Starting phenix.real_space_refine (version: dev) on Thu Apr 7 02:02:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odl_12842/04_2022/7odl_12842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odl_12842/04_2022/7odl_12842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odl_12842/04_2022/7odl_12842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odl_12842/04_2022/7odl_12842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odl_12842/04_2022/7odl_12842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odl_12842/04_2022/7odl_12842_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 24338 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7958 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 46, 'TRANS': 975} Chain breaks: 8 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7948 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 46, 'TRANS': 975} Chain breaks: 8 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 7952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7952 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 46, 'TRANS': 975} Chain breaks: 8 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.20, per 1000 atoms: 0.54 Number of scatterers: 24338 At special positions: 0 Unit cell: (139.65, 154.35, 162.75, 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 111 16.00 O 4696 8.00 N 3999 7.00 C 15532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 Atom "HETATM24336 O5 NAG C1311 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1134 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " 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: 8.43 Conformation dependent library (CDL) restraints added in 3.2 seconds 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 36 sheets defined 22.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.808A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.597A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.866A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 782 removed outlier: 3.588A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 removed outlier: 3.612A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 removed outlier: 3.731A pdb=" N CYS A 840 " --> pdb=" O TYR A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 851 through 854 No H-bonds generated for 'chain 'A' and resid 851 through 854' Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.623A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 917 No H-bonds generated for 'chain 'A' and resid 914 through 917' Processing helix chain 'A' and resid 920 through 937 removed outlier: 3.529A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.009A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 3.871A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 384 through 389 removed outlier: 5.355A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.782A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 782 removed outlier: 3.846A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.583A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 839 No H-bonds generated for 'chain 'B' and resid 837 through 839' Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 851 through 854 No H-bonds generated for 'chain 'B' and resid 851 through 854' Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.663A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 920 through 937 removed outlier: 3.507A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.036A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 981 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.086A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.813A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.553A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 782 removed outlier: 3.789A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 837 through 840 removed outlier: 3.644A pdb=" N CYS C 840 " --> pdb=" O TYR C 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 837 through 840' Processing helix chain 'C' and resid 843 through 846 Processing helix chain 'C' and resid 851 through 854 No H-bonds generated for 'chain 'C' and resid 851 through 854' Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.513A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 937 removed outlier: 3.579A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 4.249A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 removed outlier: 3.750A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1032 removed outlier: 3.899A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.280A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.698A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.873A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.679A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= G, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'A' and resid 472 through 474 Processing sheet with id= I, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.393A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 670 through 674 Processing sheet with id= K, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.643A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.562A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.112A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 48 through 55 Processing sheet with id= P, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.814A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= R, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.330A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= T, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.800A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 692 through 696 removed outlier: 6.452A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.590A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 717 through 728 removed outlier: 5.956A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.739A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.621A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.316A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.661A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.490A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.559A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AE, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AF, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.515A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 670 through 674 Processing sheet with id= AH, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.655A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.945A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.654A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2250 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: 10.30 Time building geometry restraints manager: 9.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7733 1.34 - 1.46: 6073 1.46 - 1.59: 10922 1.59 - 1.71: 0 1.71 - 1.84: 135 Bond restraints: 24863 Sorted by residual: bond pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" N VAL B 36 " pdb=" CA VAL B 36 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL C1133 " pdb=" CA VAL C1133 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.95e+00 bond pdb=" N VAL B 42 " pdb=" CA VAL B 42 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.56e+00 bond pdb=" N TYR A 269 " pdb=" CA TYR A 269 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.21e-02 6.83e+03 8.14e+00 ... (remaining 24858 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.90: 646 106.90 - 113.68: 13680 113.68 - 120.46: 9246 120.46 - 127.24: 10024 127.24 - 134.02: 204 Bond angle restraints: 33800 Sorted by residual: angle pdb=" C2 NAG A1302 " pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 109.64 105.06 4.58 5.38e-01 3.45e+00 7.24e+01 angle pdb=" N LEU A 293 " pdb=" CA LEU A 293 " pdb=" C LEU A 293 " ideal model delta sigma weight residual 113.88 106.20 7.68 1.23e+00 6.61e-01 3.90e+01 angle pdb=" CA GLY C 566 " pdb=" C GLY C 566 " pdb=" O GLY C 566 " ideal model delta sigma weight residual 120.94 117.40 3.54 7.80e-01 1.64e+00 2.06e+01 angle pdb=" N ILE B 666 " pdb=" CA ILE B 666 " pdb=" C ILE B 666 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N SER B 704 " pdb=" CA SER B 704 " pdb=" C SER B 704 " ideal model delta sigma weight residual 107.73 113.95 -6.22 1.61e+00 3.86e-01 1.49e+01 ... (remaining 33795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13240 17.91 - 35.81: 1186 35.81 - 53.72: 213 53.72 - 71.63: 50 71.63 - 89.53: 28 Dihedral angle restraints: 14717 sinusoidal: 5804 harmonic: 8913 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 38.34 54.66 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 38.78 54.22 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -32.39 -53.61 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 14714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3583 0.093 - 0.185: 336 0.185 - 0.278: 10 0.278 - 0.370: 0 0.370 - 0.463: 1 Chirality restraints: 3930 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA ASP A 294 " pdb=" N ASP A 294 " pdb=" C ASP A 294 " pdb=" CB ASP A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3927 not shown) Planarity restraints: 4368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " 0.067 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" CG ASN C1134 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " 0.147 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " -0.439 2.00e-02 2.50e+03 pdb=" C1 NAG C1311 " 0.298 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.065 2.00e-02 2.50e+03 5.40e-02 3.64e+01 pdb=" C7 NAG A1302 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.086 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO B 217 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.035 5.00e-02 4.00e+02 ... (remaining 4365 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 136 2.60 - 3.18: 19560 3.18 - 3.75: 32689 3.75 - 4.33: 49812 4.33 - 4.90: 84109 Nonbonded interactions: 186306 Sorted by model distance: nonbonded pdb=" O3 NAG B1302 " pdb=" O7 NAG B1302 " model vdw 2.028 2.440 nonbonded pdb=" O3 NAG C1311 " pdb=" O7 NAG C1311 " model vdw 2.086 2.440 nonbonded pdb=" O3 NAG C1303 " pdb=" O7 NAG C1303 " model vdw 2.189 2.440 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.200 2.520 nonbonded pdb=" O CYS B 617 " pdb=" OG1 THR B 618 " model vdw 2.203 2.440 ... (remaining 186301 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 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 189 or (resid 190 and ( \ name N or name CA or name C or name O or name CB )) or resid 191 through 1139 or \ resid 1301 through 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 1139 or resid 1301 thro \ ugh 1311)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 15532 2.51 5 N 3999 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 4.620 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.190 Process input model: 59.760 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24863 Z= 0.221 Angle : 0.581 7.683 33800 Z= 0.338 Chirality : 0.048 0.463 3930 Planarity : 0.003 0.064 4338 Dihedral : 14.460 89.532 8873 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3012 helix: 0.64 (0.21), residues: 639 sheet: 0.43 (0.21), residues: 624 loop : -2.04 (0.13), residues: 1749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 241 average time/residue: 0.4097 time to fit residues: 151.6474 Evaluate side-chains 205 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 2.997 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3667 time to fit residues: 8.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 0.0020 chunk 92 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 8.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 779 GLN A1135 ASN B 388 ASN B 675 GLN C 334 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 24863 Z= 0.276 Angle : 0.606 8.469 33800 Z= 0.328 Chirality : 0.049 0.564 3930 Planarity : 0.004 0.059 4338 Dihedral : 6.833 72.125 3499 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.96 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3012 helix: 0.54 (0.21), residues: 660 sheet: 0.86 (0.21), residues: 639 loop : -2.03 (0.13), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 210 average time/residue: 0.4370 time to fit residues: 145.5458 Evaluate side-chains 200 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 2.898 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2331 time to fit residues: 12.5416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 388 ASN B 969 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24863 Z= 0.286 Angle : 0.599 8.313 33800 Z= 0.324 Chirality : 0.049 0.574 3930 Planarity : 0.004 0.061 4338 Dihedral : 6.754 64.296 3499 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.91 % Favored : 94.02 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3012 helix: 0.57 (0.21), residues: 639 sheet: 0.92 (0.21), residues: 645 loop : -2.02 (0.13), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 206 average time/residue: 0.3866 time to fit residues: 124.1400 Evaluate side-chains 194 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 3.000 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2307 time to fit residues: 10.3164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.4980 chunk 209 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 690 GLN B 907 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 24863 Z= 0.138 Angle : 0.488 9.313 33800 Z= 0.264 Chirality : 0.044 0.536 3930 Planarity : 0.003 0.047 4338 Dihedral : 6.182 58.586 3499 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3012 helix: 1.06 (0.22), residues: 624 sheet: 1.08 (0.20), residues: 663 loop : -1.86 (0.13), residues: 1725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 207 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 219 average time/residue: 0.3886 time to fit residues: 131.9915 Evaluate side-chains 195 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 2.793 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2070 time to fit residues: 8.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 265 optimal weight: 0.3980 chunk 74 optimal weight: 20.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.116 24863 Z= 0.227 Angle : 0.548 11.400 33800 Z= 0.295 Chirality : 0.046 0.545 3930 Planarity : 0.004 0.053 4338 Dihedral : 6.289 59.708 3499 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3012 helix: 0.86 (0.21), residues: 627 sheet: 1.11 (0.21), residues: 642 loop : -1.86 (0.13), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 202 average time/residue: 0.3929 time to fit residues: 123.7158 Evaluate side-chains 197 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2199 time to fit residues: 11.4166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 296 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 24863 Z= 0.264 Angle : 0.586 17.376 33800 Z= 0.316 Chirality : 0.048 0.573 3930 Planarity : 0.004 0.057 4338 Dihedral : 6.403 59.704 3499 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3012 helix: 0.69 (0.21), residues: 627 sheet: 1.05 (0.21), residues: 642 loop : -1.90 (0.13), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 200 average time/residue: 0.3864 time to fit residues: 120.9493 Evaluate side-chains 196 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2092 time to fit residues: 10.9560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.885 24863 Z= 0.605 Angle : 0.856 106.034 33800 Z= 0.390 Chirality : 0.048 0.575 3930 Planarity : 0.004 0.058 4338 Dihedral : 6.409 59.671 3499 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3012 helix: 0.67 (0.21), residues: 627 sheet: 1.04 (0.21), residues: 642 loop : -1.90 (0.13), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 187 average time/residue: 0.3895 time to fit residues: 113.0603 Evaluate side-chains 185 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2209 time to fit residues: 7.4703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.885 24863 Z= 0.605 Angle : 0.856 106.031 33800 Z= 0.390 Chirality : 0.048 0.575 3930 Planarity : 0.004 0.058 4338 Dihedral : 6.409 59.671 3499 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3012 helix: 0.67 (0.21), residues: 627 sheet: 1.04 (0.21), residues: 642 loop : -1.90 (0.13), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.4181 time to fit residues: 115.1691 Evaluate side-chains 176 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 274 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.885 24863 Z= 0.605 Angle : 0.856 106.030 33800 Z= 0.390 Chirality : 0.048 0.575 3930 Planarity : 0.004 0.058 4338 Dihedral : 6.409 59.671 3499 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3012 helix: 0.67 (0.21), residues: 627 sheet: 1.04 (0.21), residues: 642 loop : -1.90 (0.13), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.4310 time to fit residues: 116.0598 Evaluate side-chains 176 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 2.9990 chunk 177 optimal weight: 0.0980 chunk 137 optimal weight: 0.0980 chunk 202 optimal weight: 0.0770 chunk 304 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.885 24863 Z= 0.605 Angle : 0.856 106.029 33800 Z= 0.390 Chirality : 0.048 0.575 3930 Planarity : 0.004 0.058 4338 Dihedral : 6.409 59.671 3499 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3012 helix: 0.67 (0.21), residues: 627 sheet: 1.04 (0.21), residues: 642 loop : -1.90 (0.13), residues: 1743 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.4165 time to fit residues: 112.4344 Evaluate side-chains 176 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.886 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100005 restraints weight = 30303.063| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.07 r_work: 0.3028 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.2962 rms_B_bonded: 2.20 restraints_weight: 0.1250 r_work: 0.2923 rms_B_bonded: 2.62 restraints_weight: 0.0625 r_work: 0.2869 rms_B_bonded: 3.34 restraints_weight: 0.0312 r_work: 0.2786 rms_B_bonded: 4.63 restraints_weight: 0.0156 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.885 24863 Z= 0.605 Angle : 0.856 106.029 33800 Z= 0.390 Chirality : 0.048 0.575 3930 Planarity : 0.004 0.058 4338 Dihedral : 6.409 59.671 3499 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3012 helix: 0.67 (0.21), residues: 627 sheet: 1.04 (0.21), residues: 642 loop : -1.90 (0.13), residues: 1743 =============================================================================== Job complete usr+sys time: 3500.38 seconds wall clock time: 65 minutes 38.04 seconds (3938.04 seconds total)