Starting phenix.real_space_refine on Mon Jun 23 18:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhx_34806/06_2025/8hhx_34806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhx_34806/06_2025/8hhx_34806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hhx_34806/06_2025/8hhx_34806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhx_34806/06_2025/8hhx_34806.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhx_34806/06_2025/8hhx_34806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhx_34806/06_2025/8hhx_34806.cif" } resolution = 3.62 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= 0.002 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 120 5.16 5 C 17425 2.51 5 N 4532 2.21 5 O 5358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27435 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6373 Classifications: {'peptide': 822} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 39, 'TRANS': 782} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7871 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 958} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7646 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 931} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1682 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "G" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1614 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 831 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} 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: "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: "U" 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: "V" 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: "W" 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.96, per 1000 atoms: 0.58 Number of scatterers: 27435 At special positions: 0 Unit cell: (161.85, 174.3, 185.92, 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 120 16.00 O 5358 8.00 N 4532 7.00 C 17425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 224 " - pdb=" SG CYS G 216 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG D 1 " - " ASN A1074 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG P 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " Time building additional restraints: 7.37 Conformation dependent library (CDL) restraints added in 3.8 seconds 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6490 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 63 sheets defined 21.9% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.996A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.997A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.549A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.847A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.755A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.980A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.797A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.869A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.937A pdb=" N SER B 373 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.597A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.576A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.798A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.632A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.560A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.200A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.549A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.445A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.386A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.665A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.501A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.558A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.930A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.429A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.656A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.977A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.526A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.238A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 126 through 132 removed outlier: 3.530A pdb=" N GLU G 129 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.989A pdb=" N ASN G 175 " --> pdb=" O GLN G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 193 removed outlier: 4.198A pdb=" N TRP G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS G 193 " --> pdb=" O GLN G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.695A pdb=" N ASN I 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.652A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.646A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.777A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 205 removed outlier: 6.358A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.518A pdb=" N VAL A 551 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.305A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.931A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 656 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.051A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.568A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.612A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.977A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 317 removed outlier: 5.897A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.218A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.818A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 719 removed outlier: 6.818A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.586A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.201A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.860A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.745A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.948A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.662A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.748A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 394 through 396 removed outlier: 3.715A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.506A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 719 removed outlier: 7.104A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1053 through 1056 removed outlier: 3.653A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF4, first strand: chain 'C' and resid 1089 through 1090 removed outlier: 3.531A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.077A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 95 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS F 96 " --> pdb=" O TRP F 111 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP F 111 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN F 98 " --> pdb=" O ASP F 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.512A pdb=" N VAL F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 59 " --> pdb=" O VAL F 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AG2, first strand: chain 'G' and resid 21 through 23 removed outlier: 4.539A pdb=" N ALA G 75 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 74 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP G 69 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 76 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 67 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.900A pdb=" N VAL G 49 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 38 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR G 91 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AG5, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AG6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AG7, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.840A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.660A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 70 through 73 removed outlier: 3.608A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2085 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: 10.67 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7410 1.33 - 1.46: 6924 1.46 - 1.58: 13562 1.58 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 28051 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CB PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.79e+00 bond pdb=" N ILE B 850 " pdb=" CA ILE B 850 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N VAL A 143 " pdb=" CA VAL A 143 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.27e+00 ... (remaining 28046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 37882 2.88 - 5.77: 261 5.77 - 8.65: 22 8.65 - 11.53: 5 11.53 - 14.41: 1 Bond angle restraints: 38171 Sorted by residual: angle pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" CD PRO C 272 " ideal model delta sigma weight residual 112.00 97.59 14.41 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N PRO C 272 " pdb=" CD PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 103.20 95.22 7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C ASP A 737 " pdb=" CA ASP A 737 " pdb=" CB ASP A 737 " ideal model delta sigma weight residual 110.77 118.42 -7.65 1.67e+00 3.59e-01 2.10e+01 angle pdb=" N GLN C 954 " pdb=" CA GLN C 954 " pdb=" CB GLN C 954 " ideal model delta sigma weight residual 110.32 117.74 -7.42 1.70e+00 3.46e-01 1.90e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" CB GLN A 774 " ideal model delta sigma weight residual 110.12 116.37 -6.25 1.47e+00 4.63e-01 1.81e+01 ... (remaining 38166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 16284 24.86 - 49.72: 739 49.72 - 74.59: 88 74.59 - 99.45: 20 99.45 - 124.31: 1 Dihedral angle restraints: 17132 sinusoidal: 7034 harmonic: 10098 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.48 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -164.92 78.92 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -163.24 77.24 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 17129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4430 0.190 - 0.380: 4 0.380 - 0.570: 0 0.570 - 0.760: 1 0.760 - 0.950: 1 Chirality restraints: 4436 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4433 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 271 " 0.098 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO B 272 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 271 " 0.091 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO C 272 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.049 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN A 616 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.051 2.00e-02 2.50e+03 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 557 2.67 - 3.23: 26207 3.23 - 3.79: 40161 3.79 - 4.34: 53517 4.34 - 4.90: 86634 Nonbonded interactions: 207076 Sorted by model distance: nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.114 3.040 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.144 3.040 nonbonded pdb=" O THR B 961 " pdb=" OE1 GLN B 965 " model vdw 2.151 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B1067 " pdb=" O ASN B1108 " model vdw 2.197 3.040 ... (remaining 207071 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 'B' and (resid 25 through 146 or resid 164 through 165 or resid 186 throu \ gh 463 or resid 491 through 1140 or resid 1301 through 1307)) selection = (chain 'C' and (resid 25 through 69 or resid 81 through 146 or resid 148 through \ 149 or resid 186 through 243 or resid 264 through 1140 or resid 1301 through 13 \ 07)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 63.070 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.120 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 28122 Z= 0.187 Angle : 0.664 18.597 38348 Z= 0.345 Chirality : 0.050 0.950 4436 Planarity : 0.005 0.146 4881 Dihedral : 13.430 124.309 10534 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 0.17 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.21 (0.14), residues: 3419 helix: 0.24 (0.21), residues: 624 sheet: -0.85 (0.23), residues: 535 loop : -1.13 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.014 0.001 HIS A1048 PHE 0.024 0.001 PHE C1103 TYR 0.021 0.001 TYR A 873 ARG 0.004 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 28) link_NAG-ASN : angle 3.82678 ( 84) link_BETA1-4 : bond 0.00557 ( 7) link_BETA1-4 : angle 1.47726 ( 21) hydrogen bonds : bond 0.21112 ( 766) hydrogen bonds : angle 9.57611 ( 2085) SS BOND : bond 0.00408 ( 36) SS BOND : angle 1.27540 ( 72) covalent geometry : bond 0.00378 (28051) covalent geometry : angle 0.63726 (38171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 414 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 ASP cc_start: 0.5105 (t70) cc_final: 0.4796 (t70) outliers start: 5 outliers final: 2 residues processed: 418 average time/residue: 0.3653 time to fit residues: 247.7523 Evaluate side-chains 329 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 270 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 164 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 164 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.252260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.219674 restraints weight = 43546.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218749 restraints weight = 51838.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.220289 restraints weight = 43068.155| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28122 Z= 0.143 Angle : 0.617 10.756 38348 Z= 0.319 Chirality : 0.047 0.330 4436 Planarity : 0.005 0.107 4881 Dihedral : 7.090 110.454 4457 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.11 % Favored : 93.86 % Rotamer: Outliers : 0.86 % Allowed : 6.91 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.14 (0.14), residues: 3419 helix: 0.34 (0.21), residues: 618 sheet: -0.61 (0.23), residues: 568 loop : -1.14 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.011 0.001 HIS A1048 PHE 0.019 0.001 PHE B 275 TYR 0.019 0.001 TYR C1110 ARG 0.005 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 28) link_NAG-ASN : angle 2.90879 ( 84) link_BETA1-4 : bond 0.00679 ( 7) link_BETA1-4 : angle 1.14670 ( 21) hydrogen bonds : bond 0.05088 ( 766) hydrogen bonds : angle 7.40435 ( 2085) SS BOND : bond 0.00267 ( 36) SS BOND : angle 1.15894 ( 72) covalent geometry : bond 0.00315 (28051) covalent geometry : angle 0.60074 (38171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 372 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 387 average time/residue: 0.3718 time to fit residues: 235.4467 Evaluate side-chains 351 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 334 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 178 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 306 optimal weight: 0.0030 chunk 213 optimal weight: 0.0570 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 394 ASN B 540 ASN B 774 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 955 ASN C1011 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.253789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.220935 restraints weight = 43506.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.217974 restraints weight = 51923.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.219989 restraints weight = 48307.492| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28122 Z= 0.114 Angle : 0.572 12.039 38348 Z= 0.292 Chirality : 0.045 0.335 4436 Planarity : 0.004 0.080 4881 Dihedral : 6.513 107.789 4455 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 1.10 % Allowed : 9.54 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.03 (0.14), residues: 3419 helix: 0.42 (0.21), residues: 622 sheet: -0.56 (0.23), residues: 566 loop : -1.07 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 353 HIS 0.008 0.001 HIS A1048 PHE 0.016 0.001 PHE A 817 TYR 0.022 0.001 TYR A1007 ARG 0.005 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 28) link_NAG-ASN : angle 2.66027 ( 84) link_BETA1-4 : bond 0.00548 ( 7) link_BETA1-4 : angle 1.24631 ( 21) hydrogen bonds : bond 0.04377 ( 766) hydrogen bonds : angle 6.71475 ( 2085) SS BOND : bond 0.00218 ( 36) SS BOND : angle 0.95261 ( 72) covalent geometry : bond 0.00248 (28051) covalent geometry : angle 0.55757 (38171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 364 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 773 GLU cc_start: 0.6028 (pt0) cc_final: 0.5040 (tt0) REVERT: C 902 MET cc_start: 0.7624 (mmt) cc_final: 0.7225 (mmt) REVERT: C 1106 GLN cc_start: 0.7250 (pm20) cc_final: 0.7037 (pt0) REVERT: F 57 ASN cc_start: 0.5731 (p0) cc_final: 0.5380 (p0) outliers start: 33 outliers final: 20 residues processed: 386 average time/residue: 0.3601 time to fit residues: 227.2012 Evaluate side-chains 344 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 233 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 167 optimal weight: 0.3980 chunk 242 optimal weight: 3.9990 chunk 172 optimal weight: 0.0970 chunk 333 optimal weight: 20.0000 chunk 281 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 110 optimal weight: 40.0000 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 965 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.251755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.219092 restraints weight = 44153.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.217621 restraints weight = 53405.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219608 restraints weight = 44665.661| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28122 Z= 0.133 Angle : 0.573 11.415 38348 Z= 0.292 Chirality : 0.046 0.330 4436 Planarity : 0.004 0.071 4881 Dihedral : 6.221 104.784 4455 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 1.60 % Allowed : 10.94 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.00 (0.14), residues: 3419 helix: 0.52 (0.21), residues: 616 sheet: -0.55 (0.23), residues: 565 loop : -1.06 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.008 0.001 HIS A1048 PHE 0.020 0.001 PHE B 201 TYR 0.037 0.001 TYR A1007 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 28) link_NAG-ASN : angle 2.52135 ( 84) link_BETA1-4 : bond 0.00633 ( 7) link_BETA1-4 : angle 1.28561 ( 21) hydrogen bonds : bond 0.04315 ( 766) hydrogen bonds : angle 6.50109 ( 2085) SS BOND : bond 0.00234 ( 36) SS BOND : angle 0.82805 ( 72) covalent geometry : bond 0.00300 (28051) covalent geometry : angle 0.56038 (38171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 357 time to evaluate : 3.039 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: C 878 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7775 (tt) REVERT: C 886 TRP cc_start: 0.6532 (p90) cc_final: 0.5914 (p90) REVERT: F 57 ASN cc_start: 0.5987 (p0) cc_final: 0.5532 (p0) outliers start: 48 outliers final: 35 residues processed: 387 average time/residue: 0.3761 time to fit residues: 237.9279 Evaluate side-chains 368 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 106 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 294 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 913 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 710 ASN C1005 GLN C1011 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.247652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.212747 restraints weight = 43012.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.212716 restraints weight = 43677.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.214180 restraints weight = 36206.827| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28122 Z= 0.188 Angle : 0.626 11.396 38348 Z= 0.321 Chirality : 0.047 0.347 4436 Planarity : 0.005 0.067 4881 Dihedral : 6.262 101.822 4455 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.33 % Allowed : 11.77 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.22 (0.14), residues: 3419 helix: 0.34 (0.20), residues: 611 sheet: -0.73 (0.23), residues: 562 loop : -1.19 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.008 0.001 HIS A1048 PHE 0.026 0.002 PHE C 718 TYR 0.036 0.002 TYR A1007 ARG 0.005 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 28) link_NAG-ASN : angle 2.59623 ( 84) link_BETA1-4 : bond 0.00466 ( 7) link_BETA1-4 : angle 1.31895 ( 21) hydrogen bonds : bond 0.04770 ( 766) hydrogen bonds : angle 6.57978 ( 2085) SS BOND : bond 0.00278 ( 36) SS BOND : angle 1.11650 ( 72) covalent geometry : bond 0.00428 (28051) covalent geometry : angle 0.61252 (38171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 358 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4443 (OUTLIER) cc_final: 0.4167 (mp0) REVERT: A 660 TYR cc_start: 0.6731 (p90) cc_final: 0.6355 (p90) REVERT: A 902 MET cc_start: 0.7120 (mmp) cc_final: 0.6659 (mmp) REVERT: A 906 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: A 990 GLU cc_start: 0.5387 (mm-30) cc_final: 0.5042 (mm-30) REVERT: B 347 PHE cc_start: 0.3909 (m-80) cc_final: 0.3513 (m-10) REVERT: C 818 ILE cc_start: 0.7464 (mp) cc_final: 0.6629 (mt) REVERT: C 1005 GLN cc_start: 0.7454 (tp40) cc_final: 0.7172 (tp-100) REVERT: C 1106 GLN cc_start: 0.7685 (pm20) cc_final: 0.6912 (pm20) REVERT: F 57 ASN cc_start: 0.5941 (p0) cc_final: 0.5512 (p0) outliers start: 70 outliers final: 46 residues processed: 406 average time/residue: 0.4043 time to fit residues: 271.6458 Evaluate side-chains 376 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 328 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 176 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 309 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 710 ASN C1011 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.250700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.214786 restraints weight = 42976.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.216027 restraints weight = 36856.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.216093 restraints weight = 33589.756| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28122 Z= 0.120 Angle : 0.580 13.816 38348 Z= 0.296 Chirality : 0.046 0.392 4436 Planarity : 0.004 0.060 4881 Dihedral : 5.919 100.359 4455 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.46 % Allowed : 13.43 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.09 (0.14), residues: 3419 helix: 0.44 (0.21), residues: 613 sheet: -0.61 (0.23), residues: 566 loop : -1.12 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 353 HIS 0.007 0.001 HIS A1048 PHE 0.022 0.001 PHE B 201 TYR 0.038 0.001 TYR A1007 ARG 0.004 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 28) link_NAG-ASN : angle 2.50411 ( 84) link_BETA1-4 : bond 0.00521 ( 7) link_BETA1-4 : angle 1.30328 ( 21) hydrogen bonds : bond 0.04265 ( 766) hydrogen bonds : angle 6.30917 ( 2085) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.88269 ( 72) covalent geometry : bond 0.00266 (28051) covalent geometry : angle 0.56769 (38171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 352 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4386 (OUTLIER) cc_final: 0.4062 (mp0) REVERT: A 660 TYR cc_start: 0.6618 (p90) cc_final: 0.6316 (p90) REVERT: C 702 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7560 (mp0) REVERT: F 57 ASN cc_start: 0.6009 (p0) cc_final: 0.5597 (p0) outliers start: 44 outliers final: 29 residues processed: 385 average time/residue: 0.3642 time to fit residues: 228.9672 Evaluate side-chains 366 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 336 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 71 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 114 optimal weight: 40.0000 chunk 150 optimal weight: 0.0670 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 774 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.250660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.217223 restraints weight = 43893.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.215062 restraints weight = 55058.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.216736 restraints weight = 49923.175| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28122 Z= 0.135 Angle : 0.594 13.299 38348 Z= 0.301 Chirality : 0.046 0.367 4436 Planarity : 0.004 0.060 4881 Dihedral : 5.803 98.052 4455 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.63 % Allowed : 13.96 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.09 (0.14), residues: 3419 helix: 0.46 (0.21), residues: 616 sheet: -0.63 (0.23), residues: 566 loop : -1.12 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.007 0.001 HIS A1048 PHE 0.012 0.001 PHE A 192 TYR 0.036 0.001 TYR A1007 ARG 0.008 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 28) link_NAG-ASN : angle 2.41907 ( 84) link_BETA1-4 : bond 0.00509 ( 7) link_BETA1-4 : angle 1.26903 ( 21) hydrogen bonds : bond 0.04294 ( 766) hydrogen bonds : angle 6.24588 ( 2085) SS BOND : bond 0.00286 ( 36) SS BOND : angle 0.89029 ( 72) covalent geometry : bond 0.00306 (28051) covalent geometry : angle 0.58282 (38171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4336 (OUTLIER) cc_final: 0.4009 (mp0) REVERT: A 660 TYR cc_start: 0.6701 (p90) cc_final: 0.6480 (p90) REVERT: A 740 MET cc_start: 0.3602 (tpp) cc_final: 0.3203 (ttt) REVERT: A 902 MET cc_start: 0.6919 (mmp) cc_final: 0.6688 (mmp) REVERT: F 57 ASN cc_start: 0.6000 (p0) cc_final: 0.5590 (p0) outliers start: 49 outliers final: 39 residues processed: 376 average time/residue: 0.3613 time to fit residues: 222.7176 Evaluate side-chains 369 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 108 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 277 optimal weight: 0.0670 chunk 100 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 536 ASN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 710 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.250378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.215104 restraints weight = 43397.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.214561 restraints weight = 42137.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.215785 restraints weight = 35905.702| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28122 Z= 0.124 Angle : 0.591 13.879 38348 Z= 0.299 Chirality : 0.046 0.363 4436 Planarity : 0.004 0.059 4881 Dihedral : 5.654 96.076 4455 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.73 % Allowed : 14.13 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.03 (0.14), residues: 3419 helix: 0.51 (0.21), residues: 617 sheet: -0.61 (0.23), residues: 564 loop : -1.08 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 353 HIS 0.007 0.001 HIS A1048 PHE 0.022 0.001 PHE B 201 TYR 0.040 0.001 TYR A1007 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 28) link_NAG-ASN : angle 2.45319 ( 84) link_BETA1-4 : bond 0.00530 ( 7) link_BETA1-4 : angle 1.26307 ( 21) hydrogen bonds : bond 0.04172 ( 766) hydrogen bonds : angle 6.17359 ( 2085) SS BOND : bond 0.00258 ( 36) SS BOND : angle 0.81579 ( 72) covalent geometry : bond 0.00280 (28051) covalent geometry : angle 0.57928 (38171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 348 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4317 (OUTLIER) cc_final: 0.3984 (mp0) REVERT: A 660 TYR cc_start: 0.6735 (p90) cc_final: 0.6501 (p90) REVERT: F 57 ASN cc_start: 0.6056 (p0) cc_final: 0.5633 (p0) outliers start: 52 outliers final: 45 residues processed: 382 average time/residue: 0.3593 time to fit residues: 226.8281 Evaluate side-chains 376 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 330 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 252 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 301 optimal weight: 20.0000 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.251292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.218078 restraints weight = 43851.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.215461 restraints weight = 54474.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.217317 restraints weight = 50502.514| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28122 Z= 0.125 Angle : 0.599 16.788 38348 Z= 0.302 Chirality : 0.046 0.337 4436 Planarity : 0.004 0.059 4881 Dihedral : 5.495 92.692 4455 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.96 % Allowed : 14.36 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.04 (0.14), residues: 3419 helix: 0.46 (0.21), residues: 619 sheet: -0.57 (0.23), residues: 564 loop : -1.09 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.023 0.001 HIS A1048 PHE 0.022 0.001 PHE B 201 TYR 0.034 0.001 TYR A1007 ARG 0.005 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 28) link_NAG-ASN : angle 2.30521 ( 84) link_BETA1-4 : bond 0.00549 ( 7) link_BETA1-4 : angle 1.24637 ( 21) hydrogen bonds : bond 0.04153 ( 766) hydrogen bonds : angle 6.11800 ( 2085) SS BOND : bond 0.00248 ( 36) SS BOND : angle 0.81017 ( 72) covalent geometry : bond 0.00282 (28051) covalent geometry : angle 0.58887 (38171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4323 (OUTLIER) cc_final: 0.3972 (mp0) REVERT: A 660 TYR cc_start: 0.6728 (p90) cc_final: 0.6477 (p90) REVERT: A 1038 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8346 (mmmt) REVERT: B 1029 MET cc_start: 0.5066 (OUTLIER) cc_final: 0.4841 (ttm) REVERT: B 1038 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7679 (mmtm) REVERT: F 57 ASN cc_start: 0.6073 (p0) cc_final: 0.5641 (p0) outliers start: 59 outliers final: 47 residues processed: 380 average time/residue: 0.3640 time to fit residues: 227.8096 Evaluate side-chains 385 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 300 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 278 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.246595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.211773 restraints weight = 43124.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.212468 restraints weight = 44739.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.213332 restraints weight = 36527.993| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 28122 Z= 0.201 Angle : 0.674 13.153 38348 Z= 0.344 Chirality : 0.048 0.349 4436 Planarity : 0.005 0.062 4881 Dihedral : 5.764 89.073 4455 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.89 % Allowed : 14.59 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: -1.29 (0.14), residues: 3419 helix: 0.16 (0.20), residues: 620 sheet: -0.82 (0.22), residues: 574 loop : -1.20 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 353 HIS 0.025 0.001 HIS A1048 PHE 0.025 0.002 PHE A 192 TYR 0.028 0.002 TYR A1007 ARG 0.007 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 28) link_NAG-ASN : angle 2.41676 ( 84) link_BETA1-4 : bond 0.00528 ( 7) link_BETA1-4 : angle 1.27531 ( 21) hydrogen bonds : bond 0.04762 ( 766) hydrogen bonds : angle 6.44850 ( 2085) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.02426 ( 72) covalent geometry : bond 0.00461 (28051) covalent geometry : angle 0.66401 (38171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 352 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4334 (OUTLIER) cc_final: 0.3986 (mp0) REVERT: A 660 TYR cc_start: 0.6917 (p90) cc_final: 0.6647 (p90) REVERT: A 740 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.3212 (ttt) REVERT: A 1038 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8290 (mmmt) REVERT: B 347 PHE cc_start: 0.3980 (m-80) cc_final: 0.3609 (m-10) REVERT: B 1038 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7742 (mmtm) REVERT: C 716 THR cc_start: 0.7387 (p) cc_final: 0.7075 (t) REVERT: F 57 ASN cc_start: 0.6058 (p0) cc_final: 0.5648 (p0) outliers start: 57 outliers final: 48 residues processed: 386 average time/residue: 0.3721 time to fit residues: 233.9928 Evaluate side-chains 388 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 256 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 258 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 901 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C1011 GLN C1106 GLN G 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.249123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.213819 restraints weight = 43301.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.214487 restraints weight = 39568.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.214811 restraints weight = 36342.017| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28122 Z= 0.138 Angle : 0.631 15.907 38348 Z= 0.319 Chirality : 0.047 0.402 4436 Planarity : 0.004 0.060 4881 Dihedral : 5.598 88.073 4455 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.73 % Allowed : 15.03 % Favored : 83.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.78 % 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: -1.21 (0.14), residues: 3419 helix: 0.24 (0.21), residues: 619 sheet: -0.76 (0.23), residues: 568 loop : -1.15 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.020 0.001 HIS A1048 PHE 0.028 0.001 PHE C1103 TYR 0.026 0.001 TYR A1007 ARG 0.006 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 28) link_NAG-ASN : angle 2.28418 ( 84) link_BETA1-4 : bond 0.00541 ( 7) link_BETA1-4 : angle 1.27408 ( 21) hydrogen bonds : bond 0.04395 ( 766) hydrogen bonds : angle 6.28104 ( 2085) SS BOND : bond 0.00366 ( 36) SS BOND : angle 1.08742 ( 72) covalent geometry : bond 0.00312 (28051) covalent geometry : angle 0.62090 (38171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8902.70 seconds wall clock time: 156 minutes 21.23 seconds (9381.23 seconds total)