Starting phenix.real_space_refine on Tue Mar 19 10:43:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lym_23595/03_2024/7lym_23595.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lym_23595/03_2024/7lym_23595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lym_23595/03_2024/7lym_23595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lym_23595/03_2024/7lym_23595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lym_23595/03_2024/7lym_23595.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lym_23595/03_2024/7lym_23595.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 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 102 5.16 5 C 15258 2.51 5 N 3936 2.21 5 O 4620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23916 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7818 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7819 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 7 Chain: "C" Number of atoms: 7817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7817 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.46, per 1000 atoms: 0.52 Number of scatterers: 23916 At special positions: 0 Unit cell: (128.28, 133.625, 175.316, 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 102 16.00 O 4620 8.00 N 3936 7.00 C 15258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.01 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 3.7 seconds 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 47 sheets defined 27.7% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.605A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.150A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.523A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.916A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.326A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.012A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.741A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.577A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.876A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.058A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.696A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.799A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.479A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.891A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.648A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.508A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.011A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.705A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.000A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.579A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.691A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.769A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.236A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.687A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.073A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.126A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.905A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.810A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.206A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.534A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.066A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.336A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.537A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.516A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 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 965 removed outlier: 4.090A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.649A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.982A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.754A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.608A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.306A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.553A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.888A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.383A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.133A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.779A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.093A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.597A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.597A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.920A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.679A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.618A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.777A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.277A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.237A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.549A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.973A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.761A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.630A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.401A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.922A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.793A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.911A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.989A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.697A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.940A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.990A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.482A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2901 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: 11.07 Time building geometry restraints manager: 8.61 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: 6252 1.33 - 1.46: 4575 1.46 - 1.58: 13488 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24441 Sorted by residual: bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.541 -0.027 5.50e-03 3.31e+04 2.44e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.54e+01 bond pdb=" C5 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 24436 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.15: 429 105.15 - 112.67: 11531 112.67 - 120.19: 11590 120.19 - 127.71: 9582 127.71 - 135.24: 117 Bond angle restraints: 33249 Sorted by residual: angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP C 737 " pdb=" CB ASP C 737 " pdb=" CG ASP C 737 " ideal model delta sigma weight residual 112.60 107.16 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.14 -5.34 1.00e+00 1.00e+00 2.85e+01 angle pdb=" OE1 GLN B1106 " pdb=" CD GLN B1106 " pdb=" NE2 GLN B1106 " ideal model delta sigma weight residual 122.60 117.38 5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" OE1 GLN B1054 " pdb=" CD GLN B1054 " pdb=" NE2 GLN B1054 " ideal model delta sigma weight residual 122.60 117.79 4.81 1.00e+00 1.00e+00 2.31e+01 ... (remaining 33244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13944 17.73 - 35.46: 801 35.46 - 53.20: 128 53.20 - 70.93: 55 70.93 - 88.66: 36 Dihedral angle restraints: 14964 sinusoidal: 6228 harmonic: 8736 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -163.32 77.32 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -143.93 57.93 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CA PHE B 133 " pdb=" C PHE B 133 " pdb=" N GLN B 134 " pdb=" CA GLN B 134 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 14961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 3877 0.278 - 0.556: 16 0.556 - 0.834: 0 0.834 - 1.111: 0 1.111 - 1.389: 1 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.82e+01 chirality pdb=" CA ASP B 745 " pdb=" N ASP B 745 " pdb=" C ASP B 745 " pdb=" CB ASP B 745 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ASN A 487 " pdb=" N ASN A 487 " pdb=" C ASN A 487 " pdb=" CB ASN A 487 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 3891 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.257 2.00e-02 2.50e+03 1.38e-01 4.78e+02 pdb=" CG TRP B 886 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.128 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.201 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.154 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.122 2.00e-02 2.50e+03 1.22e-01 1.86e+02 pdb=" CG ASN B 709 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.174 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.154 2.00e-02 2.50e+03 8.47e-02 1.44e+02 pdb=" CG TYR A 904 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.129 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 12536 3.01 - 3.48: 23138 3.48 - 3.95: 39207 3.95 - 4.43: 43141 4.43 - 4.90: 73318 Nonbonded interactions: 191340 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.536 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.538 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.539 2.440 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.546 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.557 2.440 ... (remaining 191335 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 'A' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 589 or (resid 590 and (name N o \ r name CA or name C or name O or name CB )) or resid 591 through 1147 or resid 1 \ 301 through 1308)) selection = (chain 'B' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 479 or (resid 480 and (name N o \ r name CA or name C or name O or name CB )) or resid 481 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1147 or resid 1301 through 1308 \ )) } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.660 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 63.180 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.150 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.013 0.076 24441 Z= 0.856 Angle : 1.732 12.187 33249 Z= 1.164 Chirality : 0.097 1.389 3894 Planarity : 0.013 0.138 4254 Dihedral : 12.920 88.659 9234 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.27 % Favored : 94.35 % Rotamer: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 2958 helix: -1.24 (0.16), residues: 688 sheet: 0.24 (0.21), residues: 540 loop : -0.76 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.257 0.029 TRP B 886 HIS 0.010 0.002 HIS A 207 PHE 0.071 0.011 PHE C 718 TYR 0.154 0.020 TYR A 904 ARG 0.009 0.001 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 302 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8655 (m-10) cc_final: 0.8392 (m-80) REVERT: A 117 LEU cc_start: 0.7279 (tp) cc_final: 0.7056 (tp) REVERT: A 353 TRP cc_start: 0.8606 (p-90) cc_final: 0.8074 (p-90) REVERT: A 405 ASP cc_start: 0.6515 (m-30) cc_final: 0.6142 (m-30) REVERT: A 449 TYR cc_start: 0.7508 (m-80) cc_final: 0.7169 (m-80) REVERT: A 458 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8133 (tmtt) REVERT: A 902 MET cc_start: 0.9012 (mmm) cc_final: 0.8727 (tpt) REVERT: B 347 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7266 (t80) REVERT: B 547 THR cc_start: 0.8612 (p) cc_final: 0.8359 (t) REVERT: C 994 ASP cc_start: 0.7777 (t70) cc_final: 0.7402 (t0) REVERT: C 1047 TYR cc_start: 0.8892 (m-80) cc_final: 0.8673 (m-80) outliers start: 22 outliers final: 5 residues processed: 322 average time/residue: 0.3765 time to fit residues: 189.0518 Evaluate side-chains 139 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN B 388 ASN B 957 GLN C 321 GLN C 460 ASN C 675 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24441 Z= 0.192 Angle : 0.640 10.297 33249 Z= 0.341 Chirality : 0.047 0.303 3894 Planarity : 0.004 0.036 4254 Dihedral : 6.948 59.262 3915 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 1.57 % Allowed : 5.80 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2958 helix: 0.84 (0.20), residues: 670 sheet: 0.11 (0.19), residues: 637 loop : -0.42 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 64 HIS 0.005 0.001 HIS C 519 PHE 0.025 0.002 PHE A 92 TYR 0.018 0.002 TYR A1067 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7546 (m-80) cc_final: 0.7254 (m-10) REVERT: A 458 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8224 (tttt) REVERT: A 512 VAL cc_start: 0.8926 (t) cc_final: 0.8679 (p) REVERT: A 823 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 979 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7144 (t0) REVERT: B 347 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 902 MET cc_start: 0.8755 (tpt) cc_final: 0.8472 (tpt) REVERT: C 353 TRP cc_start: 0.5288 (p-90) cc_final: 0.5075 (p-90) REVERT: C 505 TYR cc_start: 0.5717 (OUTLIER) cc_final: 0.5020 (m-80) REVERT: C 979 ASP cc_start: 0.7240 (m-30) cc_final: 0.6884 (t0) REVERT: C 994 ASP cc_start: 0.8048 (t70) cc_final: 0.7747 (t0) outliers start: 41 outliers final: 24 residues processed: 188 average time/residue: 0.3350 time to fit residues: 101.9499 Evaluate side-chains 142 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 272 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 243 optimal weight: 30.0000 chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 417 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 394 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24441 Z= 0.342 Angle : 0.622 8.807 33249 Z= 0.327 Chirality : 0.047 0.304 3894 Planarity : 0.004 0.036 4254 Dihedral : 6.551 57.257 3913 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.37 % Allowed : 6.61 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2958 helix: 1.01 (0.20), residues: 678 sheet: 0.08 (0.19), residues: 671 loop : -0.48 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 353 HIS 0.006 0.001 HIS C1064 PHE 0.027 0.002 PHE A 92 TYR 0.023 0.001 TYR B1067 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 125 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.6513 (t80) cc_final: 0.5913 (t80) REVERT: A 458 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8064 (tmtt) REVERT: A 823 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7638 (t80) REVERT: A 979 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7479 (t0) REVERT: A 1031 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: B 347 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.6920 (t80) REVERT: B 979 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7582 (t0) REVERT: C 167 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8576 (t) REVERT: C 353 TRP cc_start: 0.5361 (p-90) cc_final: 0.5151 (p-90) REVERT: C 505 TYR cc_start: 0.5555 (OUTLIER) cc_final: 0.4835 (m-80) REVERT: C 979 ASP cc_start: 0.7418 (m-30) cc_final: 0.6998 (t0) outliers start: 62 outliers final: 38 residues processed: 177 average time/residue: 0.3363 time to fit residues: 101.8888 Evaluate side-chains 156 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 259 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24441 Z= 0.184 Angle : 0.550 11.495 33249 Z= 0.288 Chirality : 0.045 0.279 3894 Planarity : 0.003 0.038 4254 Dihedral : 6.206 54.987 3913 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.95 % Allowed : 7.87 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2958 helix: 1.43 (0.21), residues: 668 sheet: 0.01 (0.19), residues: 690 loop : -0.46 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.026 0.001 PHE C 140 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7582 (m-80) cc_final: 0.7205 (m-10) REVERT: A 458 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8057 (tmtt) REVERT: A 823 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 902 MET cc_start: 0.9228 (tpp) cc_final: 0.8959 (tpt) REVERT: A 1031 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 347 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.6903 (t80) REVERT: B 902 MET cc_start: 0.8820 (tpt) cc_final: 0.8336 (tpt) REVERT: B 979 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7507 (t0) REVERT: C 96 GLU cc_start: 0.4810 (OUTLIER) cc_final: 0.4568 (tp30) REVERT: C 212 LEU cc_start: 0.7798 (tp) cc_final: 0.7358 (tt) REVERT: C 493 GLN cc_start: 0.5315 (OUTLIER) cc_final: 0.4531 (mm-40) REVERT: C 505 TYR cc_start: 0.5493 (OUTLIER) cc_final: 0.4754 (m-80) REVERT: C 979 ASP cc_start: 0.7392 (m-30) cc_final: 0.6957 (t0) outliers start: 51 outliers final: 32 residues processed: 164 average time/residue: 0.3338 time to fit residues: 91.3499 Evaluate side-chains 148 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 4 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 260 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24441 Z= 0.205 Angle : 0.536 11.509 33249 Z= 0.278 Chirality : 0.044 0.282 3894 Planarity : 0.003 0.038 4254 Dihedral : 5.984 55.773 3913 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.14 % Allowed : 8.29 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2958 helix: 1.56 (0.21), residues: 675 sheet: 0.04 (0.19), residues: 649 loop : -0.46 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.027 0.001 PHE C 140 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7581 (m-80) cc_final: 0.7245 (m-10) REVERT: A 458 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8052 (tmtt) REVERT: A 564 GLN cc_start: 0.7639 (tp40) cc_final: 0.7379 (tp-100) REVERT: A 762 GLN cc_start: 0.7603 (tm130) cc_final: 0.7299 (tm-30) REVERT: A 823 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7565 (t80) REVERT: A 902 MET cc_start: 0.9209 (tpp) cc_final: 0.8996 (tpt) REVERT: A 1031 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 347 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.6801 (t80) REVERT: B 979 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7518 (t0) REVERT: C 96 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.4484 (tp30) REVERT: C 493 GLN cc_start: 0.5132 (OUTLIER) cc_final: 0.4304 (mm-40) REVERT: C 505 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.4699 (m-80) REVERT: C 569 ILE cc_start: 0.8836 (mm) cc_final: 0.8510 (mp) REVERT: C 979 ASP cc_start: 0.7415 (m-30) cc_final: 0.7090 (t0) outliers start: 56 outliers final: 40 residues processed: 165 average time/residue: 0.3181 time to fit residues: 87.3623 Evaluate side-chains 157 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 290 optimal weight: 2.9990 chunk 240 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1135 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 24441 Z= 0.320 Angle : 0.565 10.931 33249 Z= 0.294 Chirality : 0.045 0.298 3894 Planarity : 0.003 0.039 4254 Dihedral : 6.004 56.262 3913 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.52 % Allowed : 8.97 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2958 helix: 1.43 (0.21), residues: 675 sheet: -0.08 (0.18), residues: 703 loop : -0.48 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 PHE 0.027 0.002 PHE C 140 TYR 0.023 0.001 TYR B1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 109 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8019 (tmtt) REVERT: A 564 GLN cc_start: 0.7628 (tp40) cc_final: 0.7360 (tp-100) REVERT: A 762 GLN cc_start: 0.7767 (tm130) cc_final: 0.7352 (tm-30) REVERT: A 1031 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: B 347 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.6781 (t80) REVERT: B 979 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (t0) REVERT: C 96 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4388 (tp30) REVERT: C 493 GLN cc_start: 0.4803 (OUTLIER) cc_final: 0.3124 (mp10) REVERT: C 505 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.4672 (m-80) REVERT: C 515 PHE cc_start: 0.8081 (m-80) cc_final: 0.7764 (m-80) REVERT: C 979 ASP cc_start: 0.7448 (m-30) cc_final: 0.7046 (t0) outliers start: 66 outliers final: 45 residues processed: 166 average time/residue: 0.3204 time to fit residues: 88.9296 Evaluate side-chains 151 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 99 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 165 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24441 Z= 0.151 Angle : 0.507 11.002 33249 Z= 0.265 Chirality : 0.044 0.269 3894 Planarity : 0.003 0.040 4254 Dihedral : 5.706 54.898 3913 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.91 % Allowed : 9.97 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2958 helix: 1.84 (0.21), residues: 663 sheet: -0.00 (0.19), residues: 664 loop : -0.44 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.003 0.000 HIS C 519 PHE 0.028 0.001 PHE C 140 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 117 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7321 (t80) cc_final: 0.7109 (t80) REVERT: A 458 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8012 (tmtt) REVERT: A 564 GLN cc_start: 0.7518 (tp40) cc_final: 0.7263 (tp-100) REVERT: A 1031 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: B 394 ASN cc_start: 0.7850 (m-40) cc_final: 0.7478 (m-40) REVERT: B 698 SER cc_start: 0.8317 (t) cc_final: 0.7936 (p) REVERT: B 902 MET cc_start: 0.8790 (tpt) cc_final: 0.8356 (tpt) REVERT: B 979 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7591 (t0) REVERT: C 96 GLU cc_start: 0.5250 (OUTLIER) cc_final: 0.4847 (tp30) REVERT: C 493 GLN cc_start: 0.4907 (OUTLIER) cc_final: 0.3257 (mp10) REVERT: C 505 TYR cc_start: 0.5330 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: C 515 PHE cc_start: 0.7965 (m-80) cc_final: 0.7654 (m-80) REVERT: C 569 ILE cc_start: 0.8817 (mm) cc_final: 0.8475 (mp) REVERT: C 1050 MET cc_start: 0.7242 (ttm) cc_final: 0.7031 (ttm) outliers start: 50 outliers final: 34 residues processed: 159 average time/residue: 0.3166 time to fit residues: 85.8425 Evaluate side-chains 147 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 263 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24441 Z= 0.228 Angle : 0.519 9.138 33249 Z= 0.271 Chirality : 0.044 0.280 3894 Planarity : 0.003 0.041 4254 Dihedral : 5.613 55.455 3911 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.95 % Allowed : 10.16 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 2958 helix: 1.70 (0.21), residues: 675 sheet: 0.02 (0.19), residues: 692 loop : -0.48 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 353 HIS 0.005 0.001 HIS C1064 PHE 0.027 0.001 PHE C 140 TYR 0.021 0.001 TYR B1067 ARG 0.008 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 108 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8032 (tmtt) REVERT: A 564 GLN cc_start: 0.7504 (tp40) cc_final: 0.7243 (tp-100) REVERT: A 1031 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: B 394 ASN cc_start: 0.7880 (m-40) cc_final: 0.7510 (m-40) REVERT: B 698 SER cc_start: 0.8242 (t) cc_final: 0.7882 (p) REVERT: B 902 MET cc_start: 0.8936 (tpt) cc_final: 0.8432 (tpt) REVERT: B 1141 LEU cc_start: 0.8874 (tp) cc_final: 0.8591 (tt) REVERT: C 96 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.5100 (tp30) REVERT: C 493 GLN cc_start: 0.4906 (OUTLIER) cc_final: 0.3275 (mp10) REVERT: C 505 TYR cc_start: 0.5305 (OUTLIER) cc_final: 0.4677 (m-80) REVERT: C 515 PHE cc_start: 0.7933 (m-80) cc_final: 0.7649 (m-80) REVERT: C 569 ILE cc_start: 0.8787 (mm) cc_final: 0.8448 (mp) outliers start: 51 outliers final: 36 residues processed: 150 average time/residue: 0.3279 time to fit residues: 82.7540 Evaluate side-chains 144 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 103 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 269 optimal weight: 0.3980 chunk 276 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 268 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24441 Z= 0.151 Angle : 0.491 8.212 33249 Z= 0.258 Chirality : 0.043 0.265 3894 Planarity : 0.003 0.041 4254 Dihedral : 5.439 54.746 3911 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.76 % Allowed : 10.31 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 2958 helix: 1.89 (0.21), residues: 664 sheet: 0.07 (0.19), residues: 689 loop : -0.43 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.003 0.001 HIS C 519 PHE 0.034 0.001 PHE A 497 TYR 0.022 0.001 TYR B 904 ARG 0.007 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 115 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7260 (t80) cc_final: 0.7015 (t80) REVERT: A 458 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8044 (tmtt) REVERT: A 564 GLN cc_start: 0.7464 (tp40) cc_final: 0.7222 (tp-100) REVERT: A 1031 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 1142 GLN cc_start: 0.8590 (tp40) cc_final: 0.8288 (tp-100) REVERT: B 394 ASN cc_start: 0.7776 (m-40) cc_final: 0.7419 (m-40) REVERT: B 698 SER cc_start: 0.8384 (t) cc_final: 0.7958 (p) REVERT: B 902 MET cc_start: 0.8743 (tpt) cc_final: 0.8343 (tpt) REVERT: B 904 TYR cc_start: 0.7368 (m-10) cc_final: 0.6452 (m-10) REVERT: B 1141 LEU cc_start: 0.8756 (tp) cc_final: 0.8466 (tt) REVERT: C 212 LEU cc_start: 0.7830 (tp) cc_final: 0.7483 (tt) REVERT: C 493 GLN cc_start: 0.5094 (OUTLIER) cc_final: 0.3438 (mp10) REVERT: C 505 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.4637 (m-80) REVERT: C 515 PHE cc_start: 0.7796 (m-80) cc_final: 0.7583 (m-10) REVERT: C 569 ILE cc_start: 0.8796 (mm) cc_final: 0.8463 (mp) outliers start: 46 outliers final: 38 residues processed: 154 average time/residue: 0.3230 time to fit residues: 83.2827 Evaluate side-chains 148 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 298 optimal weight: 0.0370 chunk 275 optimal weight: 0.5980 chunk 237 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 183 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 24441 Z= 0.139 Angle : 0.483 7.663 33249 Z= 0.254 Chirality : 0.043 0.256 3894 Planarity : 0.003 0.042 4254 Dihedral : 5.284 54.334 3911 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.53 % Allowed : 11.11 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 2958 helix: 1.98 (0.21), residues: 669 sheet: 0.14 (0.19), residues: 655 loop : -0.37 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.003 0.000 HIS C 519 PHE 0.037 0.001 PHE A 497 TYR 0.021 0.001 TYR B 904 ARG 0.007 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7243 (t80) cc_final: 0.6975 (t80) REVERT: A 458 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8107 (tmtt) REVERT: A 564 GLN cc_start: 0.7448 (tp40) cc_final: 0.7201 (tp-100) REVERT: A 1031 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 394 ASN cc_start: 0.7738 (m-40) cc_final: 0.7375 (m-40) REVERT: B 698 SER cc_start: 0.8417 (t) cc_final: 0.7989 (p) REVERT: B 902 MET cc_start: 0.8765 (tpt) cc_final: 0.8517 (tpt) REVERT: B 904 TYR cc_start: 0.7422 (m-10) cc_final: 0.6453 (m-10) REVERT: B 1141 LEU cc_start: 0.8747 (tp) cc_final: 0.8460 (tt) REVERT: C 493 GLN cc_start: 0.5076 (OUTLIER) cc_final: 0.3398 (mp10) REVERT: C 505 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4619 (m-80) REVERT: C 569 ILE cc_start: 0.8766 (mm) cc_final: 0.8440 (mp) outliers start: 40 outliers final: 33 residues processed: 149 average time/residue: 0.3378 time to fit residues: 83.3106 Evaluate side-chains 144 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 238 optimal weight: 40.0000 chunk 99 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.140564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106209 restraints weight = 45122.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104291 restraints weight = 35705.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.105992 restraints weight = 36640.550| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24441 Z= 0.316 Angle : 0.554 8.814 33249 Z= 0.287 Chirality : 0.045 0.287 3894 Planarity : 0.003 0.044 4254 Dihedral : 5.547 56.283 3911 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.79 % Allowed : 11.23 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 2958 helix: 1.60 (0.21), residues: 677 sheet: 0.05 (0.19), residues: 694 loop : -0.44 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 353 HIS 0.006 0.001 HIS C1064 PHE 0.042 0.002 PHE A 497 TYR 0.023 0.001 TYR B1067 ARG 0.006 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.97 seconds wall clock time: 67 minutes 23.58 seconds (4043.58 seconds total)