Starting phenix.real_space_refine on Mon May 26 15:03:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yh7_33822/05_2025/7yh7_33822.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh7_33822/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yh7_33822/05_2025/7yh7_33822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh7_33822/05_2025/7yh7_33822.map" model { file = "/net/cci-nas-00/data/ceres_data/7yh7_33822/05_2025/7yh7_33822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh7_33822/05_2025/7yh7_33822.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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): 1.68s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP: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: 16.98, per 1000 atoms: 0.60 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: 7.03 Conformation dependent library (CDL) restraints added in 3.7 seconds 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6618 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 63 sheets defined 22.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.19 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: 13.02 Time building geometry restraints manager: 8.24 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 1141 or resid 1301 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 1141 o \ r resid 1301 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 1141 or resid 1301 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: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 66.130 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (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 TRP 0.007 0.001 TRP P 36 HIS 0.005 0.000 HIS C 519 PHE 0.030 0.001 PHE S 76 TYR 0.012 0.001 TYR A 873 ARG 0.007 0.000 ARG V 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 34) link_NAG-ASN : angle 3.64198 ( 102) link_BETA1-4 : bond 0.00508 ( 8) link_BETA1-4 : angle 0.92968 ( 24) hydrogen bonds : bond 0.22104 ( 1029) hydrogen bonds : angle 7.71025 ( 2880) SS BOND : bond 0.00260 ( 44) SS BOND : angle 1.09360 ( 88) covalent geometry : bond 0.00272 (28956) covalent geometry : angle 0.51095 (39395) *********************** 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 : 3.216 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: 0.8775 (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: 0.6807 (mt) REVERT: C 393 THR cc_start: 0.7584 (p) cc_final: 0.7164 (p) REVERT: C 516 GLU cc_start: 0.7376 (pm20) cc_final: 0.7014 (pm20) REVERT: S 83 MET cc_start: 0.2551 (mpp) cc_final: 0.0859 (ptp) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.4018 time to fit residues: 121.1217 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 : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 207 optimal weight: 0.3980 chunk 322 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 A 804 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.134965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080950 restraints weight = 72945.145| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.25 r_work: 0.2992 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29042 Z= 0.174 Angle : 0.593 10.673 39609 Z= 0.305 Chirality : 0.045 0.226 4568 Planarity : 0.005 0.070 5044 Dihedral : 6.713 58.894 4729 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 0.52 % Allowed : 6.56 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3490 helix: 2.15 (0.21), residues: 667 sheet: 0.28 (0.17), residues: 1000 loop : -1.06 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS P 35 PHE 0.025 0.001 PHE B 168 TYR 0.022 0.001 TYR B1067 ARG 0.007 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 34) link_NAG-ASN : angle 3.15693 ( 102) link_BETA1-4 : bond 0.00399 ( 8) link_BETA1-4 : angle 0.93063 ( 24) hydrogen bonds : bond 0.06466 ( 1029) hydrogen bonds : angle 5.95703 ( 2880) SS BOND : bond 0.00450 ( 44) SS BOND : angle 1.27817 ( 88) covalent geometry : bond 0.00411 (28956) covalent geometry : angle 0.56921 (39395) *********************** 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 135 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8106 (t80) cc_final: 0.7845 (t80) REVERT: B 170 TYR cc_start: 0.7943 (t80) cc_final: 0.7513 (t80) REVERT: B 189 LEU cc_start: 0.8396 (mp) cc_final: 0.8129 (mp) REVERT: B 979 ASP cc_start: 0.9053 (t70) cc_final: 0.8722 (t0) REVERT: C 509 ARG cc_start: 0.4982 (mtt180) cc_final: 0.4649 (mtt180) REVERT: S 83 MET cc_start: 0.2483 (mpp) cc_final: 0.1262 (ptp) outliers start: 16 outliers final: 5 residues processed: 130 average time/residue: 0.4017 time to fit residues: 86.1384 Evaluate side-chains 112 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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 134 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ** 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 992 GLN ** P 35 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 = 0.4132 r_free = 0.4132 target = 0.137209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082576 restraints weight = 71549.206| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.45 r_work: 0.2959 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29042 Z= 0.195 Angle : 0.584 11.117 39609 Z= 0.299 Chirality : 0.045 0.219 4568 Planarity : 0.004 0.067 5044 Dihedral : 6.162 57.693 4729 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 0.94 % Allowed : 9.59 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3490 helix: 1.93 (0.21), residues: 674 sheet: 0.10 (0.16), residues: 1000 loop : -1.03 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.008 0.001 HIS C 519 PHE 0.022 0.001 PHE A 906 TYR 0.023 0.001 TYR C 170 ARG 0.006 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 34) link_NAG-ASN : angle 3.03901 ( 102) link_BETA1-4 : bond 0.00242 ( 8) link_BETA1-4 : angle 0.99956 ( 24) hydrogen bonds : bond 0.06747 ( 1029) hydrogen bonds : angle 5.63418 ( 2880) SS BOND : bond 0.00380 ( 44) SS BOND : angle 1.29110 ( 88) covalent geometry : bond 0.00471 (28956) covalent geometry : angle 0.56054 (39395) *********************** 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 138 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7996 (t80) cc_final: 0.7745 (t80) REVERT: B 170 TYR cc_start: 0.7873 (t80) cc_final: 0.7307 (t80) REVERT: B 979 ASP cc_start: 0.9205 (t70) cc_final: 0.8905 (t0) REVERT: C 410 ILE cc_start: 0.8154 (mm) cc_final: 0.7906 (pt) REVERT: C 509 ARG cc_start: 0.5170 (mtt180) cc_final: 0.4841 (mtt180) REVERT: P 32 PHE cc_start: 0.6372 (m-80) cc_final: 0.6030 (m-80) REVERT: S 34 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4533 (tmm) REVERT: S 83 MET cc_start: 0.2224 (mpp) cc_final: 0.0906 (ptp) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 0.4182 time to fit residues: 92.9636 Evaluate side-chains 122 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 3.158 ------------------------------------------------------------------------------- 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 A residue 878 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1094 VAL 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 58 optimal weight: 0.5980 chunk 333 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4151 r_free = 0.4151 target = 0.136185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082964 restraints weight = 73171.672| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.31 r_work: 0.3003 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1642 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 : 0.512 11.633 39609 Z= 0.261 Chirality : 0.043 0.209 4568 Planarity : 0.004 0.065 5044 Dihedral : 5.483 57.446 4729 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 0.84 % Allowed : 11.34 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3490 helix: 2.22 (0.21), residues: 675 sheet: 0.21 (0.17), residues: 977 loop : -0.90 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.007 0.001 HIS C 519 PHE 0.013 0.001 PHE B 497 TYR 0.019 0.001 TYR C 453 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 34) link_NAG-ASN : angle 2.85866 ( 102) link_BETA1-4 : bond 0.00361 ( 8) link_BETA1-4 : angle 0.84525 ( 24) hydrogen bonds : bond 0.05299 ( 1029) hydrogen bonds : angle 5.25297 ( 2880) SS BOND : bond 0.00298 ( 44) SS BOND : angle 1.01791 ( 88) covalent geometry : bond 0.00230 (28956) covalent geometry : angle 0.48919 (39395) *********************** 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 142 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7988 (t80) cc_final: 0.7746 (t80) REVERT: A 409 GLN cc_start: 0.6836 (mt0) cc_final: 0.6564 (mt0) REVERT: B 979 ASP cc_start: 0.9038 (t70) cc_final: 0.8747 (t0) REVERT: C 378 LYS cc_start: 0.7938 (tptm) cc_final: 0.7667 (tptm) REVERT: C 509 ARG cc_start: 0.5111 (mtt180) cc_final: 0.4792 (mtt180) REVERT: P 32 PHE cc_start: 0.6691 (m-80) cc_final: 0.6430 (m-80) REVERT: S 34 MET cc_start: 0.4853 (OUTLIER) cc_final: 0.4550 (tmm) REVERT: S 83 MET cc_start: 0.2189 (mpp) cc_final: 0.0683 (ptp) outliers start: 26 outliers final: 15 residues processed: 135 average time/residue: 0.3894 time to fit residues: 87.5007 Evaluate side-chains 117 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 2.877 ------------------------------------------------------------------------------- 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 738 CYS 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 582 LEU Chi-restraints excluded: chain C residue 934 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 46 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 288 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** A1005 GLN B 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.135701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082420 restraints weight = 73680.978| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.06 r_work: 0.2931 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 29042 Z= 0.268 Angle : 0.630 10.944 39609 Z= 0.323 Chirality : 0.046 0.223 4568 Planarity : 0.004 0.064 5044 Dihedral : 5.807 56.975 4729 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.14 % Allowed : 12.22 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3490 helix: 1.71 (0.20), residues: 674 sheet: -0.01 (0.16), residues: 1001 loop : -1.06 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1102 HIS 0.009 0.001 HIS C 519 PHE 0.021 0.002 PHE C 906 TYR 0.024 0.002 TYR B1067 ARG 0.005 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 34) link_NAG-ASN : angle 2.96240 ( 102) link_BETA1-4 : bond 0.00274 ( 8) link_BETA1-4 : angle 1.20899 ( 24) hydrogen bonds : bond 0.07507 ( 1029) hydrogen bonds : angle 5.58906 ( 2880) SS BOND : bond 0.00500 ( 44) SS BOND : angle 1.53156 ( 88) covalent geometry : bond 0.00655 (28956) covalent geometry : angle 0.60824 (39395) *********************** 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 137 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.6964 (mt0) cc_final: 0.6720 (mt0) REVERT: A 581 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 170 TYR cc_start: 0.7789 (t80) cc_final: 0.7358 (t80) REVERT: B 451 TYR cc_start: 0.4780 (m-80) cc_final: 0.4432 (m-10) REVERT: C 509 ARG cc_start: 0.5304 (mtt180) cc_final: 0.4936 (mtt180) REVERT: S 34 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.4019 (tmm) REVERT: S 83 MET cc_start: 0.2039 (mpp) cc_final: 0.0300 (ptp) outliers start: 35 outliers final: 23 residues processed: 133 average time/residue: 0.3918 time to fit residues: 86.6002 Evaluate side-chains 118 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 390 LEU 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 125 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 1094 VAL 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 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 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 253 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 330 optimal weight: 0.0870 chunk 195 optimal weight: 0.1980 chunk 163 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 320 optimal weight: 30.0000 chunk 182 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 784 GLN A1005 GLN B 957 GLN C 506 GLN C 914 ASN C1002 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.140462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087271 restraints weight = 73700.910| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.19 r_work: 0.3010 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29042 Z= 0.100 Angle : 0.508 11.195 39609 Z= 0.259 Chirality : 0.043 0.206 4568 Planarity : 0.004 0.060 5044 Dihedral : 5.090 57.328 4729 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 12.64 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3490 helix: 2.24 (0.21), residues: 672 sheet: 0.15 (0.16), residues: 983 loop : -0.88 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.006 0.001 HIS C 519 PHE 0.018 0.001 PHE C 168 TYR 0.021 0.001 TYR C 453 ARG 0.005 0.000 ARG P 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 34) link_NAG-ASN : angle 2.64426 ( 102) link_BETA1-4 : bond 0.00421 ( 8) link_BETA1-4 : angle 0.88236 ( 24) hydrogen bonds : bond 0.05143 ( 1029) hydrogen bonds : angle 5.08641 ( 2880) SS BOND : bond 0.00252 ( 44) SS BOND : angle 1.02502 ( 88) covalent geometry : bond 0.00208 (28956) covalent geometry : angle 0.48885 (39395) *********************** 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 139 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.6760 (mt0) cc_final: 0.6522 (mt0) REVERT: A 581 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8572 (p) REVERT: B 84 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 170 TYR cc_start: 0.7722 (t80) cc_final: 0.7341 (t80) REVERT: B 560 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8523 (mp) REVERT: C 509 ARG cc_start: 0.5219 (mtt180) cc_final: 0.4877 (mtt180) REVERT: P 32 PHE cc_start: 0.6104 (m-80) cc_final: 0.5780 (t80) REVERT: S 34 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.3864 (tmm) REVERT: S 83 MET cc_start: 0.2060 (mpp) cc_final: 0.0692 (ptp) REVERT: V 34 MET cc_start: 0.4158 (mmp) cc_final: 0.3922 (mmp) outliers start: 39 outliers final: 21 residues processed: 129 average time/residue: 0.3928 time to fit residues: 83.4452 Evaluate side-chains 118 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 517 LEU 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 B residue 84 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 163 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 222 optimal weight: 40.0000 chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 315 optimal weight: 20.0000 chunk 133 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.135479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081543 restraints weight = 72150.578| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.40 r_work: 0.2987 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2079 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= 0.143 Angle : 0.520 11.127 39609 Z= 0.264 Chirality : 0.043 0.209 4568 Planarity : 0.004 0.059 5044 Dihedral : 5.010 56.617 4729 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.17 % Allowed : 13.29 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3490 helix: 2.24 (0.21), residues: 673 sheet: 0.19 (0.16), residues: 979 loop : -0.89 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.006 0.001 HIS C 519 PHE 0.013 0.001 PHE B1121 TYR 0.028 0.001 TYR C 453 ARG 0.010 0.000 ARG P 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 34) link_NAG-ASN : angle 2.63214 ( 102) link_BETA1-4 : bond 0.00254 ( 8) link_BETA1-4 : angle 0.97725 ( 24) hydrogen bonds : bond 0.05614 ( 1029) hydrogen bonds : angle 5.09528 ( 2880) SS BOND : bond 0.00298 ( 44) SS BOND : angle 1.13283 ( 88) covalent geometry : bond 0.00342 (28956) covalent geometry : angle 0.50083 (39395) *********************** 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 133 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7349 (t80) REVERT: A 409 GLN cc_start: 0.6699 (mt0) cc_final: 0.6459 (mt0) REVERT: A 581 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 84 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 170 TYR cc_start: 0.7952 (t80) cc_final: 0.7457 (t80) REVERT: B 560 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 509 ARG cc_start: 0.5204 (mtt180) cc_final: 0.4862 (mtt180) REVERT: P 32 PHE cc_start: 0.6013 (m-80) cc_final: 0.5734 (t80) REVERT: P 98 ARG cc_start: 0.4362 (ptm-80) cc_final: 0.4111 (ptm-80) REVERT: S 34 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3852 (tmm) REVERT: S 83 MET cc_start: 0.1964 (mpp) cc_final: 0.0570 (ptp) outliers start: 36 outliers final: 23 residues processed: 128 average time/residue: 0.4150 time to fit residues: 87.4324 Evaluate side-chains 121 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE 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 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 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 123 VAL 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 146 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 2 optimal weight: 0.3980 chunk 264 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 205 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 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 = 0.4122 r_free = 0.4122 target = 0.135742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082761 restraints weight = 74010.477| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.12 r_work: 0.2986 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2200 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= 0.150 Angle : 0.529 11.014 39609 Z= 0.269 Chirality : 0.043 0.210 4568 Planarity : 0.004 0.059 5044 Dihedral : 4.987 56.632 4729 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.23 % Allowed : 13.75 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3490 helix: 2.18 (0.21), residues: 673 sheet: 0.21 (0.16), residues: 1003 loop : -0.91 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 353 HIS 0.006 0.001 HIS C 519 PHE 0.022 0.001 PHE B 168 TYR 0.037 0.001 TYR B 495 ARG 0.009 0.000 ARG P 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 34) link_NAG-ASN : angle 2.60644 ( 102) link_BETA1-4 : bond 0.00247 ( 8) link_BETA1-4 : angle 0.99516 ( 24) hydrogen bonds : bond 0.05845 ( 1029) hydrogen bonds : angle 5.09861 ( 2880) SS BOND : bond 0.00299 ( 44) SS BOND : angle 1.14552 ( 88) covalent geometry : bond 0.00359 (28956) covalent geometry : angle 0.51039 (39395) *********************** 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 147 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 3.184 Fit side-chains revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7336 (t80) REVERT: A 409 GLN cc_start: 0.6700 (mt0) cc_final: 0.6463 (mt0) REVERT: A 581 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8632 (p) REVERT: B 84 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7761 (mm) REVERT: B 170 TYR cc_start: 0.7856 (t80) cc_final: 0.7418 (t80) REVERT: B 560 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8558 (mp) REVERT: C 509 ARG cc_start: 0.5310 (mtt180) cc_final: 0.4938 (mtt180) REVERT: P 32 PHE cc_start: 0.6132 (m-80) cc_final: 0.5871 (t80) REVERT: S 34 MET cc_start: 0.4365 (OUTLIER) cc_final: 0.3905 (tmm) REVERT: S 83 MET cc_start: 0.1974 (mpp) cc_final: 0.0467 (ptp) outliers start: 38 outliers final: 28 residues processed: 138 average time/residue: 0.4031 time to fit residues: 92.2047 Evaluate side-chains 134 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 390 LEU 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 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 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain P residue 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 68 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 320 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 318 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 914 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.135187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081832 restraints weight = 74022.427| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.09 r_work: 0.2939 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 29042 Z= 0.240 Angle : 0.606 10.803 39609 Z= 0.309 Chirality : 0.045 0.222 4568 Planarity : 0.004 0.061 5044 Dihedral : 5.357 56.808 4729 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.30 % Allowed : 14.33 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3490 helix: 1.94 (0.20), residues: 671 sheet: 0.11 (0.16), residues: 996 loop : -1.01 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1102 HIS 0.008 0.001 HIS C 519 PHE 0.018 0.002 PHE B1121 TYR 0.053 0.002 TYR B 495 ARG 0.005 0.000 ARG P 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 34) link_NAG-ASN : angle 2.74192 ( 102) link_BETA1-4 : bond 0.00256 ( 8) link_BETA1-4 : angle 1.15351 ( 24) hydrogen bonds : bond 0.07020 ( 1029) hydrogen bonds : angle 5.34862 ( 2880) SS BOND : bond 0.00384 ( 44) SS BOND : angle 1.37114 ( 88) covalent geometry : bond 0.00585 (28956) covalent geometry : angle 0.58678 (39395) *********************** 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 144 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 409 GLN cc_start: 0.6886 (mt0) cc_final: 0.6558 (mt0) REVERT: A 581 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 84 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7688 (mm) REVERT: B 170 TYR cc_start: 0.7651 (t80) cc_final: 0.7241 (t80) REVERT: B 560 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (mp) REVERT: C 357 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7512 (ttt-90) REVERT: C 509 ARG cc_start: 0.5454 (mtt180) cc_final: 0.5061 (mtt180) REVERT: P 32 PHE cc_start: 0.6005 (m-80) cc_final: 0.5776 (t80) REVERT: S 34 MET cc_start: 0.3902 (OUTLIER) cc_final: 0.3485 (tmm) REVERT: S 83 MET cc_start: 0.1810 (mpp) cc_final: 0.0317 (ptp) outliers start: 40 outliers final: 30 residues processed: 134 average time/residue: 0.3888 time to fit residues: 86.0614 Evaluate side-chains 137 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 517 LEU 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 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 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain S residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 276 optimal weight: 0.9990 chunk 225 optimal weight: 30.0000 chunk 254 optimal weight: 0.0170 chunk 211 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 342 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 450 ASN A 498 GLN A 544 ASN B 957 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 914 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.132999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080388 restraints weight = 73081.364| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.17 r_work: 0.3005 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2368 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= 0.101 Angle : 0.521 11.011 39609 Z= 0.264 Chirality : 0.043 0.205 4568 Planarity : 0.004 0.057 5044 Dihedral : 4.935 56.935 4729 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.04 % Allowed : 14.79 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3490 helix: 2.28 (0.21), residues: 672 sheet: 0.27 (0.16), residues: 1021 loop : -0.93 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 PHE 0.020 0.001 PHE B 168 TYR 0.034 0.001 TYR C 380 ARG 0.008 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 34) link_NAG-ASN : angle 2.55739 ( 102) link_BETA1-4 : bond 0.00358 ( 8) link_BETA1-4 : angle 0.93615 ( 24) hydrogen bonds : bond 0.05357 ( 1029) hydrogen bonds : angle 5.03665 ( 2880) SS BOND : bond 0.00261 ( 44) SS BOND : angle 1.02490 ( 88) covalent geometry : bond 0.00213 (28956) covalent geometry : angle 0.50269 (39395) ********************** 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 140 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 3.068 Fit side-chains revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7194 (t80) REVERT: A 581 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 84 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7700 (mm) REVERT: B 170 TYR cc_start: 0.7647 (t80) cc_final: 0.7306 (t80) REVERT: B 560 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (mp) REVERT: C 509 ARG cc_start: 0.5397 (mtt180) cc_final: 0.5015 (mtt180) REVERT: P 32 PHE cc_start: 0.6081 (m-80) cc_final: 0.5750 (t80) REVERT: S 83 MET cc_start: 0.1808 (mpp) cc_final: 0.0262 (ptp) outliers start: 32 outliers final: 20 residues processed: 130 average time/residue: 0.4044 time to fit residues: 86.5152 Evaluate side-chains 127 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE 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 B residue 84 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 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 240 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 296 optimal weight: 50.0000 chunk 352 optimal weight: 0.0770 chunk 302 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 258 optimal weight: 0.0030 chunk 224 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 overall best weight: 2.6154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078187 restraints weight = 73273.645| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.13 r_work: 0.2980 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29042 Z= 0.173 Angle : 0.552 10.898 39609 Z= 0.280 Chirality : 0.044 0.212 4568 Planarity : 0.004 0.059 5044 Dihedral : 5.003 56.422 4729 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.94 % Allowed : 14.92 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3490 helix: 2.17 (0.21), residues: 672 sheet: 0.24 (0.16), residues: 1022 loop : -0.94 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1102 HIS 0.007 0.001 HIS C 519 PHE 0.015 0.001 PHE B1121 TYR 0.026 0.001 TYR C 453 ARG 0.006 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 34) link_NAG-ASN : angle 2.61497 ( 102) link_BETA1-4 : bond 0.00233 ( 8) link_BETA1-4 : angle 1.04935 ( 24) hydrogen bonds : bond 0.06129 ( 1029) hydrogen bonds : angle 5.13665 ( 2880) SS BOND : bond 0.00328 ( 44) SS BOND : angle 1.20364 ( 88) covalent geometry : bond 0.00417 (28956) covalent geometry : angle 0.53374 (39395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18769.37 seconds wall clock time: 324 minutes 17.22 seconds (19457.22 seconds total)