Starting phenix.real_space_refine on Mon Aug 25 13:38:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yh7_33822/08_2025/7yh7_33822.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh7_33822/08_2025/7yh7_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_33822/08_2025/7yh7_33822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh7_33822/08_2025/7yh7_33822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yh7_33822/08_2025/7yh7_33822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh7_33822/08_2025/7yh7_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 33 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 dihedrals: 21 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.38, per 1000 atoms: 0.19 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.34 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: 6.18 Time building geometry restraints manager: 2.47 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: 16022 17.99 - 35.98: 1368 35.98 - 53.97: 262 53.97 - 71.96: 54 71.96 - 89.95: 22 Dihedral angle restraints: 17728 sinusoidal: 7407 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 17725 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: 8.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.890 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 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 : 13.546 89.947 10978 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 aren 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 covalent geometry : bond 0.00272 (28956) covalent geometry : angle 0.51095 (39395) SS BOND : bond 0.00260 ( 44) SS BOND : angle 1.09360 ( 88) hydrogen bonds : bond 0.22104 ( 1029) hydrogen bonds : angle 7.71025 ( 2880) link_BETA1-4 : bond 0.00508 ( 8) link_BETA1-4 : angle 0.92968 ( 24) link_NAG-ASN : bond 0.00753 ( 34) link_NAG-ASN : angle 3.64198 ( 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 : 0.829 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: 0.8113 (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: 0.8885 (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: 0.1612 time to fit residues: 48.2624 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 : 1.041 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4162 r_free = 0.4162 target = 0.135892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083818 restraints weight = 73432.094| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.69 r_work: 0.3006 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29042 Z= 0.123 Angle : 0.567 10.938 39609 Z= 0.290 Chirality : 0.044 0.291 4568 Planarity : 0.004 0.070 5044 Dihedral : 6.547 58.633 4729 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 0.49 % Allowed : 6.17 % Favored : 93.34 % 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 aren not related in a simple way. whole: 0.09 (0.14), residues: 3490 helix: 2.33 (0.21), residues: 669 sheet: 0.34 (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 0.012 0.001 TRP A 436 HIS 0.010 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00272 (28956) covalent geometry : angle 0.54326 (39395) SS BOND : bond 0.00347 ( 44) SS BOND : angle 1.13076 ( 88) hydrogen bonds : bond 0.05532 ( 1029) hydrogen bonds : angle 5.82214 ( 2880) link_BETA1-4 : bond 0.00474 ( 8) link_BETA1-4 : angle 0.83258 ( 24) link_NAG-ASN : bond 0.00597 ( 34) link_NAG-ASN : angle 3.11187 ( 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 138 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8134 (t80) cc_final: 0.7853 (t80) REVERT: B 170 TYR cc_start: 0.8014 (t80) cc_final: 0.7582 (t80) REVERT: B 189 LEU cc_start: 0.8449 (mp) cc_final: 0.8214 (tp) REVERT: B 542 ASN cc_start: 0.9062 (t0) cc_final: 0.8832 (t0) REVERT: B 740 MET cc_start: 0.9125 (tpp) cc_final: 0.8855 (tpp) REVERT: B 979 ASP cc_start: 0.9030 (t70) cc_final: 0.8689 (t0) REVERT: C 509 ARG cc_start: 0.5015 (mtt180) cc_final: 0.4688 (mtt180) REVERT: S 83 MET cc_start: 0.2619 (mpp) cc_final: 0.1373 (ptp) outliers start: 15 outliers final: 5 residues processed: 134 average time/residue: 0.1612 time to fit residues: 35.6696 Evaluate side-chains 113 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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: 1.9990 chunk 328 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 281 optimal weight: 0.3980 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 317 optimal weight: 5.9990 chunk 316 optimal weight: 40.0000 chunk 172 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** U 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082768 restraints weight = 72567.174| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.45 r_work: 0.2979 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29042 Z= 0.161 Angle : 0.556 11.185 39609 Z= 0.284 Chirality : 0.044 0.210 4568 Planarity : 0.004 0.067 5044 Dihedral : 5.938 58.462 4729 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 0.88 % Allowed : 9.13 % Favored : 89.99 % 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 aren not related in a simple way. whole: 0.00 (0.14), residues: 3490 helix: 2.12 (0.21), residues: 675 sheet: 0.24 (0.17), residues: 991 loop : -0.97 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 765 TYR 0.025 0.001 TYR C 170 PHE 0.020 0.001 PHE A 906 TRP 0.012 0.001 TRP S 47 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00380 (28956) covalent geometry : angle 0.53248 (39395) SS BOND : bond 0.00341 ( 44) SS BOND : angle 1.21305 ( 88) hydrogen bonds : bond 0.06226 ( 1029) hydrogen bonds : angle 5.49453 ( 2880) link_BETA1-4 : bond 0.00247 ( 8) link_BETA1-4 : angle 1.01311 ( 24) link_NAG-ASN : bond 0.00590 ( 34) link_NAG-ASN : angle 2.98413 ( 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 144 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7966 (t80) cc_final: 0.7707 (t80) REVERT: B 170 TYR cc_start: 0.7826 (t80) cc_final: 0.7316 (t80) REVERT: B 979 ASP cc_start: 0.9057 (t70) cc_final: 0.8743 (t0) REVERT: C 410 ILE cc_start: 0.8115 (mm) cc_final: 0.7858 (pt) REVERT: C 509 ARG cc_start: 0.5105 (mtt180) cc_final: 0.4810 (mtt180) REVERT: P 32 PHE cc_start: 0.6058 (m-80) cc_final: 0.5777 (m-80) REVERT: S 34 MET cc_start: 0.4895 (OUTLIER) cc_final: 0.4569 (tmm) REVERT: S 83 MET cc_start: 0.2336 (mpp) cc_final: 0.1068 (ptp) outliers start: 27 outliers final: 14 residues processed: 138 average time/residue: 0.1579 time to fit residues: 36.3780 Evaluate side-chains 120 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 8.9990 chunk 346 optimal weight: 10.0000 chunk 214 optimal weight: 0.0270 chunk 56 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 336 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 332 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN ** C 519 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 = 0.4160 r_free = 0.4160 target = 0.136850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084233 restraints weight = 72984.401| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.20 r_work: 0.3036 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29042 Z= 0.096 Angle : 0.501 11.729 39609 Z= 0.255 Chirality : 0.043 0.204 4568 Planarity : 0.004 0.073 5044 Dihedral : 5.363 57.103 4729 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 0.88 % Allowed : 10.40 % Favored : 88.72 % 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 aren not related in a simple way. whole: 0.18 (0.14), residues: 3490 helix: 2.43 (0.21), residues: 670 sheet: 0.29 (0.17), residues: 970 loop : -0.86 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.024 0.001 TYR C 380 PHE 0.018 0.001 PHE C 168 TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00197 (28956) covalent geometry : angle 0.47782 (39395) SS BOND : bond 0.00272 ( 44) SS BOND : angle 0.95424 ( 88) hydrogen bonds : bond 0.04884 ( 1029) hydrogen bonds : angle 5.15966 ( 2880) link_BETA1-4 : bond 0.00409 ( 8) link_BETA1-4 : angle 0.84147 ( 24) link_NAG-ASN : bond 0.00586 ( 34) link_NAG-ASN : angle 2.89242 ( 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 138 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7939 (t80) cc_final: 0.7681 (t80) REVERT: A 409 GLN cc_start: 0.6832 (mt0) cc_final: 0.6530 (mt0) REVERT: B 170 TYR cc_start: 0.7840 (t80) cc_final: 0.7278 (t80) REVERT: B 979 ASP cc_start: 0.9019 (t70) cc_final: 0.8712 (t0) REVERT: C 509 ARG cc_start: 0.5170 (mtt180) cc_final: 0.4839 (mtt180) REVERT: S 34 MET cc_start: 0.4821 (OUTLIER) cc_final: 0.4539 (tmm) REVERT: S 83 MET cc_start: 0.2166 (mpp) cc_final: 0.0814 (ptp) outliers start: 27 outliers final: 11 residues processed: 133 average time/residue: 0.1506 time to fit residues: 33.2259 Evaluate side-chains 111 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 P residue 34 MET 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: 0.9990 chunk 162 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN B 957 GLN C 992 GLN ** U 16 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 = 0.4161 r_free = 0.4161 target = 0.137409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084467 restraints weight = 72595.835| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.35 r_work: 0.3016 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29042 Z= 0.106 Angle : 0.496 11.547 39609 Z= 0.252 Chirality : 0.043 0.200 4568 Planarity : 0.004 0.069 5044 Dihedral : 4.936 56.347 4729 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.01 % Allowed : 10.69 % Favored : 88.30 % 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 aren not related in a simple way. whole: 0.21 (0.14), residues: 3490 helix: 2.42 (0.21), residues: 675 sheet: 0.30 (0.17), residues: 969 loop : -0.83 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 98 TYR 0.020 0.001 TYR C 453 PHE 0.018 0.001 PHE C 168 TRP 0.009 0.001 TRP S 47 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00238 (28956) covalent geometry : angle 0.47376 (39395) SS BOND : bond 0.00275 ( 44) SS BOND : angle 0.99999 ( 88) hydrogen bonds : bond 0.04942 ( 1029) hydrogen bonds : angle 5.00421 ( 2880) link_BETA1-4 : bond 0.00316 ( 8) link_BETA1-4 : angle 0.95201 ( 24) link_NAG-ASN : bond 0.00520 ( 34) link_NAG-ASN : angle 2.78049 ( 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 140 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7931 (t80) cc_final: 0.7671 (t80) REVERT: A 409 GLN cc_start: 0.6822 (mt0) cc_final: 0.6535 (mt0) REVERT: A 581 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 979 ASP cc_start: 0.9006 (t70) cc_final: 0.8728 (t0) REVERT: C 509 ARG cc_start: 0.5202 (mtt180) cc_final: 0.4808 (mtt180) REVERT: S 34 MET cc_start: 0.4730 (OUTLIER) cc_final: 0.4323 (tmm) REVERT: S 83 MET cc_start: 0.2106 (mpp) cc_final: 0.0610 (ptp) outliers start: 31 outliers final: 19 residues processed: 135 average time/residue: 0.1928 time to fit residues: 43.1566 Evaluate side-chains 119 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 34 MET 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: 7.9990 chunk 334 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1005 GLN B 957 GLN B1135 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 914 ASN C1002 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.132938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078374 restraints weight = 72416.964| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.37 r_work: 0.2904 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 29042 Z= 0.366 Angle : 0.722 12.260 39609 Z= 0.370 Chirality : 0.050 0.235 4568 Planarity : 0.005 0.067 5044 Dihedral : 5.973 57.521 4729 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.14 % Allowed : 12.19 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3490 helix: 1.40 (0.20), residues: 680 sheet: 0.01 (0.16), residues: 991 loop : -1.11 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.027 0.002 TYR B1067 PHE 0.026 0.002 PHE A1121 TRP 0.014 0.002 TRP A1102 HIS 0.010 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00907 (28956) covalent geometry : angle 0.70018 (39395) SS BOND : bond 0.00522 ( 44) SS BOND : angle 1.82735 ( 88) hydrogen bonds : bond 0.08468 ( 1029) hydrogen bonds : angle 5.74580 ( 2880) link_BETA1-4 : bond 0.00454 ( 8) link_BETA1-4 : angle 1.35476 ( 24) link_NAG-ASN : bond 0.00593 ( 34) link_NAG-ASN : angle 3.12977 ( 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 142 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.6857 (mt0) cc_final: 0.6586 (mt0) REVERT: A 581 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8750 (p) REVERT: B 170 TYR cc_start: 0.7622 (t80) cc_final: 0.7247 (t80) REVERT: C 441 LEU cc_start: 0.7174 (mm) cc_final: 0.6866 (mt) REVERT: C 509 ARG cc_start: 0.5154 (mtt180) cc_final: 0.4870 (mtt180) REVERT: S 34 MET cc_start: 0.3911 (OUTLIER) cc_final: 0.3510 (tmm) REVERT: S 83 MET cc_start: 0.2227 (mpp) cc_final: 0.0839 (ptp) outliers start: 35 outliers final: 19 residues processed: 135 average time/residue: 0.1817 time to fit residues: 41.7350 Evaluate side-chains 117 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 980 ILE 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 C residue 101 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 351 TYR 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 1104 VAL Chi-restraints excluded: chain P residue 34 MET 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: 0.9980 chunk 131 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 762 GLN C 914 ASN ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.137979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085227 restraints weight = 73447.005| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.08 r_work: 0.2965 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2230 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= 0.138 Angle : 0.541 11.019 39609 Z= 0.276 Chirality : 0.044 0.210 4568 Planarity : 0.004 0.063 5044 Dihedral : 5.388 57.780 4729 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.20 % Allowed : 12.93 % Favored : 85.86 % 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 aren not related in a simple way. whole: -0.14 (0.14), residues: 3490 helix: 1.92 (0.20), residues: 679 sheet: 0.10 (0.16), residues: 1006 loop : -1.01 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 98 TYR 0.039 0.001 TYR B 495 PHE 0.012 0.001 PHE B1095 TRP 0.008 0.001 TRP A 886 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00326 (28956) covalent geometry : angle 0.52050 (39395) SS BOND : bond 0.00300 ( 44) SS BOND : angle 1.21473 ( 88) hydrogen bonds : bond 0.06144 ( 1029) hydrogen bonds : angle 5.24772 ( 2880) link_BETA1-4 : bond 0.00302 ( 8) link_BETA1-4 : angle 0.96326 ( 24) link_NAG-ASN : bond 0.00461 ( 34) link_NAG-ASN : angle 2.77105 ( 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 137 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7988 (t80) cc_final: 0.7784 (t80) REVERT: A 409 GLN cc_start: 0.7003 (mt0) cc_final: 0.6692 (mt0) REVERT: A 581 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 84 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7709 (mm) REVERT: B 170 TYR cc_start: 0.7778 (t80) cc_final: 0.7354 (t80) REVERT: B 560 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8618 (mp) REVERT: C 441 LEU cc_start: 0.7385 (mm) cc_final: 0.6407 (mm) REVERT: C 509 ARG cc_start: 0.5293 (mtt180) cc_final: 0.4800 (mtt180) REVERT: S 34 MET cc_start: 0.4264 (OUTLIER) cc_final: 0.3815 (tmm) REVERT: S 83 MET cc_start: 0.1952 (mpp) cc_final: 0.0465 (ptp) outliers start: 37 outliers final: 24 residues processed: 128 average time/residue: 0.1929 time to fit residues: 41.1975 Evaluate side-chains 127 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 B residue 84 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 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 241 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR 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 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain S residue 34 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 7 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 957 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.135232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081876 restraints weight = 74021.574| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.12 r_work: 0.2954 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2363 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= 0.185 Angle : 0.568 11.104 39609 Z= 0.289 Chirality : 0.044 0.213 4568 Planarity : 0.004 0.063 5044 Dihedral : 5.334 56.663 4729 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.23 % Allowed : 13.45 % Favored : 85.31 % 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 aren not related in a simple way. whole: -0.15 (0.14), residues: 3490 helix: 1.90 (0.20), residues: 678 sheet: 0.13 (0.16), residues: 997 loop : -1.02 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 98 TYR 0.033 0.001 TYR S 107 PHE 0.021 0.001 PHE B 168 TRP 0.006 0.001 TRP V 47 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00448 (28956) covalent geometry : angle 0.54736 (39395) SS BOND : bond 0.00339 ( 44) SS BOND : angle 1.29790 ( 88) hydrogen bonds : bond 0.06513 ( 1029) hydrogen bonds : angle 5.25417 ( 2880) link_BETA1-4 : bond 0.00229 ( 8) link_BETA1-4 : angle 1.11511 ( 24) link_NAG-ASN : bond 0.00417 ( 34) link_NAG-ASN : angle 2.76416 ( 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 144 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.6742 (mt0) cc_final: 0.6461 (mt0) REVERT: A 581 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8673 (p) REVERT: B 84 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7706 (mm) REVERT: B 170 TYR cc_start: 0.7773 (t80) cc_final: 0.7347 (t80) REVERT: B 560 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8635 (mp) REVERT: C 441 LEU cc_start: 0.6547 (mm) cc_final: 0.6315 (mm) REVERT: C 509 ARG cc_start: 0.5026 (mtt180) cc_final: 0.4627 (mtt180) REVERT: S 34 MET cc_start: 0.4018 (OUTLIER) cc_final: 0.3641 (tmm) REVERT: S 83 MET cc_start: 0.2015 (mpp) cc_final: 0.0554 (ptp) outliers start: 38 outliers final: 27 residues processed: 135 average time/residue: 0.1663 time to fit residues: 38.2670 Evaluate side-chains 131 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR 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 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain S residue 34 MET 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: 9.9990 chunk 305 optimal weight: 0.0970 chunk 341 optimal weight: 20.0000 chunk 322 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 328 optimal weight: 30.0000 chunk 320 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 346 optimal weight: 9.9990 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 957 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.136660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.084036 restraints weight = 73933.644| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.11 r_work: 0.2997 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2367 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= 0.126 Angle : 0.531 11.101 39609 Z= 0.269 Chirality : 0.043 0.206 4568 Planarity : 0.004 0.065 5044 Dihedral : 5.048 56.635 4729 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.20 % Allowed : 13.94 % Favored : 84.86 % 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 aren not related in a simple way. whole: 0.02 (0.14), residues: 3490 helix: 2.20 (0.21), residues: 668 sheet: 0.25 (0.16), residues: 1020 loop : -0.98 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 98 TYR 0.028 0.001 TYR B 351 PHE 0.011 0.001 PHE A 374 TRP 0.008 0.001 TRP C 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00292 (28956) covalent geometry : angle 0.51219 (39395) SS BOND : bond 0.00276 ( 44) SS BOND : angle 1.13093 ( 88) hydrogen bonds : bond 0.05632 ( 1029) hydrogen bonds : angle 5.07892 ( 2880) link_BETA1-4 : bond 0.00285 ( 8) link_BETA1-4 : angle 0.96511 ( 24) link_NAG-ASN : bond 0.00424 ( 34) link_NAG-ASN : angle 2.64432 ( 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 142 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.897 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.6688 (mt0) cc_final: 0.6375 (mt0) REVERT: A 581 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 84 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7759 (mm) REVERT: B 170 TYR cc_start: 0.7864 (t80) cc_final: 0.7456 (t80) REVERT: B 560 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8608 (mp) REVERT: C 441 LEU cc_start: 0.6551 (mm) cc_final: 0.6327 (mm) REVERT: C 509 ARG cc_start: 0.4992 (mtt180) cc_final: 0.4576 (mtt180) REVERT: S 83 MET cc_start: 0.1954 (mpp) cc_final: 0.0445 (ptp) outliers start: 37 outliers final: 28 residues processed: 134 average time/residue: 0.1828 time to fit residues: 41.1670 Evaluate side-chains 133 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 B residue 1086 LYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 241 LEU 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 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 32 PHE Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 35 HIS 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: 0.7980 chunk 272 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** 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** P 109 ASN ** U 16 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 = 0.4106 r_free = 0.4106 target = 0.134601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081355 restraints weight = 73564.320| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.09 r_work: 0.2959 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 29042 Z= 0.201 Angle : 0.582 11.106 39609 Z= 0.295 Chirality : 0.045 0.214 4568 Planarity : 0.004 0.063 5044 Dihedral : 5.244 56.625 4729 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.07 % Allowed : 14.27 % Favored : 84.66 % 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 aren not related in a simple way. whole: -0.12 (0.14), residues: 3490 helix: 1.91 (0.20), residues: 678 sheet: 0.14 (0.16), residues: 995 loop : -0.98 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 98 TYR 0.027 0.001 TYR C 453 PHE 0.018 0.001 PHE B 168 TRP 0.008 0.001 TRP A1102 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00488 (28956) covalent geometry : angle 0.56208 (39395) SS BOND : bond 0.00356 ( 44) SS BOND : angle 1.32094 ( 88) hydrogen bonds : bond 0.06666 ( 1029) hydrogen bonds : angle 5.26034 ( 2880) link_BETA1-4 : bond 0.00245 ( 8) link_BETA1-4 : angle 1.12361 ( 24) link_NAG-ASN : bond 0.00395 ( 34) link_NAG-ASN : angle 2.75019 ( 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 137 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 581 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 84 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7738 (mm) REVERT: B 170 TYR cc_start: 0.7826 (t80) cc_final: 0.7410 (t80) REVERT: B 560 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 441 LEU cc_start: 0.6443 (mm) cc_final: 0.6228 (mm) REVERT: C 509 ARG cc_start: 0.5039 (mtt180) cc_final: 0.4649 (mtt180) REVERT: S 83 MET cc_start: 0.1796 (mpp) cc_final: 0.0269 (ptp) outliers start: 33 outliers final: 29 residues processed: 130 average time/residue: 0.1823 time to fit residues: 39.7518 Evaluate side-chains 135 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 B residue 1086 LYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 241 LEU 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 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 32 PHE Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 35 HIS 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: 0.5980 chunk 133 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 322 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 348 optimal weight: 30.0000 chunk 320 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.133797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080270 restraints weight = 71681.275| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.27 r_work: 0.2988 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2549 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= 0.148 Angle : 0.541 11.110 39609 Z= 0.275 Chirality : 0.044 0.209 4568 Planarity : 0.004 0.064 5044 Dihedral : 5.085 56.719 4729 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.01 % Allowed : 14.43 % Favored : 84.56 % 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 aren not related in a simple way. whole: -0.01 (0.14), residues: 3490 helix: 2.09 (0.21), residues: 672 sheet: 0.24 (0.16), residues: 1022 loop : -0.98 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 98 TYR 0.032 0.001 TYR B 453 PHE 0.013 0.001 PHE A 374 TRP 0.008 0.001 TRP C 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00352 (28956) covalent geometry : angle 0.52175 (39395) SS BOND : bond 0.00334 ( 44) SS BOND : angle 1.19308 ( 88) hydrogen bonds : bond 0.05986 ( 1029) hydrogen bonds : angle 5.14173 ( 2880) link_BETA1-4 : bond 0.00266 ( 8) link_BETA1-4 : angle 1.00047 ( 24) link_NAG-ASN : bond 0.00393 ( 34) link_NAG-ASN : angle 2.66310 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8963.12 seconds wall clock time: 153 minutes 31.94 seconds (9211.94 seconds total)