Starting phenix.real_space_refine on Sun Nov 19 17:23:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhx_34806/11_2023/8hhx_34806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhx_34806/11_2023/8hhx_34806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhx_34806/11_2023/8hhx_34806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhx_34806/11_2023/8hhx_34806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhx_34806/11_2023/8hhx_34806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhx_34806/11_2023/8hhx_34806.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17425 2.51 5 N 4532 2.21 5 O 5358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 27435 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6373 Classifications: {'peptide': 822} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 39, 'TRANS': 782} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7871 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 958} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7646 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 931} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1682 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "G" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1614 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 831 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.14, per 1000 atoms: 0.52 Number of scatterers: 27435 At special positions: 0 Unit cell: (161.85, 174.3, 185.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5358 8.00 N 4532 7.00 C 17425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 224 " - pdb=" SG CYS G 216 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG D 1 " - " ASN A1074 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG P 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " Time building additional restraints: 10.49 Conformation dependent library (CDL) restraints added in 5.4 seconds 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6490 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 63 sheets defined 21.9% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.996A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.997A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.549A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.847A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.755A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.980A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.797A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.869A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.937A pdb=" N SER B 373 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.597A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.576A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.798A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.632A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.560A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.200A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.549A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.445A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.386A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.665A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.501A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.558A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.930A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.429A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.656A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.977A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.526A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.238A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 126 through 132 removed outlier: 3.530A pdb=" N GLU G 129 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.989A pdb=" N ASN G 175 " --> pdb=" O GLN G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 193 removed outlier: 4.198A pdb=" N TRP G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS G 193 " --> pdb=" O GLN G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.695A pdb=" N ASN I 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.652A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.646A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.777A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 205 removed outlier: 6.358A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.518A pdb=" N VAL A 551 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.305A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.931A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 656 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.051A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.568A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.612A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.977A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 317 removed outlier: 5.897A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.218A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.818A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 719 removed outlier: 6.818A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.586A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.201A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.860A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.745A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.948A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.662A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.748A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 394 through 396 removed outlier: 3.715A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.506A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 719 removed outlier: 7.104A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1053 through 1056 removed outlier: 3.653A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF4, first strand: chain 'C' and resid 1089 through 1090 removed outlier: 3.531A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.077A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 95 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS F 96 " --> pdb=" O TRP F 111 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP F 111 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN F 98 " --> pdb=" O ASP F 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.512A pdb=" N VAL F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 59 " --> pdb=" O VAL F 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AG2, first strand: chain 'G' and resid 21 through 23 removed outlier: 4.539A pdb=" N ALA G 75 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 74 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP G 69 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 76 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 67 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.900A pdb=" N VAL G 49 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 38 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR G 91 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AG5, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AG6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AG7, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.840A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.660A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 70 through 73 removed outlier: 3.608A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.40 Time building geometry restraints manager: 11.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7410 1.33 - 1.46: 6924 1.46 - 1.58: 13562 1.58 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 28051 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CB PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.79e+00 bond pdb=" N ILE B 850 " pdb=" CA ILE B 850 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N VAL A 143 " pdb=" CA VAL A 143 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.27e+00 ... (remaining 28046 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.01: 158 103.01 - 110.81: 9487 110.81 - 118.60: 12673 118.60 - 126.39: 15527 126.39 - 134.18: 326 Bond angle restraints: 38171 Sorted by residual: angle pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" CD PRO C 272 " ideal model delta sigma weight residual 112.00 97.59 14.41 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N PRO C 272 " pdb=" CD PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 103.20 95.22 7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C ASP A 737 " pdb=" CA ASP A 737 " pdb=" CB ASP A 737 " ideal model delta sigma weight residual 110.77 118.42 -7.65 1.67e+00 3.59e-01 2.10e+01 angle pdb=" N GLN C 954 " pdb=" CA GLN C 954 " pdb=" CB GLN C 954 " ideal model delta sigma weight residual 110.32 117.74 -7.42 1.70e+00 3.46e-01 1.90e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" CB GLN A 774 " ideal model delta sigma weight residual 110.12 116.37 -6.25 1.47e+00 4.63e-01 1.81e+01 ... (remaining 38166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14961 17.94 - 35.88: 1198 35.88 - 53.82: 179 53.82 - 71.76: 37 71.76 - 89.70: 22 Dihedral angle restraints: 16397 sinusoidal: 6299 harmonic: 10098 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.48 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -164.92 78.92 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -163.24 77.24 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 16394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4430 0.190 - 0.380: 4 0.380 - 0.570: 0 0.570 - 0.760: 1 0.760 - 0.950: 1 Chirality restraints: 4436 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4433 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 271 " 0.098 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO B 272 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 271 " 0.091 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO C 272 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.049 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN A 616 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.051 2.00e-02 2.50e+03 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 557 2.67 - 3.23: 26207 3.23 - 3.79: 40161 3.79 - 4.34: 53517 4.34 - 4.90: 86634 Nonbonded interactions: 207076 Sorted by model distance: nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.114 2.440 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.144 2.440 nonbonded pdb=" O THR B 961 " pdb=" OE1 GLN B 965 " model vdw 2.151 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR B1067 " pdb=" O ASN B1108 " model vdw 2.197 2.440 ... (remaining 207071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 25 through 146 or resid 164 through 165 or resid 186 throu \ gh 463 or resid 491 through 1140 or resid 1301 through 1307)) selection = (chain 'C' and (resid 25 through 69 or resid 81 through 146 or resid 148 through \ 149 or resid 186 through 243 or resid 264 through 1140 or resid 1301 through 13 \ 07)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.030 Extract box with map and model: 13.830 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 72.740 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 28051 Z= 0.258 Angle : 0.637 14.413 38171 Z= 0.339 Chirality : 0.050 0.950 4436 Planarity : 0.005 0.146 4881 Dihedral : 13.160 89.696 9799 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 0.17 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3419 helix: 0.24 (0.21), residues: 624 sheet: -0.85 (0.23), residues: 535 loop : -1.13 (0.13), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 414 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 418 average time/residue: 0.3642 time to fit residues: 247.9523 Evaluate side-chains 329 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 327 time to evaluate : 2.939 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2577 time to fit residues: 5.1729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 176 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 chunk 164 optimal weight: 0.7980 chunk 201 optimal weight: 7.9990 chunk 313 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28051 Z= 0.167 Angle : 0.569 10.141 38171 Z= 0.297 Chirality : 0.046 0.316 4436 Planarity : 0.004 0.106 4881 Dihedral : 4.161 25.834 3717 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 0.83 % Allowed : 7.05 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3419 helix: 0.44 (0.21), residues: 625 sheet: -0.54 (0.23), residues: 569 loop : -1.12 (0.13), residues: 2225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 379 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 393 average time/residue: 0.3768 time to fit residues: 241.3952 Evaluate side-chains 360 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 343 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2562 time to fit residues: 12.4704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 260 optimal weight: 0.0050 chunk 213 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 313 optimal weight: 40.0000 chunk 339 optimal weight: 7.9990 chunk 279 optimal weight: 0.0870 chunk 311 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 overall best weight: 1.9174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1113 GLN B 81 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 540 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28051 Z= 0.226 Angle : 0.572 10.500 38171 Z= 0.296 Chirality : 0.045 0.352 4436 Planarity : 0.004 0.079 4881 Dihedral : 4.227 26.647 3717 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 1.36 % Allowed : 9.54 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3419 helix: 0.41 (0.21), residues: 619 sheet: -0.67 (0.23), residues: 564 loop : -1.15 (0.13), residues: 2236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 362 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 386 average time/residue: 0.3813 time to fit residues: 238.2988 Evaluate side-chains 355 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 330 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2400 time to fit residues: 15.1594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 149 optimal weight: 0.0030 chunk 210 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 298 optimal weight: 40.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1113 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 474 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 370 ASN C 563 GLN C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28051 Z= 0.307 Angle : 0.632 9.965 38171 Z= 0.330 Chirality : 0.047 0.379 4436 Planarity : 0.005 0.074 4881 Dihedral : 4.570 28.097 3717 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.84 % Favored : 92.13 % Rotamer: Outliers : 1.96 % Allowed : 12.40 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3419 helix: 0.24 (0.21), residues: 613 sheet: -0.79 (0.23), residues: 551 loop : -1.30 (0.13), residues: 2255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 363 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 35 residues processed: 401 average time/residue: 0.3751 time to fit residues: 246.6539 Evaluate side-chains 358 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 323 time to evaluate : 2.721 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.2414 time to fit residues: 20.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 284 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 299 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 764 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28051 Z= 0.315 Angle : 0.640 11.613 38171 Z= 0.335 Chirality : 0.048 0.391 4436 Planarity : 0.005 0.069 4881 Dihedral : 4.672 28.355 3717 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.93 % Allowed : 14.30 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3419 helix: 0.03 (0.20), residues: 619 sheet: -0.98 (0.22), residues: 578 loop : -1.42 (0.13), residues: 2222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 358 time to evaluate : 3.187 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 outliers start: 58 outliers final: 30 residues processed: 398 average time/residue: 0.3529 time to fit residues: 230.2108 Evaluate side-chains 357 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 327 time to evaluate : 2.688 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.2417 time to fit residues: 17.4049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 9.9990 chunk 300 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 28051 Z= 0.369 Angle : 0.698 11.517 38171 Z= 0.364 Chirality : 0.049 0.389 4436 Planarity : 0.005 0.062 4881 Dihedral : 4.960 28.668 3717 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.13 % Allowed : 16.62 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3419 helix: -0.25 (0.20), residues: 611 sheet: -1.27 (0.22), residues: 560 loop : -1.56 (0.13), residues: 2248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 359 time to evaluate : 3.074 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 outliers start: 64 outliers final: 39 residues processed: 406 average time/residue: 0.3759 time to fit residues: 252.0951 Evaluate side-chains 370 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 331 time to evaluate : 2.707 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 2 residues processed: 39 average time/residue: 0.2655 time to fit residues: 23.5524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 332 optimal weight: 40.0000 chunk 208 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 0.1980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 764 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 501 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28051 Z= 0.328 Angle : 0.684 12.691 38171 Z= 0.354 Chirality : 0.049 0.419 4436 Planarity : 0.005 0.066 4881 Dihedral : 4.915 27.445 3717 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.53 % Allowed : 17.92 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.14), residues: 3419 helix: -0.30 (0.20), residues: 612 sheet: -1.35 (0.22), residues: 565 loop : -1.59 (0.13), residues: 2242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 355 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 391 average time/residue: 0.3804 time to fit residues: 244.7655 Evaluate side-chains 341 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 2.825 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.2607 time to fit residues: 14.5272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.0470 chunk 132 optimal weight: 10.0000 chunk 198 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 779 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28051 Z= 0.182 Angle : 0.616 14.549 38171 Z= 0.315 Chirality : 0.047 0.452 4436 Planarity : 0.004 0.063 4881 Dihedral : 4.483 22.703 3717 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.86 % Allowed : 18.92 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3419 helix: -0.05 (0.21), residues: 626 sheet: -1.10 (0.22), residues: 604 loop : -1.37 (0.13), residues: 2189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 370 time to evaluate : 2.921 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 outliers start: 26 outliers final: 11 residues processed: 387 average time/residue: 0.3729 time to fit residues: 236.3319 Evaluate side-chains 340 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 329 time to evaluate : 2.827 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2581 time to fit residues: 9.3638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 290 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 chunk 186 optimal weight: 50.0000 chunk 134 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 764 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 317 ASN B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 82 GLN ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.131 28051 Z= 0.598 Angle : 0.878 12.765 38171 Z= 0.458 Chirality : 0.056 0.419 4436 Planarity : 0.006 0.067 4881 Dihedral : 5.551 31.425 3717 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 1.56 % Allowed : 18.85 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 3419 helix: -0.80 (0.19), residues: 617 sheet: -1.49 (0.22), residues: 548 loop : -1.85 (0.12), residues: 2254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 342 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 36 residues processed: 369 average time/residue: 0.3866 time to fit residues: 234.0049 Evaluate side-chains 360 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 324 time to evaluate : 2.961 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 2 residues processed: 36 average time/residue: 0.2731 time to fit residues: 22.2240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 0.4980 chunk 327 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 273 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 211 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 949 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 450 ASN B 540 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28051 Z= 0.277 Angle : 0.695 13.704 38171 Z= 0.355 Chirality : 0.049 0.413 4436 Planarity : 0.005 0.065 4881 Dihedral : 5.071 25.716 3717 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.50 % Allowed : 19.78 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3419 helix: -0.44 (0.20), residues: 613 sheet: -1.48 (0.22), residues: 580 loop : -1.67 (0.13), residues: 2226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 342 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 351 average time/residue: 0.3732 time to fit residues: 216.0115 Evaluate side-chains 330 residues out of total 3021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 320 time to evaluate : 2.880 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2485 time to fit residues: 8.9008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 252 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 474 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B1119 ASN C 710 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.244153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.208297 restraints weight = 43145.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.209010 restraints weight = 39143.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.209361 restraints weight = 34652.406| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28051 Z= 0.213 Angle : 0.647 14.744 38171 Z= 0.330 Chirality : 0.048 0.434 4436 Planarity : 0.005 0.065 4881 Dihedral : 4.707 24.228 3717 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.27 % Allowed : 20.71 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3419 helix: -0.26 (0.21), residues: 620 sheet: -1.31 (0.21), residues: 604 loop : -1.53 (0.13), residues: 2195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5425.30 seconds wall clock time: 100 minutes 21.61 seconds (6021.61 seconds total)