 1.80 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 329 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.38e+00 chirality pdb=" CB VAL B 129 " pdb=" CA VAL B 129 " pdb=" CG1 VAL B 129 " pdb=" CG2 VAL B 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.16e+00 ... (remaining 3885 not shown) Planarity restraints: 4174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.333 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG A1309 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " -0.135 5.00e-02 4.00e+02 1.99e-01 6.36e+01 pdb=" N PRO A 230 " 0.344 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.117 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " -0.113 5.00e-02 4.00e+02 1.63e-01 4.27e+01 pdb=" N PRO A 561 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.083 5.00e-02 4.00e+02 ... (remaining 4171 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 4 1.88 - 2.64: 357 2.64 - 3.39: 30299 3.39 - 4.15: 57261 4.15 - 4.90: 102077 Nonbonded interactions: 189998 Sorted by model distance: nonbonded pdb=" OD1 ASN C 280 " pdb=" OG1 THR C 284 " model vdw 1.127 3.040 nonbonded pdb=" OE2 GLU B 131 " pdb=" CD1 ILE B 229 " model vdw 1.609 3.460 nonbonded pdb=" CD2 LEU B 558 " pdb=" CZ PHE B 560 " model vdw 1.665 3.760 nonbonded pdb=" CD2 LEU B 558 " pdb=" CE2 PHE B 560 " model vdw 1.793 3.760 nonbonded pdb=" OE1 GLU B 131 " pdb=" ND2 ASN B 164 " model vdw 2.043 3.120 ... (remaining 189993 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 26 through 65 or resid 74 through 138 or resid 154 through \ 172 or resid 188 through 425 or resid 428 through 457 or resid 490 through 516 \ or resid 530 through 1147 or resid 1301 through 1304)) selection = (chain 'B' and (resid 26 through 137 or resid 153 through 208 or resid 211 throu \ gh 827 or resid 851 through 1145 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'O' 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: 75.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 59.350 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 24150 Z= 0.345 Angle : 1.230 18.882 32956 Z= 0.707 Chirality : 0.069 0.840 3888 Planarity : 0.010 0.286 4142 Dihedral : 14.385 106.941 9453 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 0.16 % Allowed : 6.84 % Favored : 93.01 % Cbeta Deviations : 0.07 % 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: 0.61 (0.14), residues: 2856 helix: 1.19 (0.18), residues: 679 sheet: 1.14 (0.21), residues: 500 loop : -0.11 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 353 HIS 0.013 0.002 HIS B1081 PHE 0.085 0.004 PHE A 400 TYR 0.053 0.003 TYR A 423 ARG 0.017 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 32) link_NAG-ASN : angle 3.49887 ( 96) link_BETA1-4 : bond 0.00787 ( 22) link_BETA1-4 : angle 2.75890 ( 66) hydrogen bonds : bond 0.12618 ( 947) hydrogen bonds : angle 7.55722 ( 2709) SS BOND : bond 0.00928 ( 34) SS BOND : angle 2.87448 ( 68) covalent geometry : bond 0.00752 (24062) covalent geometry : angle 1.20604 (32726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.7154 (m-40) cc_final: 0.6779 (t0) REVERT: A 190 ARG cc_start: 0.6724 (ptm160) cc_final: 0.6028 (ptp90) REVERT: A 498 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7885 (mtm180) REVERT: A 646 ARG cc_start: 0.8006 (mtp180) cc_final: 0.7730 (mmm160) REVERT: A 978 ASN cc_start: 0.7238 (m110) cc_final: 0.6998 (m110) REVERT: B 312 GLN cc_start: 0.7530 (mp10) cc_final: 0.7201 (mt0) REVERT: B 1140 GLN cc_start: 0.6834 (tt0) cc_final: 0.6538 (mm110) REVERT: C 121 ASN cc_start: 0.7287 (m-40) cc_final: 0.6849 (t0) REVERT: C 237 ARG cc_start: 0.7397 (ttp-170) cc_final: 0.7080 (ttp-110) REVERT: C 571 ASP cc_start: 0.7793 (m-30) cc_final: 0.7213 (t0) REVERT: C 628 GLN cc_start: 0.7498 (mt0) cc_final: 0.7254 (mt0) REVERT: C 1005 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7741 (mt0) outliers start: 4 outliers final: 1 residues processed: 267 average time/residue: 1.1057 time to fit residues: 349.7757 Evaluate side-chains 210 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 414 GLN A 907 ASN A 955 ASN A1048 HIS B 319 GLN B 542 ASN B 611 GLN B 899 GLN C 115 GLN C 280 ASN C 613 GLN C 955 ASN C1010 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.185319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133006 restraints weight = 28131.008| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.87 r_work: 0.3307 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24150 Z= 0.162 Angle : 0.686 12.154 32956 Z= 0.352 Chirality : 0.048 0.524 3888 Planarity : 0.005 0.113 4142 Dihedral : 8.278 61.832 4224 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.64 % Allowed : 7.07 % Favored : 91.29 % 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: 0.76 (0.15), residues: 2856 helix: 2.45 (0.19), residues: 668 sheet: 0.75 (0.20), residues: 556 loop : -0.41 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 103 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.002 PHE C 65 TYR 0.023 0.002 TYR A 423 ARG 0.007 0.001 ARG B1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 32) link_NAG-ASN : angle 3.16161 ( 96) link_BETA1-4 : bond 0.00809 ( 22) link_BETA1-4 : angle 2.60728 ( 66) hydrogen bonds : bond 0.05062 ( 947) hydrogen bonds : angle 6.05842 ( 2709) SS BOND : bond 0.00477 ( 34) SS BOND : angle 1.36048 ( 68) covalent geometry : bond 0.00364 (24062) covalent geometry : angle 0.65355 (32726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.7454 (m-40) cc_final: 0.7160 (t0) REVERT: A 54 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 351 TYR cc_start: 0.7268 (p90) cc_final: 0.7022 (p90) REVERT: A 405 ASN cc_start: 0.8866 (m-40) cc_final: 0.8644 (m-40) REVERT: A 646 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7756 (mmm160) REVERT: A 978 ASN cc_start: 0.7290 (m110) cc_final: 0.7042 (m110) REVERT: A 1005 GLN cc_start: 0.8410 (mt0) cc_final: 0.8108 (mm-40) REVERT: B 28 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6697 (t80) REVERT: B 30 ASN cc_start: 0.7409 (p0) cc_final: 0.7079 (t0) REVERT: B 312 GLN cc_start: 0.7610 (mp10) cc_final: 0.7301 (mt0) REVERT: B 902 TYR cc_start: 0.7551 (t80) cc_final: 0.7013 (t80) REVERT: B 1140 GLN cc_start: 0.6856 (tt0) cc_final: 0.6360 (mm110) REVERT: C 129 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7259 (tttm) REVERT: C 170 TYR cc_start: 0.7057 (t80) cc_final: 0.6685 (t80) REVERT: C 237 ARG cc_start: 0.7388 (ttp-170) cc_final: 0.6994 (ttp-110) REVERT: C 302 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8601 (p) REVERT: C 318 PHE cc_start: 0.5386 (m-80) cc_final: 0.5166 (m-10) REVERT: C 690 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6798 (mm-40) REVERT: C 888 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7728 (t80) REVERT: C 1005 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7946 (mt0) outliers start: 42 outliers final: 14 residues processed: 285 average time/residue: 1.1772 time to fit residues: 404.1171 Evaluate side-chains 233 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 88 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 339 HIS A 606 ASN A 907 ASN B 319 GLN B 542 ASN C 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131233 restraints weight = 28152.080| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.65 r_work: 0.3311 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 24150 Z= 0.222 Angle : 0.667 10.658 32956 Z= 0.341 Chirality : 0.049 0.395 3888 Planarity : 0.005 0.097 4142 Dihedral : 6.378 53.968 4224 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.42 % Allowed : 8.32 % Favored : 89.26 % 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: 0.50 (0.15), residues: 2856 helix: 2.44 (0.19), residues: 677 sheet: 0.40 (0.20), residues: 576 loop : -0.63 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 103 HIS 0.008 0.001 HIS C1058 PHE 0.018 0.002 PHE B 896 TYR 0.021 0.002 TYR A 423 ARG 0.005 0.001 ARG B 993 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 32) link_NAG-ASN : angle 3.01413 ( 96) link_BETA1-4 : bond 0.00776 ( 22) link_BETA1-4 : angle 2.32048 ( 66) hydrogen bonds : bond 0.05215 ( 947) hydrogen bonds : angle 5.90983 ( 2709) SS BOND : bond 0.01218 ( 34) SS BOND : angle 1.69263 ( 68) covalent geometry : bond 0.00536 (24062) covalent geometry : angle 0.63653 (32726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 287 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 314 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: A 351 TYR cc_start: 0.7498 (p90) cc_final: 0.7246 (p90) REVERT: A 405 ASN cc_start: 0.8786 (m-40) cc_final: 0.8586 (m-40) REVERT: A 498 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7855 (mtt-85) REVERT: A 748 GLU cc_start: 0.7666 (mp0) cc_final: 0.7434 (mp0) REVERT: A 964 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8053 (ttmt) REVERT: A 1119 ASN cc_start: 0.8200 (m-40) cc_final: 0.7914 (m-40) REVERT: B 28 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6764 (t80) REVERT: B 30 ASN cc_start: 0.7484 (p0) cc_final: 0.7264 (t0) REVERT: B 235 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7298 (mtm180) REVERT: B 303 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 312 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: B 1140 GLN cc_start: 0.7205 (tt0) cc_final: 0.6748 (mm110) REVERT: C 41 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8346 (mttt) REVERT: C 129 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7585 (tttm) REVERT: C 237 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7219 (ttp-110) REVERT: C 302 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8688 (p) REVERT: C 317 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8241 (m-40) REVERT: C 888 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8073 (t80) outliers start: 62 outliers final: 29 residues processed: 267 average time/residue: 1.1478 time to fit residues: 361.8201 Evaluate side-chains 240 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 183 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1005 GLN B 905 ASN C 607 GLN C 787 GLN C1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123129 restraints weight = 28396.201| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.84 r_work: 0.3240 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24150 Z= 0.191 Angle : 0.620 11.882 32956 Z= 0.317 Chirality : 0.047 0.373 3888 Planarity : 0.004 0.082 4142 Dihedral : 5.717 57.593 4224 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 2.66 % Allowed : 9.53 % Favored : 87.81 % 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 (0.15), residues: 2856 helix: 2.43 (0.19), residues: 675 sheet: 0.20 (0.20), residues: 584 loop : -0.77 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 633 HIS 0.007 0.001 HIS C1058 PHE 0.035 0.002 PHE C 318 TYR 0.025 0.002 TYR C 612 ARG 0.004 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 32) link_NAG-ASN : angle 2.91823 ( 96) link_BETA1-4 : bond 0.00690 ( 22) link_BETA1-4 : angle 1.97418 ( 66) hydrogen bonds : bond 0.04825 ( 947) hydrogen bonds : angle 5.78530 ( 2709) SS BOND : bond 0.00487 ( 34) SS BOND : angle 1.34180 ( 68) covalent geometry : bond 0.00459 (24062) covalent geometry : angle 0.59193 (32726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5638 (t80) REVERT: A 314 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: A 498 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7874 (mtt-85) REVERT: A 740 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: A 748 GLU cc_start: 0.7604 (mp0) cc_final: 0.7378 (mp0) REVERT: A 1127 ASP cc_start: 0.8455 (t0) cc_final: 0.8237 (t0) REVERT: B 28 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6810 (t80) REVERT: B 30 ASN cc_start: 0.7516 (p0) cc_final: 0.7308 (t0) REVERT: B 235 ARG cc_start: 0.7596 (mtm180) cc_final: 0.7272 (mtm180) REVERT: B 303 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 312 GLN cc_start: 0.7853 (mp10) cc_final: 0.7428 (mt0) REVERT: B 324 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7681 (mp) REVERT: B 1140 GLN cc_start: 0.7083 (tt0) cc_final: 0.6560 (mm110) REVERT: C 129 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7465 (tttm) REVERT: C 170 TYR cc_start: 0.7160 (t80) cc_final: 0.6752 (t80) REVERT: C 237 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.7195 (ttp-110) REVERT: C 595 VAL cc_start: 0.7748 (t) cc_final: 0.7417 (t) REVERT: C 725 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: C 1005 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8230 (mt0) outliers start: 68 outliers final: 36 residues processed: 266 average time/residue: 1.1902 time to fit residues: 372.0091 Evaluate side-chains 243 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 168 optimal weight: 0.0270 chunk 289 optimal weight: 0.3980 chunk 191 optimal weight: 0.9980 chunk 271 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 339 HIS A1005 GLN B 319 GLN B 562 GLN C 314 GLN C 613 GLN C 628 GLN C 703 ASN C 751 ASN C1125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.179606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126916 restraints weight = 28306.980| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.22 r_work: 0.3214 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24150 Z= 0.117 Angle : 0.553 11.902 32956 Z= 0.283 Chirality : 0.044 0.345 3888 Planarity : 0.004 0.072 4142 Dihedral : 5.138 53.479 4224 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 1.95 % Allowed : 10.51 % Favored : 87.54 % 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: 0.42 (0.15), residues: 2856 helix: 2.54 (0.19), residues: 680 sheet: 0.16 (0.20), residues: 577 loop : -0.69 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 633 HIS 0.003 0.001 HIS C 954 PHE 0.036 0.001 PHE A 400 TYR 0.019 0.001 TYR C1067 ARG 0.009 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 32) link_NAG-ASN : angle 2.70440 ( 96) link_BETA1-4 : bond 0.00626 ( 22) link_BETA1-4 : angle 1.69581 ( 66) hydrogen bonds : bond 0.04151 ( 947) hydrogen bonds : angle 5.57465 ( 2709) SS BOND : bond 0.00307 ( 34) SS BOND : angle 1.60565 ( 68) covalent geometry : bond 0.00262 (24062) covalent geometry : angle 0.52421 (32726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.7825 (m-40) cc_final: 0.7171 (t160) REVERT: A 646 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7637 (mtm110) REVERT: A 748 GLU cc_start: 0.7375 (mp0) cc_final: 0.7094 (mp0) REVERT: A 1092 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7789 (pt0) REVERT: A 1119 ASN cc_start: 0.8357 (m-40) cc_final: 0.8061 (m-40) REVERT: A 1127 ASP cc_start: 0.8565 (t0) cc_final: 0.8303 (t0) REVERT: B 28 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6625 (t80) REVERT: B 303 SER cc_start: 0.8827 (m) cc_final: 0.8380 (p) REVERT: B 886 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 1000 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: B 1140 GLN cc_start: 0.6593 (tt0) cc_final: 0.6018 (mm110) REVERT: C 34 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6361 (mtp85) REVERT: C 41 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8226 (mttt) REVERT: C 170 TYR cc_start: 0.6983 (t80) cc_final: 0.6616 (t80) REVERT: C 237 ARG cc_start: 0.7208 (ttp-170) cc_final: 0.6948 (ttp-110) REVERT: C 302 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8211 (p) REVERT: C 307 THR cc_start: 0.8943 (p) cc_final: 0.8690 (p) REVERT: C 751 ASN cc_start: 0.8809 (m-40) cc_final: 0.8416 (m-40) REVERT: C 754 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (mp) REVERT: C 886 TRP cc_start: 0.7718 (p90) cc_final: 0.7511 (p90) REVERT: C 888 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8166 (t80) REVERT: C 1045 LYS cc_start: 0.8209 (mmmt) cc_final: 0.8004 (mmmt) outliers start: 50 outliers final: 19 residues processed: 249 average time/residue: 1.1540 time to fit residues: 338.8220 Evaluate side-chains 228 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 611 GLN C 280 ASN C 703 ASN C1125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124370 restraints weight = 28114.074| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.21 r_work: 0.3149 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24150 Z= 0.221 Angle : 0.643 21.050 32956 Z= 0.326 Chirality : 0.048 0.559 3888 Planarity : 0.004 0.063 4142 Dihedral : 5.505 54.654 4224 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 2.81 % Allowed : 10.55 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2856 helix: 2.33 (0.19), residues: 680 sheet: 0.06 (0.19), residues: 604 loop : -0.85 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 886 HIS 0.008 0.001 HIS C1058 PHE 0.031 0.002 PHE A 400 TYR 0.024 0.002 TYR A 423 ARG 0.008 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 32) link_NAG-ASN : angle 3.39269 ( 96) link_BETA1-4 : bond 0.00634 ( 22) link_BETA1-4 : angle 1.68087 ( 66) hydrogen bonds : bond 0.04872 ( 947) hydrogen bonds : angle 5.73285 ( 2709) SS BOND : bond 0.00520 ( 34) SS BOND : angle 1.72189 ( 68) covalent geometry : bond 0.00540 (24062) covalent geometry : angle 0.60917 (32726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5222 (t80) REVERT: A 30 ASN cc_start: 0.7868 (m-40) cc_final: 0.7097 (t0) REVERT: A 287 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7924 (t0) REVERT: A 452 TRP cc_start: 0.7217 (m100) cc_final: 0.6711 (m100) REVERT: A 646 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7663 (mmm160) REVERT: A 907 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8396 (m-40) REVERT: A 995 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7106 (ttm-80) REVERT: A 1092 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7818 (pt0) REVERT: A 1127 ASP cc_start: 0.8597 (t0) cc_final: 0.8306 (t0) REVERT: B 28 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6379 (t80) REVERT: B 303 SER cc_start: 0.8827 (m) cc_final: 0.8346 (p) REVERT: B 312 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: B 324 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7474 (mp) REVERT: B 736 CYS cc_start: 0.8087 (t) cc_final: 0.7878 (t) REVERT: B 1000 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: B 1140 GLN cc_start: 0.6612 (tt0) cc_final: 0.5982 (mm110) REVERT: C 41 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8306 (mttt) REVERT: C 237 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6891 (ttp80) REVERT: C 316 SER cc_start: 0.8546 (t) cc_final: 0.8169 (p) REVERT: C 568 ASP cc_start: 0.7365 (t70) cc_final: 0.6896 (t0) REVERT: C 751 ASN cc_start: 0.8767 (m-40) cc_final: 0.8364 (m-40) REVERT: C 888 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8422 (t80) REVERT: C 1005 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8216 (mt0) outliers start: 72 outliers final: 37 residues processed: 253 average time/residue: 1.4116 time to fit residues: 421.8175 Evaluate side-chains 253 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 284 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 259 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 787 GLN C1125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.177160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118259 restraints weight = 28406.738| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.37 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24150 Z= 0.155 Angle : 0.574 13.503 32956 Z= 0.293 Chirality : 0.045 0.336 3888 Planarity : 0.004 0.062 4142 Dihedral : 5.175 54.771 4224 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 2.58 % Allowed : 11.52 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2856 helix: 2.41 (0.19), residues: 682 sheet: 0.09 (0.19), residues: 599 loop : -0.86 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS C1058 PHE 0.043 0.001 PHE A 400 TYR 0.018 0.001 TYR A 423 ARG 0.011 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 32) link_NAG-ASN : angle 2.70196 ( 96) link_BETA1-4 : bond 0.00622 ( 22) link_BETA1-4 : angle 1.54947 ( 66) hydrogen bonds : bond 0.04374 ( 947) hydrogen bonds : angle 5.60375 ( 2709) SS BOND : bond 0.00389 ( 34) SS BOND : angle 1.49535 ( 68) covalent geometry : bond 0.00370 (24062) covalent geometry : angle 0.54904 (32726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 210 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5310 (t80) REVERT: A 30 ASN cc_start: 0.7931 (m-40) cc_final: 0.7201 (t0) REVERT: A 351 TYR cc_start: 0.7268 (p90) cc_final: 0.6835 (p90) REVERT: A 452 TRP cc_start: 0.7293 (m100) cc_final: 0.6785 (m100) REVERT: A 646 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7753 (mmm160) REVERT: A 995 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6901 (mtp-110) REVERT: A 1092 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7852 (pt0) REVERT: A 1127 ASP cc_start: 0.8554 (t0) cc_final: 0.8267 (t0) REVERT: B 28 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6191 (t80) REVERT: B 303 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 312 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: B 823 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7710 (mmmt) REVERT: B 1000 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: B 1140 GLN cc_start: 0.6701 (tt0) cc_final: 0.6085 (mm110) REVERT: C 41 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8426 (mttt) REVERT: C 237 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.7043 (ttp80) REVERT: C 302 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8351 (p) REVERT: C 307 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 316 SER cc_start: 0.8534 (t) cc_final: 0.8278 (p) REVERT: C 317 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8310 (m110) REVERT: C 751 ASN cc_start: 0.8875 (m-40) cc_final: 0.8505 (m-40) REVERT: C 754 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8715 (mp) REVERT: C 886 TRP cc_start: 0.7881 (p90) cc_final: 0.7630 (p90) REVERT: C 888 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8427 (t80) REVERT: C 995 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7560 (ttm-80) REVERT: C 1005 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8325 (mt0) outliers start: 66 outliers final: 26 residues processed: 251 average time/residue: 1.1261 time to fit residues: 334.6802 Evaluate side-chains 244 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 59 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 319 GLN B 760 GLN C 675 GLN C 703 ASN C1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.177050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117611 restraints weight = 28534.062| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.40 r_work: 0.3150 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24150 Z= 0.205 Angle : 0.606 10.521 32956 Z= 0.310 Chirality : 0.046 0.355 3888 Planarity : 0.004 0.056 4142 Dihedral : 5.293 55.786 4224 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 2.62 % Allowed : 11.68 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2856 helix: 2.33 (0.19), residues: 682 sheet: 0.10 (0.20), residues: 600 loop : -0.94 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 633 HIS 0.007 0.001 HIS C1058 PHE 0.061 0.002 PHE A 400 TYR 0.023 0.001 TYR A 423 ARG 0.011 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 32) link_NAG-ASN : angle 2.65972 ( 96) link_BETA1-4 : bond 0.00598 ( 22) link_BETA1-4 : angle 1.53012 ( 66) hydrogen bonds : bond 0.04735 ( 947) hydrogen bonds : angle 5.70481 ( 2709) SS BOND : bond 0.00482 ( 34) SS BOND : angle 1.77369 ( 68) covalent geometry : bond 0.00499 (24062) covalent geometry : angle 0.58117 (32726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.5210 (t80) REVERT: A 30 ASN cc_start: 0.7944 (m-40) cc_final: 0.7153 (t0) REVERT: A 351 TYR cc_start: 0.7375 (p90) cc_final: 0.6937 (p90) REVERT: A 452 TRP cc_start: 0.7424 (m100) cc_final: 0.6895 (m100) REVERT: A 646 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7739 (mmm160) REVERT: A 740 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7702 (ttp) REVERT: A 907 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8529 (m-40) REVERT: A 995 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.7061 (ttm-80) REVERT: A 1092 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7882 (pt0) REVERT: A 1119 ASN cc_start: 0.8364 (m-40) cc_final: 0.8114 (m-40) REVERT: A 1127 ASP cc_start: 0.8550 (t0) cc_final: 0.8240 (t0) REVERT: B 28 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6228 (t80) REVERT: B 303 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8499 (p) REVERT: B 312 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: B 823 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7686 (mmmt) REVERT: B 1000 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: B 1140 GLN cc_start: 0.6679 (tt0) cc_final: 0.6054 (mm110) REVERT: C 41 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (mttt) REVERT: C 237 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.6989 (ttp80) REVERT: C 307 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8747 (p) REVERT: C 316 SER cc_start: 0.8576 (t) cc_final: 0.8298 (p) REVERT: C 317 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8355 (m110) REVERT: C 725 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: C 751 ASN cc_start: 0.8854 (m-40) cc_final: 0.8475 (m-40) REVERT: C 794 ILE cc_start: 0.8834 (mt) cc_final: 0.8589 (mm) REVERT: C 888 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8469 (t80) REVERT: C 995 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7593 (ttm-80) REVERT: C 1005 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8367 (mt0) outliers start: 67 outliers final: 34 residues processed: 243 average time/residue: 1.1861 time to fit residues: 343.3549 Evaluate side-chains 245 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 201 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 269 optimal weight: 0.0050 chunk 140 optimal weight: 9.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A1005 GLN B 760 GLN C1125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119616 restraints weight = 28346.704| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.36 r_work: 0.3196 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24150 Z= 0.123 Angle : 0.551 9.142 32956 Z= 0.282 Chirality : 0.044 0.321 3888 Planarity : 0.004 0.057 4142 Dihedral : 5.002 55.425 4224 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 1.84 % Allowed : 12.58 % Favored : 85.59 % 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: 0.26 (0.15), residues: 2856 helix: 2.49 (0.19), residues: 683 sheet: 0.10 (0.19), residues: 599 loop : -0.87 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 353 HIS 0.004 0.001 HIS A 519 PHE 0.062 0.001 PHE A 400 TYR 0.018 0.001 TYR C1067 ARG 0.012 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 32) link_NAG-ASN : angle 2.47198 ( 96) link_BETA1-4 : bond 0.00588 ( 22) link_BETA1-4 : angle 1.44758 ( 66) hydrogen bonds : bond 0.04133 ( 947) hydrogen bonds : angle 5.52314 ( 2709) SS BOND : bond 0.00305 ( 34) SS BOND : angle 1.58218 ( 68) covalent geometry : bond 0.00282 (24062) covalent geometry : angle 0.52785 (32726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5245 (t80) REVERT: A 30 ASN cc_start: 0.7949 (m-40) cc_final: 0.7179 (t0) REVERT: A 195 LYS cc_start: 0.7380 (tttt) cc_final: 0.7023 (tttm) REVERT: A 351 TYR cc_start: 0.7317 (p90) cc_final: 0.6878 (p90) REVERT: A 452 TRP cc_start: 0.7410 (m100) cc_final: 0.6887 (m100) REVERT: A 646 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7727 (mmm160) REVERT: A 995 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6831 (mtp-110) REVERT: A 1092 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7865 (pt0) REVERT: A 1119 ASN cc_start: 0.8190 (m-40) cc_final: 0.7927 (m-40) REVERT: A 1127 ASP cc_start: 0.8462 (t0) cc_final: 0.8157 (t0) REVERT: B 28 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6167 (t80) REVERT: B 303 SER cc_start: 0.8887 (m) cc_final: 0.8573 (p) REVERT: B 312 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: B 823 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7683 (mmmt) REVERT: B 1000 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: B 1140 GLN cc_start: 0.6671 (tt0) cc_final: 0.6064 (mm110) REVERT: C 237 ARG cc_start: 0.7300 (ttp-170) cc_final: 0.7010 (ttp80) REVERT: C 302 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 307 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8764 (p) REVERT: C 316 SER cc_start: 0.8504 (t) cc_final: 0.8210 (p) REVERT: C 568 ASP cc_start: 0.7472 (t70) cc_final: 0.7022 (t0) REVERT: C 751 ASN cc_start: 0.8805 (m-40) cc_final: 0.8443 (m-40) REVERT: C 754 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8695 (mp) REVERT: C 794 ILE cc_start: 0.8857 (mt) cc_final: 0.8613 (mm) REVERT: C 886 TRP cc_start: 0.7823 (p90) cc_final: 0.7444 (p90) REVERT: C 888 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8320 (t80) outliers start: 47 outliers final: 28 residues processed: 233 average time/residue: 1.0371 time to fit residues: 286.8777 Evaluate side-chains 238 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 56 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 245 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 178 optimal weight: 0.5980 chunk 182 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 268 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 542 ASN C1125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122101 restraints weight = 28504.984| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.31 r_work: 0.3219 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24150 Z= 0.117 Angle : 0.536 8.522 32956 Z= 0.274 Chirality : 0.044 0.315 3888 Planarity : 0.004 0.054 4142 Dihedral : 4.693 55.364 4224 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 1.41 % Allowed : 13.16 % Favored : 85.43 % 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: 0.34 (0.16), residues: 2856 helix: 2.57 (0.19), residues: 683 sheet: 0.17 (0.20), residues: 595 loop : -0.84 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS C 954 PHE 0.057 0.001 PHE A 400 TYR 0.019 0.001 TYR A 423 ARG 0.013 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 32) link_NAG-ASN : angle 2.32250 ( 96) link_BETA1-4 : bond 0.00563 ( 22) link_BETA1-4 : angle 1.39317 ( 66) hydrogen bonds : bond 0.03988 ( 947) hydrogen bonds : angle 5.39148 ( 2709) SS BOND : bond 0.00314 ( 34) SS BOND : angle 1.42327 ( 68) covalent geometry : bond 0.00265 (24062) covalent geometry : angle 0.51476 (32726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5251 (t80) REVERT: A 30 ASN cc_start: 0.7943 (m-40) cc_final: 0.7263 (t0) REVERT: A 195 LYS cc_start: 0.7365 (tttt) cc_final: 0.7004 (tttm) REVERT: A 351 TYR cc_start: 0.7235 (p90) cc_final: 0.6724 (p90) REVERT: A 452 TRP cc_start: 0.7375 (m100) cc_final: 0.6836 (m100) REVERT: A 646 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7679 (mmm160) REVERT: A 995 ARG cc_start: 0.7209 (ttm-80) cc_final: 0.6797 (mtp-110) REVERT: A 1092 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7831 (pt0) REVERT: A 1119 ASN cc_start: 0.8092 (m-40) cc_final: 0.7838 (m-40) REVERT: A 1127 ASP cc_start: 0.8404 (t0) cc_final: 0.8107 (t0) REVERT: B 28 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6179 (t80) REVERT: B 303 SER cc_start: 0.8848 (m) cc_final: 0.8587 (p) REVERT: B 312 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: B 1000 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: B 1140 GLN cc_start: 0.6654 (tt0) cc_final: 0.6047 (mm110) REVERT: C 237 ARG cc_start: 0.7293 (ttp-170) cc_final: 0.7021 (ttp-110) REVERT: C 302 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8374 (p) REVERT: C 307 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8747 (p) REVERT: C 316 SER cc_start: 0.8482 (t) cc_final: 0.8205 (p) REVERT: C 568 ASP cc_start: 0.7524 (t70) cc_final: 0.7044 (t0) REVERT: C 569 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8268 (pp) REVERT: C 751 ASN cc_start: 0.8764 (m-40) cc_final: 0.8380 (m-40) REVERT: C 794 ILE cc_start: 0.8849 (mt) cc_final: 0.8600 (mm) REVERT: C 886 TRP cc_start: 0.7748 (p90) cc_final: 0.7323 (p90) REVERT: C 888 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8236 (t80) outliers start: 36 outliers final: 23 residues processed: 230 average time/residue: 1.0308 time to fit residues: 283.7287 Evaluate side-chains 233 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 59 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 269 optimal weight: 0.0980 chunk 277 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C1125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.181176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122727 restraints weight = 28405.484| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.31 r_work: 0.3227 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24150 Z= 0.113 Angle : 0.530 9.598 32956 Z= 0.271 Chirality : 0.044 0.308 3888 Planarity : 0.004 0.058 4142 Dihedral : 4.567 55.651 4224 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 1.37 % Allowed : 13.48 % Favored : 85.16 % 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: 0.38 (0.16), residues: 2856 helix: 2.58 (0.19), residues: 683 sheet: 0.21 (0.20), residues: 586 loop : -0.81 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.003 0.001 HIS C 954 PHE 0.061 0.001 PHE A 400 TYR 0.019 0.001 TYR C1067 ARG 0.013 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 32) link_NAG-ASN : angle 2.27057 ( 96) link_BETA1-4 : bond 0.00550 ( 22) link_BETA1-4 : angle 1.36804 ( 66) hydrogen bonds : bond 0.03912 ( 947) hydrogen bonds : angle 5.33224 ( 2709) SS BOND : bond 0.00325 ( 34) SS BOND : angle 1.40497 ( 68) covalent geometry : bond 0.00257 (24062) covalent geometry : angle 0.50968 (32726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18472.40 seconds wall clock time: 319 minutes 56.94 seconds (19196.94 seconds total)