Starting phenix.real_space_refine on Tue Nov 19 17:01:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/11_2024/7xu6_33460_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/11_2024/7xu6_33460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/11_2024/7xu6_33460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/11_2024/7xu6_33460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/11_2024/7xu6_33460_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu6_33460/11_2024/7xu6_33460_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 123 5.16 5 C 16902 2.51 5 N 4350 2.21 5 O 5187 1.98 5 H 24902 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.83s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51464 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 16818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16818 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1037} Chain breaks: 5 Chain: "C" Number of atoms: 16817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16817 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1037} Chain breaks: 5 Chain: "B" Number of atoms: 16818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16818 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1037} Chain breaks: 5 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: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "O" 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: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 24.93, per 1000 atoms: 0.48 Number of scatterers: 51464 At special positions: 0 Unit cell: (136.869, 148.54, 163.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 O 5187 8.00 N 4350 7.00 C 16902 6.00 H 24902 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1134 " Time building additional restraints: 14.40 Conformation dependent library (CDL) restraints added in 3.8 seconds 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6114 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 25.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 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 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.211A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.919A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.506A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.621A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.818A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.708A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (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: 3.655A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.205A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.918A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.501A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.669A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.625A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.814A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.722A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (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 1033 removed outlier: 3.653A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (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 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.210A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.912A 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 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.509A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.670A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.628A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.821A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.720A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.659A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.989A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.698A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.976A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.974A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 157 removed outlier: 6.524A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.911A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.736A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.198A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.816A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 554 removed outlier: 3.846A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.084A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.604A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.060A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.187A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.550A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.799A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.968A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.971A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.965A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 152 through 157 removed outlier: 6.529A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.894A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.737A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.199A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.818A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 552 through 554 removed outlier: 3.870A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.104A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 701 through 703 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.615A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.058A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.198A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.990A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.975A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.970A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.527A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.896A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.740A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.195A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.809A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.094A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.611A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.058A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.212A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.802A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2694 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: 25.20 Time building geometry restraints manager: 16.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 24893 1.02 - 1.24: 3242 1.24 - 1.45: 8686 1.45 - 1.66: 15087 1.66 - 1.88: 153 Bond restraints: 52061 Sorted by residual: bond pdb=" NB BLA C1314 " pdb=" C4B BLA C1314 " ideal model delta sigma weight residual 1.371 1.535 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" NB BLA A1314 " pdb=" C4B BLA A1314 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" NB BLA B1314 " pdb=" C4B BLA B1314 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C4C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C4C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.375 1.536 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 52056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.15: 93255 6.15 - 12.31: 64 12.31 - 18.46: 6 18.46 - 24.62: 4 24.62 - 30.77: 2 Bond angle restraints: 93331 Sorted by residual: angle pdb=" CD GLN A 628 " pdb=" NE2 GLN A 628 " pdb="HE22 GLN A 628 " ideal model delta sigma weight residual 120.00 150.77 -30.77 3.00e+00 1.11e-01 1.05e+02 angle pdb="HE21 GLN A 628 " pdb=" NE2 GLN A 628 " pdb="HE22 GLN A 628 " ideal model delta sigma weight residual 120.00 90.10 29.90 3.00e+00 1.11e-01 9.94e+01 angle pdb="HE21 GLN C 628 " pdb=" NE2 GLN C 628 " pdb="HE22 GLN C 628 " ideal model delta sigma weight residual 120.00 95.43 24.57 3.00e+00 1.11e-01 6.71e+01 angle pdb=" CD GLN C 628 " pdb=" NE2 GLN C 628 " pdb="HE22 GLN C 628 " ideal model delta sigma weight residual 120.00 144.18 -24.18 3.00e+00 1.11e-01 6.49e+01 angle pdb=" CD GLN C 628 " pdb=" NE2 GLN C 628 " pdb="HE21 GLN C 628 " ideal model delta sigma weight residual 120.00 96.47 23.53 3.00e+00 1.11e-01 6.15e+01 ... (remaining 93326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 23129 17.74 - 35.49: 2028 35.49 - 53.23: 513 53.23 - 70.97: 177 70.97 - 88.72: 24 Dihedral angle restraints: 25871 sinusoidal: 14439 harmonic: 11432 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -27.24 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -27.26 -58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -27.38 -58.62 1 1.00e+01 1.00e-02 4.60e+01 ... (remaining 25868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3569 0.066 - 0.133: 652 0.133 - 0.199: 115 0.199 - 0.265: 5 0.265 - 0.332: 6 Chirality restraints: 4347 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4344 not shown) Planarity restraints: 7833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1314 " -0.024 2.00e-02 2.50e+03 1.37e-01 4.67e+02 pdb=" C1D BLA A1314 " 0.311 2.00e-02 2.50e+03 pdb=" C2C BLA A1314 " 0.038 2.00e-02 2.50e+03 pdb=" C3C BLA A1314 " -0.031 2.00e-02 2.50e+03 pdb=" C4C BLA A1314 " -0.125 2.00e-02 2.50e+03 pdb=" CAC BLA A1314 " 0.006 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " -0.195 2.00e-02 2.50e+03 pdb=" CMC BLA A1314 " 0.134 2.00e-02 2.50e+03 pdb=" NC BLA A1314 " -0.124 2.00e-02 2.50e+03 pdb=" OC BLA A1314 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1314 " -0.024 2.00e-02 2.50e+03 1.37e-01 4.67e+02 pdb=" C1D BLA B1314 " 0.311 2.00e-02 2.50e+03 pdb=" C2C BLA B1314 " 0.038 2.00e-02 2.50e+03 pdb=" C3C BLA B1314 " -0.031 2.00e-02 2.50e+03 pdb=" C4C BLA B1314 " -0.125 2.00e-02 2.50e+03 pdb=" CAC BLA B1314 " 0.006 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " -0.195 2.00e-02 2.50e+03 pdb=" CMC BLA B1314 " 0.133 2.00e-02 2.50e+03 pdb=" NC BLA B1314 " -0.124 2.00e-02 2.50e+03 pdb=" OC BLA B1314 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA C1314 " -0.024 2.00e-02 2.50e+03 1.37e-01 4.66e+02 pdb=" C1D BLA C1314 " 0.311 2.00e-02 2.50e+03 pdb=" C2C BLA C1314 " 0.038 2.00e-02 2.50e+03 pdb=" C3C BLA C1314 " -0.031 2.00e-02 2.50e+03 pdb=" C4C BLA C1314 " -0.125 2.00e-02 2.50e+03 pdb=" CAC BLA C1314 " 0.006 2.00e-02 2.50e+03 pdb=" CHD BLA C1314 " -0.195 2.00e-02 2.50e+03 pdb=" CMC BLA C1314 " 0.134 2.00e-02 2.50e+03 pdb=" NC BLA C1314 " -0.124 2.00e-02 2.50e+03 pdb=" OC BLA C1314 " 0.011 2.00e-02 2.50e+03 ... (remaining 7830 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 5730 2.24 - 2.83: 111847 2.83 - 3.42: 130034 3.42 - 4.01: 185789 4.01 - 4.60: 281240 Nonbonded interactions: 714640 Sorted by model distance: nonbonded pdb=" OG SER B1051 " pdb=" HD1 HIS B1064 " model vdw 1.655 2.450 nonbonded pdb=" OG SER A1051 " pdb=" HD1 HIS A1064 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN A1002 " pdb="HE22 GLN C1005 " model vdw 1.671 2.450 nonbonded pdb="HE22 GLN A1005 " pdb=" OE1 GLN B1002 " model vdw 1.671 2.450 nonbonded pdb=" OE1 GLN C1002 " pdb="HE22 GLN B1005 " model vdw 1.673 2.450 ... (remaining 714635 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 17 through 1063 or (resid 1064 and (name N or name CA or n \ ame C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or nam \ e NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or na \ me HE2)) or resid 1065 through 1140 or resid 1301 through 1314)) selection = (chain 'B' and (resid 17 through 1063 or (resid 1064 and (name N or name CA or n \ ame C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or nam \ e NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or na \ me HE2)) or resid 1065 through 1140 or resid 1301 through 1314)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.00 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: 2.740 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: 0.860 Extract box with map and model: 1.980 Check model and map are aligned: 0.360 Set scattering table: 0.470 Process input model: 108.680 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.012 0.164 27159 Z= 0.820 Angle : 0.955 15.523 36963 Z= 0.455 Chirality : 0.055 0.332 4347 Planarity : 0.006 0.137 4689 Dihedral : 14.180 88.717 10740 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.74 % Allowed : 0.56 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3231 helix: 0.18 (0.20), residues: 711 sheet: -0.65 (0.19), residues: 687 loop : -1.97 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP A 64 HIS 0.008 0.001 HIS B 245 PHE 0.015 0.002 PHE B 140 TYR 0.068 0.002 TYR C 904 ARG 0.010 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0632 (mtt) cc_final: -0.0859 (mtt) REVERT: A 516 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 629 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6602 (pp) REVERT: C 140 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (p90) REVERT: B 144 TYR cc_start: 0.6954 (t80) cc_final: 0.6633 (t80) REVERT: B 245 HIS cc_start: 0.7399 (m-70) cc_final: 0.6955 (m90) REVERT: B 731 MET cc_start: 0.9054 (ptt) cc_final: 0.8795 (ptt) outliers start: 21 outliers final: 3 residues processed: 249 average time/residue: 2.3770 time to fit residues: 718.5097 Evaluate side-chains 174 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 0.1980 chunk 294 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN A1088 HIS C1005 GLN C1088 HIS B1005 GLN B1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27159 Z= 0.196 Angle : 0.604 10.247 36963 Z= 0.315 Chirality : 0.045 0.338 4347 Planarity : 0.004 0.045 4689 Dihedral : 8.643 59.459 4919 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.67 % Allowed : 5.79 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3231 helix: 0.61 (0.20), residues: 723 sheet: -0.62 (0.19), residues: 681 loop : -1.80 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.012 0.001 PHE A 898 TYR 0.024 0.001 TYR B 904 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 3.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0202 (mtt) cc_final: -0.0002 (mtt) REVERT: A 228 ASP cc_start: 0.7859 (t0) cc_final: 0.7631 (t0) REVERT: C 140 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8342 (p90) REVERT: C 837 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: B 140 PHE cc_start: 0.8614 (p90) cc_final: 0.8228 (p90) REVERT: B 177 MET cc_start: -0.0363 (mtt) cc_final: -0.0735 (mtt) REVERT: B 228 ASP cc_start: 0.7996 (t0) cc_final: 0.7786 (t0) REVERT: B 837 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.5779 (m-80) REVERT: B 950 ASP cc_start: 0.7410 (m-30) cc_final: 0.7204 (m-30) outliers start: 19 outliers final: 8 residues processed: 194 average time/residue: 2.0891 time to fit residues: 504.4973 Evaluate side-chains 183 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 0.0570 chunk 294 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 292 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS C1101 HIS B 628 GLN B1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27159 Z= 0.217 Angle : 0.559 10.274 36963 Z= 0.291 Chirality : 0.044 0.306 4347 Planarity : 0.003 0.045 4689 Dihedral : 7.435 58.629 4915 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.77 % Allowed : 6.84 % Favored : 92.39 % 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: -1.22 (0.14), residues: 3231 helix: 0.81 (0.20), residues: 720 sheet: -0.53 (0.18), residues: 681 loop : -1.64 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A 519 PHE 0.016 0.001 PHE B 220 TYR 0.021 0.001 TYR B 904 ARG 0.003 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 3.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7883 (t0) cc_final: 0.7633 (t0) REVERT: A 837 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: C 140 PHE cc_start: 0.8791 (p90) cc_final: 0.8401 (p90) REVERT: C 837 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6266 (m-80) REVERT: B 140 PHE cc_start: 0.8672 (p90) cc_final: 0.8342 (p90) REVERT: B 177 MET cc_start: 0.0012 (mtt) cc_final: -0.0282 (mtt) REVERT: B 228 ASP cc_start: 0.7859 (t0) cc_final: 0.7657 (t0) REVERT: B 731 MET cc_start: 0.9216 (ptt) cc_final: 0.9005 (ptt) REVERT: B 837 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: B 950 ASP cc_start: 0.7474 (m-30) cc_final: 0.7188 (m-30) outliers start: 22 outliers final: 7 residues processed: 201 average time/residue: 2.0503 time to fit residues: 514.2735 Evaluate side-chains 183 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 313 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27159 Z= 0.273 Angle : 0.564 10.440 36963 Z= 0.296 Chirality : 0.044 0.299 4347 Planarity : 0.003 0.044 4689 Dihedral : 6.916 59.055 4913 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.81 % Allowed : 8.04 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3231 helix: 0.88 (0.20), residues: 720 sheet: -0.49 (0.19), residues: 684 loop : -1.65 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS B 245 PHE 0.016 0.001 PHE B 220 TYR 0.013 0.001 TYR B 265 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7946 (t0) cc_final: 0.7686 (t0) REVERT: A 837 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6058 (m-80) REVERT: A 950 ASP cc_start: 0.7399 (m-30) cc_final: 0.7195 (m-30) REVERT: C 140 PHE cc_start: 0.8841 (p90) cc_final: 0.8464 (p90) REVERT: C 837 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: B 140 PHE cc_start: 0.8716 (p90) cc_final: 0.8454 (p90) REVERT: B 177 MET cc_start: 0.0237 (mtt) cc_final: -0.0029 (mtt) REVERT: B 731 MET cc_start: 0.9275 (ptt) cc_final: 0.9064 (ptt) REVERT: B 837 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.5769 (m-80) REVERT: B 950 ASP cc_start: 0.7504 (m-30) cc_final: 0.7151 (m-30) REVERT: B 990 GLU cc_start: 0.7606 (tt0) cc_final: 0.7394 (mt-10) outliers start: 23 outliers final: 9 residues processed: 197 average time/residue: 2.0713 time to fit residues: 513.8320 Evaluate side-chains 184 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 965 GLN B 628 GLN B 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 27159 Z= 0.444 Angle : 0.629 11.408 36963 Z= 0.331 Chirality : 0.046 0.287 4347 Planarity : 0.004 0.044 4689 Dihedral : 6.819 58.833 4913 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.09 % Allowed : 9.54 % Favored : 89.37 % 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: -1.42 (0.14), residues: 3231 helix: 0.77 (0.21), residues: 708 sheet: -0.55 (0.19), residues: 651 loop : -1.86 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.004 0.001 HIS B 245 PHE 0.015 0.001 PHE C 898 TYR 0.021 0.002 TYR A 508 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 4.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7982 (t0) cc_final: 0.7734 (t0) REVERT: A 837 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: A 990 GLU cc_start: 0.7747 (tt0) cc_final: 0.7545 (mt-10) REVERT: C 140 PHE cc_start: 0.8934 (p90) cc_final: 0.8537 (p90) REVERT: C 837 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: B 177 MET cc_start: 0.0459 (mtt) cc_final: 0.0255 (mtt) REVERT: B 837 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.5794 (m-80) REVERT: B 990 GLU cc_start: 0.7685 (tt0) cc_final: 0.7380 (mt-10) outliers start: 31 outliers final: 8 residues processed: 202 average time/residue: 2.0122 time to fit residues: 506.7623 Evaluate side-chains 182 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 313 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 164 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27159 Z= 0.180 Angle : 0.548 10.168 36963 Z= 0.286 Chirality : 0.044 0.283 4347 Planarity : 0.003 0.043 4689 Dihedral : 6.515 57.984 4911 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.98 % Allowed : 10.18 % Favored : 88.84 % 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: -1.15 (0.14), residues: 3231 helix: 1.08 (0.21), residues: 699 sheet: -0.52 (0.19), residues: 672 loop : -1.65 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.008 0.001 HIS C 519 PHE 0.014 0.001 PHE A 898 TYR 0.014 0.001 TYR A 508 ARG 0.002 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0345 (mtt) cc_final: -0.0561 (mtt) REVERT: A 212 LEU cc_start: 0.8178 (tt) cc_final: 0.7851 (tm) REVERT: A 228 ASP cc_start: 0.7927 (t0) cc_final: 0.7631 (t0) REVERT: A 837 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: A 950 ASP cc_start: 0.7380 (m-30) cc_final: 0.7154 (m-30) REVERT: A 990 GLU cc_start: 0.7682 (tt0) cc_final: 0.7468 (mt-10) REVERT: A 1050 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8635 (ptm) REVERT: C 140 PHE cc_start: 0.8893 (p90) cc_final: 0.8513 (p90) REVERT: C 837 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: B 837 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.5677 (m-80) REVERT: B 950 ASP cc_start: 0.7510 (m-30) cc_final: 0.7212 (m-30) REVERT: B 990 GLU cc_start: 0.7644 (tt0) cc_final: 0.7423 (mt-10) outliers start: 28 outliers final: 6 residues processed: 196 average time/residue: 2.0609 time to fit residues: 505.6605 Evaluate side-chains 178 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 0.0470 chunk 177 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 312 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN C 965 GLN B 628 GLN B 955 ASN B 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27159 Z= 0.193 Angle : 0.538 9.880 36963 Z= 0.279 Chirality : 0.043 0.267 4347 Planarity : 0.003 0.044 4689 Dihedral : 6.288 58.978 4911 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.84 % Allowed : 10.63 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3231 helix: 1.17 (0.20), residues: 702 sheet: -0.44 (0.19), residues: 672 loop : -1.58 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS C 519 PHE 0.012 0.001 PHE C 898 TYR 0.015 0.001 TYR C 508 ARG 0.001 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0251 (mtt) cc_final: -0.0460 (mtt) REVERT: A 212 LEU cc_start: 0.8204 (tt) cc_final: 0.7884 (tm) REVERT: A 228 ASP cc_start: 0.7824 (t0) cc_final: 0.7550 (t0) REVERT: A 828 LEU cc_start: 0.7499 (mm) cc_final: 0.7120 (tp) REVERT: A 837 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: A 986 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (ttpp) REVERT: A 990 GLU cc_start: 0.7647 (tt0) cc_final: 0.7360 (mt-10) REVERT: A 1050 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8609 (ptm) REVERT: C 140 PHE cc_start: 0.8883 (p90) cc_final: 0.8533 (p90) REVERT: C 837 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: B 837 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.5652 (m-80) REVERT: B 950 ASP cc_start: 0.7497 (m-30) cc_final: 0.7194 (m-30) outliers start: 24 outliers final: 8 residues processed: 192 average time/residue: 2.0516 time to fit residues: 495.4823 Evaluate side-chains 184 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27159 Z= 0.294 Angle : 0.563 10.336 36963 Z= 0.294 Chirality : 0.044 0.262 4347 Planarity : 0.004 0.044 4689 Dihedral : 6.270 59.803 4911 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.91 % Allowed : 11.02 % Favored : 88.07 % 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: -1.09 (0.14), residues: 3231 helix: 1.17 (0.21), residues: 702 sheet: -0.43 (0.19), residues: 666 loop : -1.65 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B 245 PHE 0.013 0.001 PHE B 898 TYR 0.022 0.001 TYR B 508 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0010 (mtt) cc_final: -0.0192 (mtt) REVERT: A 212 LEU cc_start: 0.8200 (tt) cc_final: 0.7881 (tm) REVERT: A 228 ASP cc_start: 0.7968 (t0) cc_final: 0.7712 (t0) REVERT: A 828 LEU cc_start: 0.7545 (mm) cc_final: 0.7098 (tp) REVERT: A 837 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: A 986 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7906 (ttpp) REVERT: A 1050 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (ptm) REVERT: C 140 PHE cc_start: 0.8916 (p90) cc_final: 0.8585 (p90) REVERT: C 837 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: B 837 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.5680 (m-80) outliers start: 26 outliers final: 14 residues processed: 198 average time/residue: 1.9676 time to fit residues: 488.7552 Evaluate side-chains 188 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27159 Z= 0.201 Angle : 0.538 9.659 36963 Z= 0.280 Chirality : 0.043 0.260 4347 Planarity : 0.003 0.046 4689 Dihedral : 6.163 59.949 4911 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.74 % Allowed : 11.47 % Favored : 87.79 % 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: -0.97 (0.14), residues: 3231 helix: 1.25 (0.20), residues: 711 sheet: -0.38 (0.19), residues: 672 loop : -1.58 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.013 0.001 PHE B 220 TYR 0.019 0.001 TYR B 508 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0164 (mtt) cc_final: -0.0386 (mtt) REVERT: A 212 LEU cc_start: 0.8193 (tt) cc_final: 0.7872 (tm) REVERT: A 228 ASP cc_start: 0.7913 (t0) cc_final: 0.7646 (t0) REVERT: A 828 LEU cc_start: 0.7572 (mm) cc_final: 0.7101 (tp) REVERT: A 837 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.6147 (m-80) REVERT: A 986 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7933 (ttpp) REVERT: C 140 PHE cc_start: 0.8884 (p90) cc_final: 0.8592 (p90) REVERT: C 516 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7245 (tm-30) REVERT: C 837 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: B 212 LEU cc_start: 0.8094 (tt) cc_final: 0.7793 (tt) REVERT: B 837 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.5698 (m-80) REVERT: B 950 ASP cc_start: 0.7465 (m-30) cc_final: 0.7265 (m-30) outliers start: 21 outliers final: 8 residues processed: 191 average time/residue: 1.9531 time to fit residues: 475.4859 Evaluate side-chains 187 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27159 Z= 0.249 Angle : 0.548 9.844 36963 Z= 0.285 Chirality : 0.044 0.256 4347 Planarity : 0.003 0.046 4689 Dihedral : 6.142 59.796 4911 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.70 % Allowed : 12.11 % Favored : 87.19 % 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: -0.97 (0.14), residues: 3231 helix: 1.31 (0.20), residues: 711 sheet: -0.35 (0.19), residues: 666 loop : -1.61 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.001 PHE A 220 TYR 0.024 0.001 TYR B 508 ARG 0.002 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0094 (mtt) cc_final: -0.0205 (mtt) REVERT: A 212 LEU cc_start: 0.8192 (tt) cc_final: 0.7872 (tm) REVERT: A 228 ASP cc_start: 0.7896 (t0) cc_final: 0.7631 (t0) REVERT: A 828 LEU cc_start: 0.7570 (mm) cc_final: 0.7102 (tp) REVERT: A 837 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6023 (m-80) REVERT: A 986 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7931 (ttpp) REVERT: C 140 PHE cc_start: 0.8888 (p90) cc_final: 0.8609 (p90) REVERT: C 837 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: B 101 ILE cc_start: 0.9092 (mm) cc_final: 0.8717 (pp) REVERT: B 212 LEU cc_start: 0.8094 (tt) cc_final: 0.7794 (tt) REVERT: B 837 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.5667 (m-80) outliers start: 20 outliers final: 10 residues processed: 190 average time/residue: 1.8957 time to fit residues: 456.9801 Evaluate side-chains 187 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 264 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090288 restraints weight = 140380.450| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.16 r_work: 0.3134 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27159 Z= 0.251 Angle : 0.547 9.804 36963 Z= 0.286 Chirality : 0.044 0.257 4347 Planarity : 0.003 0.047 4689 Dihedral : 6.142 59.717 4911 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.63 % Allowed : 12.14 % Favored : 87.23 % 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: -0.96 (0.14), residues: 3231 helix: 1.31 (0.20), residues: 711 sheet: -0.34 (0.19), residues: 666 loop : -1.61 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C 519 PHE 0.013 0.001 PHE B 220 TYR 0.025 0.001 TYR A 508 ARG 0.002 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12551.64 seconds wall clock time: 278 minutes 12.89 seconds (16692.89 seconds total)