Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 02:20:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcp_32427/10_2023/7wcp_32427_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcp_32427/10_2023/7wcp_32427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcp_32427/10_2023/7wcp_32427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcp_32427/10_2023/7wcp_32427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcp_32427/10_2023/7wcp_32427_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcp_32427/10_2023/7wcp_32427_neut.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 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 126 5.16 5 C 18007 2.51 5 N 4745 2.21 5 O 5450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 28328 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7736 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 9 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 7653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7653 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7683 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "M" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 15.17, per 1000 atoms: 0.54 Number of scatterers: 28328 At special positions: 0 Unit cell: (204.12, 153.36, 189, 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 126 16.00 O 5450 8.00 N 4745 7.00 C 18007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.02 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=2.06 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=2.87 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.91 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 4.1 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6824 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 60 sheets defined 19.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.546A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.133A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.721A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.922A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.533A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.553A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.080A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.558A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.675A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.243A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 917' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.772A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.133A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.645A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1032 removed outlier: 3.512A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.521A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.395A 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: 3.785A 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 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.191A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.525A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.563A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.520A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.091A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.707A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.789A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.721A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.911A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.651A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 757 Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.553A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 936 removed outlier: 3.547A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 955 removed outlier: 3.697A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.803A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1032 removed outlier: 3.599A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.630A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.630A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.629A pdb=" N SER N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.550A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.229A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.305A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.806A 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: 3.639A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.576A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.090A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.859A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.839A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.687A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.454A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 728 removed outlier: 6.625A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.788A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.780A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.572A 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: 8.104A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.503A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.838A 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 removed outlier: 3.931A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.548A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.074A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 573 through 576 removed outlier: 6.502A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.562A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.224A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.550A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.347A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.417A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.976A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.018A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 7.000A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.211A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.321A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.681A pdb=" N LEU D 80 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.967A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.681A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.966A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.680A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.967A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.24 Time building geometry restraints manager: 11.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.27: 4681 1.27 - 1.42: 7771 1.42 - 1.58: 16337 1.58 - 1.73: 6 1.73 - 1.88: 154 Bond restraints: 28949 Sorted by residual: bond pdb=" C ASN C 616 " pdb=" O ASN C 616 " ideal model delta sigma weight residual 1.234 1.123 0.111 1.20e-02 6.94e+03 8.62e+01 bond pdb=" C GLU C1072 " pdb=" O GLU C1072 " ideal model delta sigma weight residual 1.233 1.115 0.118 1.32e-02 5.74e+03 8.00e+01 bond pdb=" C THR C1076 " pdb=" O THR C1076 " ideal model delta sigma weight residual 1.235 1.122 0.113 1.28e-02 6.10e+03 7.84e+01 bond pdb=" C VAL A 615 " pdb=" O VAL A 615 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.29e-02 6.01e+03 6.54e+01 bond pdb=" CA GLU C1072 " pdb=" C GLU C1072 " ideal model delta sigma weight residual 1.527 1.419 0.108 1.41e-02 5.03e+03 5.89e+01 ... (remaining 28944 not shown) Histogram of bond angle deviations from ideal: 64.78 - 79.63: 1 79.63 - 94.48: 1 94.48 - 109.32: 3938 109.32 - 124.17: 34758 124.17 - 139.02: 694 Bond angle restraints: 39392 Sorted by residual: angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CD PRO C 330 " ideal model delta sigma weight residual 125.00 64.78 60.22 4.10e+00 5.95e-02 2.16e+02 angle pdb=" C ASN C 657 " pdb=" CA ASN C 657 " pdb=" CB ASN C 657 " ideal model delta sigma weight residual 109.56 89.04 20.52 1.65e+00 3.67e-01 1.55e+02 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 133.54 -13.70 1.25e+00 6.40e-01 1.20e+02 angle pdb=" N VAL A 915 " pdb=" CA VAL A 915 " pdb=" C VAL A 915 " ideal model delta sigma weight residual 112.96 104.40 8.56 1.00e+00 1.00e+00 7.32e+01 angle pdb=" C ASN C 334 " pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta sigma weight residual 120.87 109.57 11.30 1.42e+00 4.96e-01 6.33e+01 ... (remaining 39387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15503 17.98 - 35.96: 1367 35.96 - 53.93: 283 53.93 - 71.91: 47 71.91 - 89.89: 35 Dihedral angle restraints: 17235 sinusoidal: 6604 harmonic: 10631 Sorted by residual: dihedral pdb=" C ASN C 657 " pdb=" N ASN C 657 " pdb=" CA ASN C 657 " pdb=" CB ASN C 657 " ideal model delta harmonic sigma weight residual -122.60 -95.76 -26.84 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " pdb=" CA PRO B 987 " ideal model delta harmonic sigma weight residual 180.00 130.89 49.11 0 5.00e+00 4.00e-02 9.65e+01 dihedral pdb=" C CYS C 617 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " pdb=" CB CYS C 617 " ideal model delta harmonic sigma weight residual -122.60 -145.44 22.84 0 2.50e+00 1.60e-01 8.34e+01 ... (remaining 17232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 4342 0.176 - 0.353: 120 0.353 - 0.529: 8 0.529 - 0.706: 4 0.706 - 0.882: 2 Chirality restraints: 4476 Sorted by residual: chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" CA ASN C 331 " pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CB ASN C 331 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CG LEU B 821 " pdb=" CB LEU B 821 " pdb=" CD1 LEU B 821 " pdb=" CD2 LEU B 821 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4473 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.183 5.00e-02 4.00e+02 2.24e-01 8.05e+01 pdb=" N PRO C 330 " -0.372 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.171 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.050 2.00e-02 2.50e+03 4.71e-02 3.89e+01 pdb=" CG PHE C 906 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.036 2.00e-02 2.50e+03 3.56e-02 2.22e+01 pdb=" CG PHE A 906 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.007 2.00e-02 2.50e+03 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 34 2.31 - 2.96: 13448 2.96 - 3.61: 39553 3.61 - 4.25: 64655 4.25 - 4.90: 110979 Nonbonded interactions: 228669 Sorted by model distance: nonbonded pdb=" CG PRO C 330 " pdb=" CA GLN C 580 " model vdw 1.667 3.870 nonbonded pdb=" CG PRO C 330 " pdb=" CB GLN C 580 " model vdw 1.831 3.840 nonbonded pdb=" CG PRO C 330 " pdb=" CG GLN C 580 " model vdw 1.946 3.840 nonbonded pdb=" CD1 ILE C 332 " pdb=" CA PRO C 527 " model vdw 1.996 3.890 nonbonded pdb=" CB PRO C 330 " pdb=" CB GLN C 580 " model vdw 2.022 3.840 ... (remaining 228664 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 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 187 or (resid 188 and (name N or name CA or name C or name O or name CB \ )) or resid 189 or (resid 190 and (name N or name CA or name C or name O or name \ CB )) or resid 191 through 194 or (resid 195 through 198 and (name N or name CA \ or name C or name O or name CB )) or resid 199 through 209 or resid 217 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or r \ esid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 through 243 or resid 264 through 327 or resid 330 through 620 or re \ sid 641 through 1146)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or r \ esid 158 through 175 or (resid 176 through 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or nam \ e C or name O or name CB )) or resid 191 through 195 or (resid 196 through 198 a \ nd (name N or name CA or name C or name O or name CB )) or resid 199 through 236 \ or (resid 237 and (name N or name CA or name C or name O or name CB )) or resid \ 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or r \ esid 240 through 289 or (resid 290 and (name N or name CA or name C or name O or \ name CB )) or resid 291 through 620 or resid 641 through 1146)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 327 or re \ sid 330 through 1146)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 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: 15.500 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 76.990 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.180 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.014 0.137 28949 Z= 0.921 Angle : 1.274 60.217 39392 Z= 0.692 Chirality : 0.080 0.882 4476 Planarity : 0.009 0.224 5118 Dihedral : 14.693 89.891 10282 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.61 % Favored : 92.17 % Rotamer: Outliers : 1.57 % Allowed : 0.93 % Favored : 97.50 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.12), residues: 3602 helix: -2.31 (0.16), residues: 683 sheet: -0.50 (0.16), residues: 892 loop : -2.30 (0.12), residues: 2027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 15 residues processed: 248 average time/residue: 0.4082 time to fit residues: 165.0863 Evaluate side-chains 183 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.3227 time to fit residues: 12.8104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 6.9990 chunk 273 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 282 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 960 ASN A1135 ASN B 762 GLN B 957 GLN B1071 GLN C 606 ASN C 613 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 28949 Z= 0.222 Angle : 0.640 16.210 39392 Z= 0.337 Chirality : 0.046 0.331 4476 Planarity : 0.006 0.089 5118 Dihedral : 5.995 38.732 3947 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 0.77 % Allowed : 6.36 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 3602 helix: -0.83 (0.19), residues: 670 sheet: -0.41 (0.16), residues: 918 loop : -2.03 (0.12), residues: 2014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 214 average time/residue: 0.4064 time to fit residues: 142.1781 Evaluate side-chains 184 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2838 time to fit residues: 11.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 328 optimal weight: 20.0000 chunk 354 optimal weight: 10.0000 chunk 292 optimal weight: 0.2980 chunk 325 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN C 901 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28949 Z= 0.370 Angle : 0.649 12.808 39392 Z= 0.338 Chirality : 0.048 0.254 4476 Planarity : 0.005 0.083 5118 Dihedral : 5.589 38.761 3947 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 1.32 % Allowed : 10.05 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.81 (0.13), residues: 3602 helix: -0.26 (0.20), residues: 664 sheet: -0.46 (0.16), residues: 925 loop : -1.95 (0.13), residues: 2013 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 213 average time/residue: 0.3999 time to fit residues: 139.6529 Evaluate side-chains 194 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 3.221 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2640 time to fit residues: 15.5717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 7.9990 chunk 246 optimal weight: 0.0060 chunk 170 optimal weight: 0.5980 chunk 36 optimal weight: 0.0060 chunk 156 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 312 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 overall best weight: 0.4812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1135 ASN C 954 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28949 Z= 0.154 Angle : 0.551 11.678 39392 Z= 0.288 Chirality : 0.044 0.293 4476 Planarity : 0.005 0.082 5118 Dihedral : 5.130 36.558 3947 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 0.74 % Allowed : 11.88 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.50 (0.13), residues: 3602 helix: 0.37 (0.21), residues: 650 sheet: -0.33 (0.17), residues: 906 loop : -1.83 (0.13), residues: 2046 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 3.221 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 206 average time/residue: 0.3965 time to fit residues: 135.3720 Evaluate side-chains 182 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2604 time to fit residues: 8.9702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 0.0470 chunk 313 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 556 ASN B 762 GLN C 950 ASN C 954 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 28949 Z= 0.223 Angle : 0.558 10.878 39392 Z= 0.292 Chirality : 0.045 0.226 4476 Planarity : 0.005 0.082 5118 Dihedral : 4.997 36.803 3947 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 1.00 % Allowed : 12.97 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.38 (0.13), residues: 3602 helix: 0.51 (0.21), residues: 658 sheet: -0.29 (0.17), residues: 906 loop : -1.76 (0.13), residues: 2038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 3.556 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 203 average time/residue: 0.4161 time to fit residues: 141.7919 Evaluate side-chains 181 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2958 time to fit residues: 14.3551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 3.9990 chunk 314 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 349 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28949 Z= 0.216 Angle : 0.549 10.330 39392 Z= 0.287 Chirality : 0.045 0.246 4476 Planarity : 0.005 0.080 5118 Dihedral : 4.900 35.535 3947 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 1.06 % Allowed : 13.84 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % 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: -1.29 (0.14), residues: 3602 helix: 0.62 (0.21), residues: 658 sheet: -0.26 (0.17), residues: 912 loop : -1.70 (0.13), residues: 2032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 212 average time/residue: 0.3878 time to fit residues: 136.8161 Evaluate side-chains 187 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2641 time to fit residues: 14.5353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 199 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 197 optimal weight: 0.0060 chunk 294 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 347 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28949 Z= 0.193 Angle : 0.544 10.096 39392 Z= 0.282 Chirality : 0.044 0.232 4476 Planarity : 0.004 0.082 5118 Dihedral : 4.792 35.662 3947 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.35 % Allowed : 15.00 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % 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: -1.20 (0.14), residues: 3602 helix: 0.77 (0.21), residues: 656 sheet: -0.24 (0.17), residues: 915 loop : -1.65 (0.13), residues: 2031 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 193 average time/residue: 0.4087 time to fit residues: 130.7769 Evaluate side-chains 173 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 3.343 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2597 time to fit residues: 5.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.0170 chunk 138 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 221 optimal weight: 0.5980 chunk 237 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 580 GLN B1071 GLN C 907 ASN C 955 ASN C 957 GLN L 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28949 Z= 0.141 Angle : 0.520 9.029 39392 Z= 0.270 Chirality : 0.043 0.228 4476 Planarity : 0.004 0.081 5118 Dihedral : 4.555 35.872 3947 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.51 % Allowed : 15.32 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % 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 (0.14), residues: 3602 helix: 0.93 (0.21), residues: 662 sheet: -0.20 (0.17), residues: 905 loop : -1.60 (0.13), residues: 2035 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 212 average time/residue: 0.3974 time to fit residues: 140.4072 Evaluate side-chains 186 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 3.060 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3354 time to fit residues: 9.3176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 324 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 30.0000 chunk 254 optimal weight: 0.0020 chunk 99 optimal weight: 0.5980 chunk 292 optimal weight: 0.7980 chunk 306 optimal weight: 8.9990 chunk 323 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 751 ASN B 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28949 Z= 0.185 Angle : 0.527 8.765 39392 Z= 0.274 Chirality : 0.044 0.190 4476 Planarity : 0.004 0.082 5118 Dihedral : 4.561 35.163 3947 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.39 % Allowed : 15.70 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % 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: -1.07 (0.14), residues: 3602 helix: 0.90 (0.21), residues: 667 sheet: -0.20 (0.17), residues: 915 loop : -1.56 (0.13), residues: 2020 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 3.064 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 187 average time/residue: 0.3748 time to fit residues: 116.8230 Evaluate side-chains 181 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2643 time to fit residues: 7.4882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 3.9990 chunk 342 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 221 optimal weight: 0.0050 chunk 175 optimal weight: 0.8980 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28949 Z= 0.283 Angle : 0.570 8.534 39392 Z= 0.297 Chirality : 0.045 0.181 4476 Planarity : 0.005 0.081 5118 Dihedral : 4.797 34.981 3947 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 0.13 % Allowed : 15.90 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % 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: -1.16 (0.14), residues: 3602 helix: 0.69 (0.21), residues: 669 sheet: -0.23 (0.17), residues: 921 loop : -1.59 (0.13), residues: 2012 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 181 average time/residue: 0.4013 time to fit residues: 120.3309 Evaluate side-chains 175 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2533 time to fit residues: 5.3078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 0.3980 chunk 305 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 79 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.175303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107219 restraints weight = 47463.193| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.73 r_work: 0.3150 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28949 Z= 0.158 Angle : 0.528 10.434 39392 Z= 0.275 Chirality : 0.044 0.245 4476 Planarity : 0.004 0.082 5118 Dihedral : 4.609 35.660 3947 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.06 % Allowed : 16.22 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.06 % 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: -1.05 (0.14), residues: 3602 helix: 0.89 (0.21), residues: 667 sheet: -0.16 (0.17), residues: 902 loop : -1.55 (0.13), residues: 2033 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6269.85 seconds wall clock time: 115 minutes 1.20 seconds (6901.20 seconds total)