Starting phenix.real_space_refine on Sun Jul 5 14:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh7_33822/07_2026/7yh7_33822.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 119 5.16 5 C 18022 2.51 5 N 4667 2.21 5 O 5510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28318 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7369 Classifications: {'peptide': 945} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 893} Chain breaks: 12 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 7487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7487 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 51, 'TRANS': 908} Chain breaks: 11 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7481 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 51, 'TRANS': 909} Chain breaks: 10 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 823 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 823 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "S" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "U" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 823 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "V" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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 chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.72, per 1000 atoms: 0.20 Number of scatterers: 28318 At special positions: 0 Unit cell: (127.3, 169.51, 206.36, 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 119 16.00 O 5510 8.00 N 4667 7.00 C 18022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 90 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 90 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 90 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6618 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 63 sheets defined 22.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.596A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.246A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.264A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.634A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.609A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 940 removed outlier: 7.136A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.861A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.568A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.585A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.463A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.282A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.186A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.880A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.570A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.683A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.577A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.101A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.537A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.443A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.314A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.324A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.917A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.799A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.824A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.251A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.730A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.067A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 85 removed outlier: 3.996A pdb=" N ASP Q 84 " --> pdb=" O GLN Q 81 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU Q 85 " --> pdb=" O THR Q 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 81 through 85' Processing helix chain 'R' and resid 81 through 85 removed outlier: 3.562A pdb=" N ASP R 84 " --> pdb=" O GLN R 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU R 85 " --> pdb=" O THR R 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 81 through 85' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.732A pdb=" N THR S 91 " --> pdb=" O PRO S 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 85 removed outlier: 3.552A pdb=" N ASP U 84 " --> pdb=" O GLN U 81 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU U 85 " --> pdb=" O THR U 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 81 through 85' Processing helix chain 'V' and resid 28 through 32 Processing helix chain 'V' and resid 87 through 91 removed outlier: 4.056A pdb=" N THR V 91 " --> pdb=" O PRO V 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.518A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 4.136A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.871A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.147A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.624A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.612A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.612A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.704A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.325A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.821A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.042A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.534A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.978A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.227A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.645A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.594A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.347A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.367A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.682A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.623A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.516A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.240A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.822A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.636A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.655A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.535A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.177A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.177A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.545A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 9 through 10 removed outlier: 3.600A pdb=" N VAL Q 10 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP Q 37 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 9 through 10 removed outlier: 3.600A pdb=" N VAL Q 10 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP Q 94 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU Q 99 " --> pdb=" O ASP Q 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.813A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER P 25 " --> pdb=" O GLN P 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR P 78 " --> pdb=" O ASP P 73 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.569A pdb=" N THR P 119 " --> pdb=" O TYR P 94 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR P 94 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET P 34 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 9 through 10 removed outlier: 4.134A pdb=" N ALA R 86 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN R 39 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU R 48 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 9 through 10 removed outlier: 4.134A pdb=" N ALA R 86 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP R 94 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 99 " --> pdb=" O ASP R 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.515A pdb=" N VAL R 18 " --> pdb=" O ILE R 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.815A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.534A pdb=" N TYR S 94 " --> pdb=" O THR S 119 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET S 34 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.534A pdb=" N TYR S 94 " --> pdb=" O THR S 119 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE S 114 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 9 through 12 removed outlier: 4.166A pdb=" N ALA U 86 " --> pdb=" O VAL U 108 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN U 39 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU U 48 " --> pdb=" O GLN U 39 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 9 through 12 removed outlier: 4.166A pdb=" N ALA U 86 " --> pdb=" O VAL U 108 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP U 94 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU U 99 " --> pdb=" O ASP U 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 18 through 23 removed outlier: 3.812A pdb=" N VAL U 18 " --> pdb=" O ILE U 77 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 3 through 7 removed outlier: 3.566A pdb=" N GLN V 3 " --> pdb=" O SER V 25 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER V 25 " --> pdb=" O GLN V 3 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL V 5 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR V 78 " --> pdb=" O ASP V 73 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 11 through 12 removed outlier: 3.657A pdb=" N GLN V 39 " --> pdb=" O VAL V 93 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET V 34 " --> pdb=" O VAL V 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 2880 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: 5.80 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9032 1.34 - 1.46: 7180 1.46 - 1.58: 12594 1.58 - 1.70: 1 1.70 - 1.82: 149 Bond restraints: 28956 Sorted by residual: bond pdb=" CB PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.16e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 28951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 38573 1.58 - 3.16: 728 3.16 - 4.74: 75 4.74 - 6.32: 15 6.32 - 7.90: 4 Bond angle restraints: 39395 Sorted by residual: angle pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" CD PRO A 217 " ideal model delta sigma weight residual 112.00 104.80 7.20 1.40e+00 5.10e-01 2.65e+01 angle pdb=" C ASN C 801 " pdb=" CA ASN C 801 " pdb=" CB ASN C 801 " ideal model delta sigma weight residual 110.16 116.29 -6.13 1.66e+00 3.63e-01 1.36e+01 angle pdb=" C LEU B 518 " pdb=" N HIS B 519 " pdb=" CA HIS B 519 " ideal model delta sigma weight residual 121.54 127.88 -6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA ASN C1134 " pdb=" CB ASN C1134 " pdb=" CG ASN C1134 " ideal model delta sigma weight residual 112.60 115.41 -2.81 1.00e+00 1.00e+00 7.92e+00 angle pdb=" C LEU C 518 " pdb=" N HIS C 519 " pdb=" CA HIS C 519 " ideal model delta sigma weight residual 122.89 127.66 -4.77 1.72e+00 3.38e-01 7.68e+00 ... (remaining 39390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15242 17.99 - 35.98: 1314 35.98 - 53.97: 205 53.97 - 71.96: 42 71.96 - 89.95: 22 Dihedral angle restraints: 16825 sinusoidal: 6504 harmonic: 10321 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 93.00 174.23 -81.23 1 1.00e+01 1.00e-02 8.14e+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 93.00 171.50 -78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 19.59 73.41 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 16822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3908 0.063 - 0.125: 638 0.125 - 0.188: 17 0.188 - 0.250: 4 0.250 - 0.313: 1 Chirality restraints: 4568 Sorted by residual: chirality pdb=" CA ASN A 343 " pdb=" N ASN A 343 " pdb=" C ASN A 343 " pdb=" CB ASN A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4565 not shown) Planarity restraints: 5078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " 0.089 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO A 217 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.029 2.00e-02 2.50e+03 2.61e-02 8.52e+00 pdb=" CG ASN A 343 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO B 987 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.039 5.00e-02 4.00e+02 ... (remaining 5075 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1642 2.73 - 3.27: 26880 3.27 - 3.82: 43024 3.82 - 4.36: 49045 4.36 - 4.90: 89501 Nonbonded interactions: 210092 Sorted by model distance: nonbonded pdb=" OE1 GLN C 762 " pdb=" NH2 ARG C 765 " model vdw 2.190 3.120 nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 393 " pdb=" OE2 GLU B 516 " model vdw 2.215 3.040 nonbonded pdb=" O PRO U 7 " pdb=" OG1 THR U 106 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" OE2 GLU A 516 " model vdw 2.228 3.040 ... (remaining 210087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 95 or resid 101 through \ 133 or resid 167 through 196 or resid 200 through 209 or resid 216 through 217 o \ r (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 19 through 223 or (resid 224 and (name N or name CA or name C or name O or name \ CB )) or resid 225 through 240 or resid 265 through 866 or (resid 867 through 86 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 869 through \ 939 or (resid 940 and (name N or name CA or name C or name O or name CB )) or re \ sid 941 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1307)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 95 or resid 101 through \ 107 or resid 116 through 122 or resid 126 through 133 or resid 167 through 209 o \ r resid 216 through 231 or resid 237 through 585 or (resid 586 and (name N or na \ me CA or name C or name O or name CB )) or resid 587 through 676 or resid 692 th \ rough 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) \ or resid 746 through 826 or resid 856 through 866 or (resid 867 through 868 and \ (name N or name CA or name C or name O or name CB )) or resid 869 through 920 o \ r (resid 921 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 22 through 939 or (resid 940 and (name N or name CA or name C or name O or name \ CB )) or resid 941 through 987 or (resid 988 through 989 and (name N or name CA \ or name C or name O or name CB )) or resid 990 through 1117 or (resid 1118 and ( \ name N or name CA or name C or name O or name CB )) or resid 1119 through 1307)) \ selection = (chain 'C' and (resid 27 through 66 or resid 82 through 95 or resid 101 through \ 107 or resid 116 through 122 or resid 126 through 133 or resid 167 through 172 o \ r resid 188 through 196 or resid 200 through 209 or resid 216 through 217 or (re \ sid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 th \ rough 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) \ or resid 225 through 231 or resid 237 through 240 or resid 265 through 585 or ( \ resid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 \ through 676 or resid 692 through 826 or resid 856 through 920 or (resid 921 and \ (name N or name CA or name C or name O or name CB )) or resid 922 through 1117 o \ r (resid 1118 and (name N or name CA or name C or name O or name CB )) or resid \ 1119 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 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 : 0.003 0.102 29042 Z= 0.133 Angle : 0.545 11.907 39609 Z= 0.261 Chirality : 0.044 0.313 4568 Planarity : 0.004 0.130 5044 Dihedral : 13.428 89.947 10075 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3490 helix: 2.23 (0.21), residues: 664 sheet: 0.29 (0.17), residues: 965 loop : -1.02 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 16 TYR 0.012 0.001 TYR A 873 PHE 0.030 0.001 PHE S 76 TRP 0.007 0.001 TRP P 36 HIS 0.005 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (28956) covalent geometry : angle 0.51095 / 0.25 (39395) SS BOND : bond 0.00260 / 0.17 ( 44) SS BOND : angle 1.09360 / 0.59 ( 88) hydrogen bonds : bond 0.22104 / 14.36 ( 1029) hydrogen bonds : angle 7.71025 / 5.37 ( 2880) link_BETA1-4 : bond 0.00508 / 0.34 ( 8) link_BETA1-4 : angle 0.92968 / 0.59 ( 24) link_NAG-ASN : bond 0.00753 / 0.48 ( 34) link_NAG-ASN : angle 3.64198 / 2.18 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 TYR cc_start: 0.8183 (t80) cc_final: 0.7671 (t80) REVERT: B 189 LEU cc_start: 0.8112 (mp) cc_final: 0.7853 (mp) REVERT: B 542 ASN cc_start: 0.9000 (t0) cc_final: 0.8774 (t0) REVERT: B 740 MET cc_start: 0.8830 (tpp) cc_final: 0.8484 (tpp) REVERT: B 979 ASP cc_start: 0.8886 (t70) cc_final: 0.8485 (t0) REVERT: C 105 ILE cc_start: 0.7192 (tt) cc_final: 0.6805 (mt) REVERT: C 393 THR cc_start: 0.7584 (p) cc_final: 0.7161 (p) REVERT: C 516 GLU cc_start: 0.7376 (pm20) cc_final: 0.7010 (pm20) REVERT: S 83 MET cc_start: 0.2551 (mpp) cc_final: 0.0858 (ptp) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.1707 time to fit residues: 51.7071 Evaluate side-chains 120 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0020 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 122 ASN B 957 GLN B1106 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.138957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086609 restraints weight = 72345.036| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.87 r_work: 0.3008 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29042 Z= 0.123 Angle : 0.565 11.018 39609 Z= 0.290 Chirality : 0.044 0.316 4568 Planarity : 0.004 0.070 5044 Dihedral : 3.792 19.753 3826 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.62 % Rotamer: Outliers : 0.52 % Allowed : 5.95 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3490 helix: 2.33 (0.21), residues: 669 sheet: 0.36 (0.17), residues: 986 loop : -0.98 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.021 0.001 TYR C 453 PHE 0.027 0.001 PHE B 168 TRP 0.011 0.001 TRP A 436 HIS 0.011 0.001 HIS P 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (28956) covalent geometry : angle 0.54128 / 0.28 (39395) SS BOND : bond 0.00339 / 0.22 ( 44) SS BOND : angle 1.13564 / 0.66 ( 88) hydrogen bonds : bond 0.05638 / 3.58 ( 1029) hydrogen bonds : angle 5.87421 / 4.03 ( 2880) link_BETA1-4 : bond 0.00374 / 0.23 ( 8) link_BETA1-4 : angle 0.86750 / 0.53 ( 24) link_NAG-ASN : bond 0.00614 / 0.39 ( 34) link_NAG-ASN : angle 3.07828 / 1.99 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8165 (t80) cc_final: 0.7876 (t80) REVERT: B 170 TYR cc_start: 0.8126 (t80) cc_final: 0.7657 (t80) REVERT: B 189 LEU cc_start: 0.8449 (mp) cc_final: 0.8140 (mp) REVERT: B 542 ASN cc_start: 0.9057 (t0) cc_final: 0.8823 (t0) REVERT: B 740 MET cc_start: 0.9108 (tpp) cc_final: 0.8849 (tpp) REVERT: B 979 ASP cc_start: 0.9024 (t70) cc_final: 0.8677 (t0) REVERT: C 509 ARG cc_start: 0.5005 (mtt180) cc_final: 0.4671 (mtt180) REVERT: S 83 MET cc_start: 0.2625 (mpp) cc_final: 0.1432 (ptp) outliers start: 16 outliers final: 5 residues processed: 135 average time/residue: 0.1819 time to fit residues: 40.6338 Evaluate side-chains 112 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 582 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 201 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 316 optimal weight: 50.0000 chunk 172 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 957 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 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 = 0.4140 r_free = 0.4140 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082036 restraints weight = 73760.445| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.21 r_work: 0.2980 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29042 Z= 0.166 Angle : 0.560 11.104 39609 Z= 0.286 Chirality : 0.044 0.202 4568 Planarity : 0.004 0.067 5044 Dihedral : 3.891 19.463 3826 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 0.78 % Allowed : 9.10 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3490 helix: 2.12 (0.21), residues: 674 sheet: 0.25 (0.17), residues: 991 loop : -0.98 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.027 0.001 TYR C 170 PHE 0.021 0.001 PHE A 906 TRP 0.013 0.001 TRP S 47 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (28956) covalent geometry : angle 0.53690 / 0.28 (39395) SS BOND : bond 0.00351 / 0.23 ( 44) SS BOND : angle 1.21399 / 0.73 ( 88) hydrogen bonds : bond 0.06241 / 3.96 ( 1029) hydrogen bonds : angle 5.54387 / 3.79 ( 2880) link_BETA1-4 : bond 0.00232 / 0.12 ( 8) link_BETA1-4 : angle 0.95968 / 0.59 ( 24) link_NAG-ASN : bond 0.00567 / 0.36 ( 34) link_NAG-ASN : angle 2.97252 / 1.93 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7936 (t80) cc_final: 0.7682 (t80) REVERT: B 170 TYR cc_start: 0.7720 (t80) cc_final: 0.7259 (t80) REVERT: B 979 ASP cc_start: 0.9056 (t70) cc_final: 0.8741 (t0) REVERT: C 410 ILE cc_start: 0.8117 (mm) cc_final: 0.7867 (pt) REVERT: C 509 ARG cc_start: 0.5127 (mtt180) cc_final: 0.4779 (mtt180) REVERT: P 32 PHE cc_start: 0.6178 (m-80) cc_final: 0.5722 (m-80) REVERT: S 34 MET cc_start: 0.4929 (OUTLIER) cc_final: 0.4588 (tmm) REVERT: S 83 MET cc_start: 0.2294 (mpp) cc_final: 0.1030 (ptp) outliers start: 24 outliers final: 14 residues processed: 136 average time/residue: 0.1828 time to fit residues: 41.2427 Evaluate side-chains 117 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain S residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 236 optimal weight: 0.9990 chunk 346 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 332 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086400 restraints weight = 73298.345| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.11 r_work: 0.3002 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29042 Z= 0.125 Angle : 0.522 11.517 39609 Z= 0.266 Chirality : 0.043 0.200 4568 Planarity : 0.004 0.065 5044 Dihedral : 3.770 18.822 3826 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 0.84 % Allowed : 10.98 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3490 helix: 2.24 (0.21), residues: 675 sheet: 0.24 (0.17), residues: 974 loop : -0.90 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 357 TYR 0.022 0.001 TYR C 170 PHE 0.016 0.001 PHE C 168 TRP 0.011 0.001 TRP S 47 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (28956) covalent geometry : angle 0.49904 / 0.26 (39395) SS BOND : bond 0.00326 / 0.22 ( 44) SS BOND : angle 1.06929 / 0.63 ( 88) hydrogen bonds : bond 0.05505 / 3.48 ( 1029) hydrogen bonds : angle 5.28803 / 3.61 ( 2880) link_BETA1-4 : bond 0.00273 / 0.15 ( 8) link_BETA1-4 : angle 0.82508 / 0.50 ( 24) link_NAG-ASN : bond 0.00529 / 0.34 ( 34) link_NAG-ASN : angle 2.88301 / 1.85 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7985 (t80) cc_final: 0.7726 (t80) REVERT: A 409 GLN cc_start: 0.6807 (mt0) cc_final: 0.6544 (mt0) REVERT: B 170 TYR cc_start: 0.7846 (t80) cc_final: 0.7257 (t80) REVERT: B 979 ASP cc_start: 0.9034 (t70) cc_final: 0.8741 (t0) REVERT: C 378 LYS cc_start: 0.7801 (tptm) cc_final: 0.7555 (tptm) REVERT: C 509 ARG cc_start: 0.5240 (mtt180) cc_final: 0.4866 (mtt180) REVERT: P 32 PHE cc_start: 0.6296 (m-80) cc_final: 0.5976 (m-80) REVERT: S 34 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4688 (tmm) REVERT: S 83 MET cc_start: 0.2145 (mpp) cc_final: 0.0611 (ptp) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.1866 time to fit residues: 39.7522 Evaluate side-chains 117 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain S residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 307 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 241 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 992 GLN ** P 35 HIS ** 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 = 0.4139 r_free = 0.4139 target = 0.136740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086085 restraints weight = 71759.878| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 5.14 r_work: 0.2917 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29042 Z= 0.147 Angle : 0.531 11.340 39609 Z= 0.271 Chirality : 0.044 0.198 4568 Planarity : 0.004 0.066 5044 Dihedral : 3.776 19.660 3826 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.17 % Allowed : 11.47 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3490 helix: 2.19 (0.21), residues: 673 sheet: 0.19 (0.16), residues: 977 loop : -0.91 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 765 TYR 0.020 0.001 TYR C 453 PHE 0.017 0.001 PHE C 168 TRP 0.009 0.001 TRP S 47 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (28956) covalent geometry : angle 0.51050 / 0.27 (39395) SS BOND : bond 0.00363 / 0.25 ( 44) SS BOND : angle 1.09322 / 0.66 ( 88) hydrogen bonds : bond 0.05813 / 3.68 ( 1029) hydrogen bonds : angle 5.20269 / 3.55 ( 2880) link_BETA1-4 : bond 0.00232 / 0.12 ( 8) link_BETA1-4 : angle 0.90952 / 0.56 ( 24) link_NAG-ASN : bond 0.00472 / 0.31 ( 34) link_NAG-ASN : angle 2.76325 / 1.76 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8025 (t80) cc_final: 0.7760 (t80) REVERT: A 409 GLN cc_start: 0.6971 (mt0) cc_final: 0.6716 (mt0) REVERT: A 581 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8564 (p) REVERT: B 979 ASP cc_start: 0.9080 (t70) cc_final: 0.8806 (t0) REVERT: C 509 ARG cc_start: 0.5317 (mtt180) cc_final: 0.4916 (mtt180) REVERT: S 34 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.4399 (tmm) REVERT: S 83 MET cc_start: 0.2077 (mpp) cc_final: 0.0673 (ptp) outliers start: 36 outliers final: 19 residues processed: 134 average time/residue: 0.1605 time to fit residues: 36.0637 Evaluate side-chains 118 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain S residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 66 optimal weight: 4.9990 chunk 334 optimal weight: 20.0000 chunk 90 optimal weight: 0.0060 chunk 245 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 326 optimal weight: 30.0000 chunk 228 optimal weight: 10.0000 chunk 320 optimal weight: 30.0000 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 957 GLN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 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 = 0.4135 r_free = 0.4135 target = 0.135669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081507 restraints weight = 72097.984| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.37 r_work: 0.2978 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29042 Z= 0.149 Angle : 0.533 11.890 39609 Z= 0.270 Chirality : 0.044 0.197 4568 Planarity : 0.004 0.063 5044 Dihedral : 3.865 45.971 3826 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.88 % Allowed : 12.51 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3490 helix: 2.18 (0.21), residues: 673 sheet: 0.23 (0.16), residues: 974 loop : -0.89 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 98 TYR 0.032 0.001 TYR B 495 PHE 0.018 0.001 PHE B 497 TRP 0.007 0.001 TRP S 47 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (28956) covalent geometry : angle 0.51270 / 0.27 (39395) SS BOND : bond 0.00389 / 0.28 ( 44) SS BOND : angle 1.18149 / 0.70 ( 88) hydrogen bonds : bond 0.05814 / 3.68 ( 1029) hydrogen bonds : angle 5.15468 / 3.52 ( 2880) link_BETA1-4 : bond 0.00264 / 0.14 ( 8) link_BETA1-4 : angle 0.88621 / 0.55 ( 24) link_NAG-ASN : bond 0.00449 / 0.30 ( 34) link_NAG-ASN : angle 2.70727 / 1.71 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7955 (t80) cc_final: 0.7723 (t80) REVERT: A 409 GLN cc_start: 0.6836 (mt0) cc_final: 0.6586 (mt0) REVERT: A 581 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8613 (p) REVERT: B 979 ASP cc_start: 0.9055 (t70) cc_final: 0.8794 (t0) REVERT: C 509 ARG cc_start: 0.5290 (mtt180) cc_final: 0.4938 (mtt180) REVERT: P 32 PHE cc_start: 0.6090 (m-80) cc_final: 0.5815 (t80) REVERT: S 34 MET cc_start: 0.4453 (OUTLIER) cc_final: 0.3801 (tmm) REVERT: S 83 MET cc_start: 0.2017 (mpp) cc_final: 0.0689 (ptp) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.1678 time to fit residues: 34.4739 Evaluate side-chains 119 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain S residue 34 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 245 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 316 optimal weight: 50.0000 chunk 42 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 957 GLN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085303 restraints weight = 73254.826| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.15 r_work: 0.2977 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29042 Z= 0.150 Angle : 0.530 11.041 39609 Z= 0.269 Chirality : 0.044 0.195 4568 Planarity : 0.004 0.062 5044 Dihedral : 3.827 38.227 3826 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.30 % Allowed : 12.74 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3490 helix: 2.18 (0.21), residues: 674 sheet: 0.24 (0.16), residues: 980 loop : -0.89 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 98 TYR 0.026 0.001 TYR B 495 PHE 0.021 0.001 PHE B 168 TRP 0.007 0.001 TRP V 47 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (28956) covalent geometry : angle 0.51082 / 0.26 (39395) SS BOND : bond 0.00303 / 0.19 ( 44) SS BOND : angle 1.24438 / 0.74 ( 88) hydrogen bonds : bond 0.05837 / 3.70 ( 1029) hydrogen bonds : angle 5.09190 / 3.48 ( 2880) link_BETA1-4 : bond 0.00236 / 0.12 ( 8) link_BETA1-4 : angle 0.91222 / 0.57 ( 24) link_NAG-ASN : bond 0.00431 / 0.29 ( 34) link_NAG-ASN : angle 2.58529 / 1.63 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8018 (t80) cc_final: 0.7775 (t80) REVERT: A 409 GLN cc_start: 0.6941 (mt0) cc_final: 0.6735 (mt0) REVERT: A 581 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (p) REVERT: B 84 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (mm) REVERT: B 170 TYR cc_start: 0.7788 (t80) cc_final: 0.7307 (t80) REVERT: B 560 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 509 ARG cc_start: 0.5370 (mtt180) cc_final: 0.4976 (mtt180) REVERT: P 32 PHE cc_start: 0.6120 (m-80) cc_final: 0.5762 (t80) REVERT: S 83 MET cc_start: 0.2041 (mpp) cc_final: 0.0588 (ptp) outliers start: 40 outliers final: 24 residues processed: 132 average time/residue: 0.1843 time to fit residues: 40.5512 Evaluate side-chains 120 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 7 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 329 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.139742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086188 restraints weight = 73890.323| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.17 r_work: 0.2981 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29042 Z= 0.139 Angle : 0.527 11.032 39609 Z= 0.267 Chirality : 0.043 0.194 4568 Planarity : 0.004 0.061 5044 Dihedral : 3.805 41.370 3826 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.10 % Allowed : 13.10 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3490 helix: 2.23 (0.21), residues: 673 sheet: 0.26 (0.16), residues: 1001 loop : -0.88 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 98 TYR 0.031 0.001 TYR C 453 PHE 0.012 0.001 PHE B1121 TRP 0.006 0.001 TRP A 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (28956) covalent geometry : angle 0.50883 / 0.26 (39395) SS BOND : bond 0.00327 / 0.21 ( 44) SS BOND : angle 1.15205 / 0.67 ( 88) hydrogen bonds : bond 0.05699 / 3.61 ( 1029) hydrogen bonds : angle 5.04874 / 3.45 ( 2880) link_BETA1-4 : bond 0.00253 / 0.14 ( 8) link_BETA1-4 : angle 0.89676 / 0.56 ( 24) link_NAG-ASN : bond 0.00406 / 0.28 ( 34) link_NAG-ASN : angle 2.54889 / 1.60 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 581 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 84 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7705 (mm) REVERT: B 170 TYR cc_start: 0.7782 (t80) cc_final: 0.7366 (t80) REVERT: B 560 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 509 ARG cc_start: 0.5335 (mtt180) cc_final: 0.4957 (mtt180) REVERT: P 32 PHE cc_start: 0.6127 (m-80) cc_final: 0.5912 (t80) REVERT: P 98 ARG cc_start: 0.4450 (ptm-80) cc_final: 0.4220 (ptm-80) REVERT: S 83 MET cc_start: 0.2008 (mpp) cc_final: 0.0575 (ptp) outliers start: 34 outliers final: 23 residues processed: 128 average time/residue: 0.1803 time to fit residues: 38.9577 Evaluate side-chains 121 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 20 optimal weight: 0.1980 chunk 129 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 341 optimal weight: 30.0000 chunk 322 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 328 optimal weight: 30.0000 chunk 320 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 346 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 804 GLN B 957 GLN ** P 35 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.132248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078600 restraints weight = 72793.851| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.20 r_work: 0.2978 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29042 Z= 0.182 Angle : 0.561 10.903 39609 Z= 0.285 Chirality : 0.044 0.198 4568 Planarity : 0.004 0.062 5044 Dihedral : 3.936 41.488 3826 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.01 % Allowed : 13.49 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3490 helix: 2.11 (0.21), residues: 672 sheet: 0.26 (0.16), residues: 990 loop : -0.92 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 98 TYR 0.034 0.001 TYR C 380 PHE 0.021 0.001 PHE B 168 TRP 0.012 0.001 TRP S 36 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (28956) covalent geometry : angle 0.54297 / 0.28 (39395) SS BOND : bond 0.00370 / 0.23 ( 44) SS BOND : angle 1.27044 / 0.75 ( 88) hydrogen bonds : bond 0.06288 / 3.99 ( 1029) hydrogen bonds : angle 5.17281 / 3.54 ( 2880) link_BETA1-4 : bond 0.00252 / 0.13 ( 8) link_BETA1-4 : angle 0.98738 / 0.62 ( 24) link_NAG-ASN : bond 0.00392 / 0.27 ( 34) link_NAG-ASN : angle 2.58100 / 1.63 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 581 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8640 (p) REVERT: B 84 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7781 (mm) REVERT: B 170 TYR cc_start: 0.7843 (t80) cc_final: 0.7378 (t80) REVERT: B 497 PHE cc_start: 0.0989 (m-80) cc_final: 0.0456 (m-80) REVERT: B 560 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 509 ARG cc_start: 0.5382 (mtt180) cc_final: 0.4991 (mtt180) REVERT: S 83 MET cc_start: 0.1973 (mpp) cc_final: 0.0433 (ptp) outliers start: 31 outliers final: 24 residues processed: 130 average time/residue: 0.1824 time to fit residues: 39.9096 Evaluate side-chains 125 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 313 optimal weight: 40.0000 chunk 93 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 336 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.133681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080418 restraints weight = 72286.381| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.22 r_work: 0.3005 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29042 Z= 0.124 Angle : 0.525 10.951 39609 Z= 0.265 Chirality : 0.043 0.245 4568 Planarity : 0.004 0.064 5044 Dihedral : 3.808 41.235 3826 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.84 % Allowed : 14.07 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3490 helix: 2.33 (0.21), residues: 667 sheet: 0.34 (0.16), residues: 1022 loop : -0.91 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 98 TYR 0.035 0.001 TYR B 495 PHE 0.014 0.001 PHE A 374 TRP 0.009 0.001 TRP S 36 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (28956) covalent geometry : angle 0.50767 / 0.26 (39395) SS BOND : bond 0.00308 / 0.19 ( 44) SS BOND : angle 1.10682 / 0.63 ( 88) hydrogen bonds : bond 0.05514 / 3.49 ( 1029) hydrogen bonds : angle 5.01637 / 3.43 ( 2880) link_BETA1-4 : bond 0.00285 / 0.16 ( 8) link_BETA1-4 : angle 0.86926 / 0.54 ( 24) link_NAG-ASN : bond 0.00413 / 0.28 ( 34) link_NAG-ASN : angle 2.48543 / 1.56 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 581 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 84 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7719 (mm) REVERT: B 170 TYR cc_start: 0.7838 (t80) cc_final: 0.7435 (t80) REVERT: B 497 PHE cc_start: 0.0475 (m-80) cc_final: 0.0093 (m-80) REVERT: B 560 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (mp) REVERT: C 509 ARG cc_start: 0.5314 (mtt180) cc_final: 0.4960 (mtt180) REVERT: P 34 MET cc_start: 0.6166 (ptp) cc_final: 0.5703 (ptp) REVERT: S 83 MET cc_start: 0.1951 (mpp) cc_final: 0.0444 (ptp) outliers start: 26 outliers final: 21 residues processed: 127 average time/residue: 0.1799 time to fit residues: 39.1614 Evaluate side-chains 126 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 250 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 322 optimal weight: 40.0000 chunk 141 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.131669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078338 restraints weight = 73094.661| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.14 r_work: 0.2981 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29042 Z= 0.180 Angle : 0.557 10.874 39609 Z= 0.283 Chirality : 0.044 0.208 4568 Planarity : 0.004 0.063 5044 Dihedral : 3.925 41.416 3826 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.94 % Allowed : 13.97 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3490 helix: 2.18 (0.21), residues: 669 sheet: 0.27 (0.16), residues: 991 loop : -0.91 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 98 TYR 0.040 0.001 TYR C 380 PHE 0.019 0.001 PHE B 168 TRP 0.016 0.001 TRP U 37 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (28956) covalent geometry : angle 0.53995 / 0.28 (39395) SS BOND : bond 0.00350 / 0.22 ( 44) SS BOND : angle 1.23872 / 0.74 ( 88) hydrogen bonds : bond 0.06151 / 3.91 ( 1029) hydrogen bonds : angle 5.12967 / 3.51 ( 2880) link_BETA1-4 : bond 0.00256 / 0.13 ( 8) link_BETA1-4 : angle 0.96880 / 0.60 ( 24) link_NAG-ASN : bond 0.00377 / 0.26 ( 34) link_NAG-ASN : angle 2.53670 / 1.60 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9036.02 seconds wall clock time: 155 minutes 2.88 seconds (9302.88 seconds total)