Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 02:51:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wch_32422/08_2023/7wch_32422_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wch_32422/08_2023/7wch_32422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wch_32422/08_2023/7wch_32422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wch_32422/08_2023/7wch_32422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wch_32422/08_2023/7wch_32422_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wch_32422/08_2023/7wch_32422_neut.pdb" } resolution = 3.19 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= 0.065 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 135 5.16 5 C 17995 2.51 5 N 4766 2.21 5 O 5423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G ARG 319": "NH1" <-> "NH2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G GLU 406": "OE1" <-> "OE2" Residue "G GLU 484": "OE1" <-> "OE2" Residue "G GLU 661": "OE1" <-> "OE2" Residue "G ARG 815": "NH1" <-> "NH2" Residue "G GLU 819": "OE1" <-> "OE2" Residue "G GLU 988": "OE1" <-> "OE2" Residue "G ARG 995": "NH1" <-> "NH2" Residue "G GLU 1017": "OE1" <-> "OE2" Residue "G PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1144": "OE1" <-> "OE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 41": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 30": "NH1" <-> "NH2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 28319 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" 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: "B" 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: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" 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: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "M" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Time building chain proxies: 13.68, per 1000 atoms: 0.48 Number of scatterers: 28319 At special positions: 0 Unit cell: (163.08, 204.12, 152.28, 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 135 16.00 O 5423 8.00 N 4766 7.00 C 17995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.28 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.91 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=1.41 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.97 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.87 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=2.05 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 D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.02 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=1.05 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.06 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.89 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.04 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.02 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.02 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 106 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " 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: 11.05 Conformation dependent library (CDL) restraints added in 3.9 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: 6854 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 70 sheets defined 19.5% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.747A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.606A 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 408 removed outlier: 3.956A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.552A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (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 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 936 removed outlier: 3.546A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.697A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.803A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1032 removed outlier: 3.599A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.545A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.604A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.956A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.655A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.554A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.080A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.847A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.559A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.675A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 917 removed outlier: 4.242A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 917' Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.771A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 4.134A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.645A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1032 removed outlier: 3.512A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.521A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.090A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.841A pdb=" N SER E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 33 " --> pdb=" O ARG E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 33' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.635A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 386 through 390 removed outlier: 3.745A pdb=" N ASP G 389 " --> pdb=" O LYS G 386 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 386 through 390' Processing helix chain 'G' and resid 405 through 408 removed outlier: 3.956A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 417 through 422 Processing helix chain 'G' and resid 438 through 443 removed outlier: 3.656A pdb=" N SER G 443 " --> pdb=" O ASN G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 744 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.835A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 811 through 815 removed outlier: 4.190A pdb=" N LYS G 814 " --> pdb=" O LYS G 811 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG G 815 " --> pdb=" O PRO G 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 811 through 815' Processing helix chain 'G' and resid 816 through 825 Processing helix chain 'G' and resid 866 through 885 removed outlier: 3.525A pdb=" N GLN G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.562A pdb=" N TYR G 917 " --> pdb=" O GLN G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 940 removed outlier: 3.520A pdb=" N LYS G 933 " --> pdb=" O SER G 929 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE G 934 " --> pdb=" O ALA G 930 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 965 removed outlier: 4.091A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 952 " --> pdb=" O LEU G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 977 through 982 removed outlier: 3.706A pdb=" N LEU G 981 " --> pdb=" O LEU G 977 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 1032 removed outlier: 3.788A pdb=" N GLN G 992 " --> pdb=" O GLU G 988 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1141 through 1145 removed outlier: 3.721A pdb=" N LEU G1145 " --> pdb=" O GLN G1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.090A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.840A pdb=" N SER L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L 33 " --> pdb=" O ARG L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 33' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.634A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 4.089A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.838A pdb=" N SER N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU N 33 " --> pdb=" O ARG N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 33' Processing helix chain 'N' and resid 80 through 84 removed outlier: 3.635A pdb=" N PHE N 84 " --> pdb=" O PRO N 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.550A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.318A pdb=" N PHE A 43 " --> pdb=" O ARG G 567 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY G 566 " --> pdb=" O ASP G 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.346A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.634A 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: 4.417A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.977A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.634A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.740A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.147A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.508A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 714 Processing sheet with id=AB7, first strand: chain 'A' and resid 719 through 728 removed outlier: 7.000A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.211A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.627A pdb=" N ILE A 788 " --> pdb=" O ASN G 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.321A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.551A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.305A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.638A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.576A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.090A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 565 " --> pdb=" O PHE G 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.633A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.630A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 665 through 667 removed outlier: 6.687A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.454A pdb=" N ALA B 701 " --> pdb=" O ILE G 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 728 removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.781A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.572A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.593A pdb=" N GLU D 10 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 52 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 57 " --> pdb=" O VAL D 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.772A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.594A pdb=" N ALA E 19 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.494A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 28 through 30 removed outlier: 8.103A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU G 96 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN G 188 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE G 201 " --> pdb=" O ASP G 228 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP G 228 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 203 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS G 207 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ALA G 222 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 47 through 55 removed outlier: 3.503A pdb=" N ASP G 53 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.932A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU G 132 " --> pdb=" O CYS G 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS G 166 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 324 through 325 removed outlier: 6.547A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.633A pdb=" N GLY G 431 " --> pdb=" O TYR G 380 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR G 380 " --> pdb=" O GLY G 431 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL G 433 " --> pdb=" O LYS G 378 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS G 378 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.871A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AF7, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.563A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G1076 " --> pdb=" O SER G1097 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G1078 " --> pdb=" O PHE G1095 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE G1095 " --> pdb=" O ALA G1078 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.224A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 1120 through 1122 Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.594A pdb=" N GLU H 10 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AG7, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.772A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.595A pdb=" N ALA L 19 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.494A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.595A pdb=" N GLU M 10 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 52 " --> pdb=" O ASN M 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN M 57 " --> pdb=" O VAL M 52 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AH5, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.773A pdb=" N LEU N 11 " --> pdb=" O GLU N 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'N' and resid 19 through 21 removed outlier: 3.594A pdb=" N ALA N 19 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.493A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2664 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: 17.79 Time building geometry restraints manager: 11.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.28: 4665 1.28 - 1.44: 8159 1.44 - 1.60: 15954 1.60 - 1.76: 29 1.76 - 1.93: 142 Bond restraints: 28949 Sorted by residual: bond pdb=" CA HIS L 92 " pdb=" C HIS L 92 " ideal model delta sigma weight residual 1.526 1.376 0.151 1.11e-02 8.12e+03 1.85e+02 bond pdb=" CA HIS N 92 " pdb=" C HIS N 92 " ideal model delta sigma weight residual 1.526 1.376 0.150 1.11e-02 8.12e+03 1.84e+02 bond pdb=" CA HIS E 92 " pdb=" C HIS E 92 " ideal model delta sigma weight residual 1.526 1.376 0.150 1.11e-02 8.12e+03 1.83e+02 bond pdb=" C GLU A1072 " pdb=" O GLU A1072 " ideal model delta sigma weight residual 1.233 1.114 0.119 1.32e-02 5.74e+03 8.09e+01 bond pdb=" C THR A1076 " pdb=" O THR A1076 " ideal model delta sigma weight residual 1.235 1.122 0.114 1.28e-02 6.10e+03 7.88e+01 ... (remaining 28944 not shown) Histogram of bond angle deviations from ideal: 64.77 - 78.73: 2 78.73 - 92.70: 3 92.70 - 106.66: 1042 106.66 - 120.62: 27634 120.62 - 134.59: 10723 Bond angle restraints: 39404 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 125.00 64.77 60.23 4.10e+00 5.95e-02 2.16e+02 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 125.00 66.10 58.90 4.10e+00 5.95e-02 2.06e+02 angle pdb=" C ASN A 334 " pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 121.42 103.86 17.56 1.43e+00 4.89e-01 1.51e+02 angle pdb=" C PRO L 96 " pdb=" N PRO L 97 " pdb=" CD PRO L 97 " ideal model delta sigma weight residual 125.00 78.82 46.18 4.10e+00 5.95e-02 1.27e+02 angle pdb=" C PRO N 96 " pdb=" N PRO N 97 " pdb=" CD PRO N 97 " ideal model delta sigma weight residual 125.00 78.83 46.17 4.10e+00 5.95e-02 1.27e+02 ... (remaining 39399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15531 17.98 - 35.96: 1394 35.96 - 53.94: 242 53.94 - 71.93: 61 71.93 - 89.91: 34 Dihedral angle restraints: 17262 sinusoidal: 6622 harmonic: 10640 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual -180.00 -121.82 -58.18 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER N 7 " pdb=" C SER N 7 " pdb=" N PRO N 8 " pdb=" CA PRO N 8 " ideal model delta harmonic sigma weight residual -180.00 -121.83 -58.17 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual -180.00 -121.84 -58.16 0 5.00e+00 4.00e-02 1.35e+02 ... (remaining 17259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 4423 0.227 - 0.455: 65 0.455 - 0.682: 7 0.682 - 0.909: 1 0.909 - 1.137: 1 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA THR G 333 " pdb=" N THR G 333 " pdb=" C THR G 333 " pdb=" CB THR G 333 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CG LEU G 821 " pdb=" CB LEU G 821 " pdb=" CD1 LEU G 821 " pdb=" CD2 LEU G 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 4494 not shown) Planarity restraints: 5109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 330 " 0.053 2.00e-02 2.50e+03 1.23e-01 1.50e+02 pdb=" C PRO G 330 " -0.211 2.00e-02 2.50e+03 pdb=" O PRO G 330 " 0.087 2.00e-02 2.50e+03 pdb=" N ASN G 331 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.183 5.00e-02 4.00e+02 2.56e-01 1.05e+02 pdb=" N PRO A 527 " -0.434 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.190 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 96 " -0.157 5.00e-02 4.00e+02 2.35e-01 8.82e+01 pdb=" N PRO N 97 " 0.402 5.00e-02 4.00e+02 pdb=" CA PRO N 97 " -0.166 5.00e-02 4.00e+02 pdb=" CD PRO N 97 " -0.080 5.00e-02 4.00e+02 ... (remaining 5106 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 13 1.97 - 2.70: 1829 2.70 - 3.44: 38517 3.44 - 4.17: 68220 4.17 - 4.90: 123189 Nonbonded interactions: 231768 Sorted by model distance: nonbonded pdb=" ND2 ASN A 334 " pdb=" CA CYS A 361 " model vdw 1.240 3.550 nonbonded pdb=" OD1 ASN B 334 " pdb=" CA CYS B 361 " model vdw 1.327 3.470 nonbonded pdb=" SG CYS A 336 " pdb=" O VAL A 362 " model vdw 1.527 3.400 nonbonded pdb=" CG PRO A 330 " pdb=" CA GLN A 580 " model vdw 1.668 3.870 nonbonded pdb=" OD1 ASN B 334 " pdb=" CB CYS B 361 " model vdw 1.680 3.440 ... (remaining 231763 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 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)) selection = (chain 'B' 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 'G' 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)) } 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 16.130 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 77.180 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.170 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.015 0.151 28949 Z= 0.979 Angle : 1.444 60.229 39404 Z= 0.745 Chirality : 0.084 1.137 4497 Planarity : 0.012 0.256 5109 Dihedral : 14.506 89.907 10270 Min Nonbonded Distance : 1.240 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.83 % Favored : 91.12 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % 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: -2.89 (0.12), residues: 3602 helix: -2.21 (0.16), residues: 647 sheet: -0.97 (0.17), residues: 950 loop : -2.35 (0.12), residues: 2005 *********************** 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 525 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 496 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 520 average time/residue: 0.4009 time to fit residues: 331.5621 Evaluate side-chains 273 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 258 time to evaluate : 2.968 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2565 time to fit residues: 11.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.9980 chunk 275 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 0.2980 chunk 330 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN A 901 GLN A 969 ASN A1005 GLN B 282 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1135 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN G 563 GLN G 950 ASN G 955 ASN G1002 GLN G1071 GLN M 57 ASN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 28949 Z= 0.243 Angle : 0.707 16.836 39404 Z= 0.370 Chirality : 0.048 0.299 4497 Planarity : 0.008 0.166 5109 Dihedral : 6.087 43.419 3920 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.39 % Favored : 93.25 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % 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: -2.17 (0.13), residues: 3602 helix: -0.78 (0.19), residues: 662 sheet: -0.73 (0.16), residues: 982 loop : -2.11 (0.13), residues: 1958 *********************** 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 355 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 299 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 341 average time/residue: 0.3683 time to fit residues: 207.5676 Evaluate side-chains 247 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.2794 time to fit residues: 17.8107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 275 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 331 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 294 optimal weight: 0.6980 chunk 328 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 440 ASN A 540 ASN A1005 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 950 ASN G 954 GLN G 955 ASN G1005 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 28949 Z= 0.226 Angle : 0.634 9.524 39404 Z= 0.331 Chirality : 0.047 0.258 4497 Planarity : 0.007 0.151 5109 Dihedral : 5.460 40.901 3920 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.52 % Favored : 93.14 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % 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: -1.77 (0.13), residues: 3602 helix: 0.05 (0.21), residues: 641 sheet: -0.57 (0.16), residues: 995 loop : -1.97 (0.13), residues: 1966 *********************** 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 314 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 260 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 302 average time/residue: 0.3623 time to fit residues: 184.0000 Evaluate side-chains 239 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.2623 time to fit residues: 16.1210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 0.5980 chunk 222 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 351 optimal weight: 30.0000 chunk 173 optimal weight: 2.9990 chunk 314 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 540 ASN B 487 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 28949 Z= 0.319 Angle : 0.654 11.355 39404 Z= 0.342 Chirality : 0.048 0.260 4497 Planarity : 0.006 0.152 5109 Dihedral : 5.349 35.309 3920 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.64 % Favored : 93.11 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -1.68 (0.13), residues: 3602 helix: 0.31 (0.21), residues: 652 sheet: -0.51 (0.16), residues: 987 loop : -2.00 (0.13), residues: 1963 *********************** 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 302 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 243 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 288 average time/residue: 0.3836 time to fit residues: 183.9198 Evaluate side-chains 239 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.2762 time to fit residues: 18.6431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 0.6980 chunk 199 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 300 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 0.0020 chunk 315 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 28949 Z= 0.191 Angle : 0.590 12.513 39404 Z= 0.309 Chirality : 0.045 0.256 4497 Planarity : 0.006 0.152 5109 Dihedral : 5.001 35.798 3920 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.27 % Favored : 93.48 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -1.47 (0.14), residues: 3602 helix: 0.65 (0.21), residues: 645 sheet: -0.42 (0.16), residues: 985 loop : -1.90 (0.13), residues: 1972 *********************** 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 285 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 276 average time/residue: 0.3719 time to fit residues: 170.3128 Evaluate side-chains 224 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 3.129 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 3 residues processed: 19 average time/residue: 0.2604 time to fit residues: 13.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 206 optimal weight: 30.0000 chunk 86 optimal weight: 0.8980 chunk 352 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 116 optimal weight: 0.4980 chunk 184 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 28949 Z= 0.257 Angle : 0.595 8.740 39404 Z= 0.312 Chirality : 0.046 0.256 4497 Planarity : 0.005 0.121 5109 Dihedral : 4.918 35.206 3920 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.77 % Favored : 92.98 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3602 helix: 0.71 (0.21), residues: 647 sheet: -0.41 (0.16), residues: 974 loop : -1.85 (0.13), residues: 1981 *********************** 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 258 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 250 average time/residue: 0.3909 time to fit residues: 162.2313 Evaluate side-chains 229 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 3.250 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 2 residues processed: 22 average time/residue: 0.2616 time to fit residues: 15.3219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 9.9990 chunk 39 optimal weight: 0.0270 chunk 200 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 296 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 350 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 161 optimal weight: 0.2980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 28949 Z= 0.182 Angle : 0.575 13.870 39404 Z= 0.298 Chirality : 0.045 0.266 4497 Planarity : 0.005 0.150 5109 Dihedral : 4.723 35.263 3920 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.24 (0.14), residues: 3602 helix: 0.93 (0.21), residues: 647 sheet: -0.29 (0.17), residues: 959 loop : -1.75 (0.13), residues: 1996 *********************** 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 265 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 255 average time/residue: 0.4029 time to fit residues: 169.9532 Evaluate side-chains 220 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 3.062 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.2685 time to fit residues: 12.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 173 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN D 59 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 28949 Z= 0.191 Angle : 0.566 8.788 39404 Z= 0.295 Chirality : 0.045 0.248 4497 Planarity : 0.005 0.120 5109 Dihedral : 4.637 34.734 3920 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.30 % Favored : 93.45 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.12 (0.14), residues: 3602 helix: 1.00 (0.21), residues: 656 sheet: -0.14 (0.17), residues: 924 loop : -1.70 (0.13), residues: 2022 *********************** 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 241 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 236 average time/residue: 0.3949 time to fit residues: 154.7588 Evaluate side-chains 215 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 3.146 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.2527 time to fit residues: 10.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 20.0000 chunk 306 optimal weight: 0.0980 chunk 326 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 309 optimal weight: 0.5980 chunk 325 optimal weight: 2.9990 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 658 ASN A 907 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN G 493 GLN ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 28949 Z= 0.229 Angle : 0.582 11.080 39404 Z= 0.303 Chirality : 0.045 0.227 4497 Planarity : 0.005 0.104 5109 Dihedral : 4.672 34.621 3920 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.30 % Favored : 93.48 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.10 (0.14), residues: 3602 helix: 1.02 (0.21), residues: 655 sheet: -0.13 (0.17), residues: 927 loop : -1.68 (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 254 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 251 average time/residue: 0.3993 time to fit residues: 164.7583 Evaluate side-chains 219 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2706 time to fit residues: 10.7671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 333 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 28949 Z= 0.201 Angle : 0.573 10.342 39404 Z= 0.299 Chirality : 0.045 0.224 4497 Planarity : 0.005 0.100 5109 Dihedral : 4.622 34.537 3920 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.19 % Favored : 93.59 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.05 (0.14), residues: 3602 helix: 1.02 (0.21), residues: 659 sheet: -0.02 (0.17), residues: 912 loop : -1.67 (0.13), residues: 2031 ********************** 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 223 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 221 average time/residue: 0.4071 time to fit residues: 149.4106 Evaluate side-chains 206 residues out of total 3198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 202 time to evaluate : 3.697 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.4195 time to fit residues: 8.3709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 266 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 296 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 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 = 0.4129 r_free = 0.4129 target = 0.145488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096052 restraints weight = 56397.145| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.71 r_work: 0.3196 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 28949 Z= 0.245 Angle : 0.591 12.809 39404 Z= 0.306 Chirality : 0.045 0.220 4497 Planarity : 0.005 0.098 5109 Dihedral : 4.669 34.400 3920 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.47 % Favored : 93.31 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.07 (0.14), residues: 3602 helix: 0.98 (0.21), residues: 665 sheet: -0.05 (0.17), residues: 925 loop : -1.69 (0.13), residues: 2012 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6220.24 seconds wall clock time: 113 minutes 45.35 seconds (6825.35 seconds total)