Starting phenix.real_space_refine (version: dev) on Sun May 15 11:07:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp9_32679/05_2022/7wp9_32679_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp9_32679/05_2022/7wp9_32679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp9_32679/05_2022/7wp9_32679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp9_32679/05_2022/7wp9_32679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp9_32679/05_2022/7wp9_32679_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp9_32679/05_2022/7wp9_32679_neut.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A ARG 902": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B ARG 631": "NH1" <-> "NH2" Residue "B ARG 643": "NH1" <-> "NH2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B ARG 762": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B ARG 812": "NH1" <-> "NH2" Residue "B ARG 844": "NH1" <-> "NH2" Residue "B ARG 902": "NH1" <-> "NH2" Residue "B GLU 915": "OE1" <-> "OE2" Residue "B ARG 980": "NH1" <-> "NH2" Residue "B ARG 992": "NH1" <-> "NH2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B ARG 1011": "NH1" <-> "NH2" Residue "B ARG 1016": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1088": "NH1" <-> "NH2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C ARG 316": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C ARG 343": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 495": "NH1" <-> "NH2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 631": "NH1" <-> "NH2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 643": "NH1" <-> "NH2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C ARG 812": "NH1" <-> "NH2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C ARG 844": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 980": "NH1" <-> "NH2" Residue "C ARG 992": "NH1" <-> "NH2" Residue "C ARG 997": "NH1" <-> "NH2" Residue "C ARG 1011": "NH1" <-> "NH2" Residue "C ARG 1016": "NH1" <-> "NH2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C ARG 1088": "NH1" <-> "NH2" Residue "C ARG 1104": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 25077 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8224 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 55, 'TRANS': 991} Chain breaks: 9 Chain: "B" Number of atoms: 8175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8175 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 54, 'TRANS': 984} Chain breaks: 13 Chain: "C" Number of atoms: 8286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8286 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 56, 'TRANS': 998} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.96, per 1000 atoms: 0.56 Number of scatterers: 25077 At special positions: 0 Unit cell: (126.072, 136.784, 175.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4802 8.00 N 4136 7.00 C 16028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 613 " " NAG A1303 " - " ASN A 706 " " NAG A1304 " - " ASN A1131 " " NAG B1301 " - " ASN B 279 " " NAG B1302 " - " ASN B 613 " " NAG B1303 " - " ASN B1131 " " NAG B1304 " - " ASN B 706 " " NAG B1305 " - " ASN B 328 " " NAG C1301 " - " ASN C 279 " " NAG C1302 " - " ASN C 613 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 706 " " NAG C1305 " - " ASN C1131 " " NAG D 1 " - " ASN A 328 " " NAG E 1 " - " ASN A 798 " " NAG F 1 " - " ASN A1095 " " NAG G 1 " - " ASN B 798 " " NAG H 1 " - " ASN B1095 " " NAG I 1 " - " ASN C 798 " " NAG J 1 " - " ASN C1095 " Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 3.5 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 49 sheets defined 22.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.677A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 743 through 750 removed outlier: 3.659A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 754 removed outlier: 3.882A pdb=" N GLY A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.809A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 820 removed outlier: 3.579A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.765A pdb=" N GLN A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 852 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.656A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.906A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 905 " --> pdb=" O TYR A 901 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.666A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.606A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.054A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.624A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 removed outlier: 3.883A pdb=" N VAL A 988 " --> pdb=" O GLU A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 989 through 1030 removed outlier: 3.654A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 3.545A pdb=" N SER A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.928A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.916A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.171A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.119A pdb=" N SER B 747 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 748 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 750 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 751 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 752 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 779 removed outlier: 3.655A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 821 removed outlier: 3.541A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 853 removed outlier: 3.826A pdb=" N ALA B 849 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 850 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 removed outlier: 3.523A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.586A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 937 removed outlier: 3.559A pdb=" N GLY B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.700A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 951 " --> pdb=" O ASP B 947 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 953 " --> pdb=" O VAL B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.532A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 985 through 1030 removed outlier: 4.421A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE B 994 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B1015 " --> pdb=" O ARG B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.851A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.984A pdb=" N LEU C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 368' Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.700A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 386' Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.825A pdb=" N CYS C 740 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 753 removed outlier: 3.709A pdb=" N GLN C 752 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.502A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.660A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 853 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.642A pdb=" N ALA C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.542A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 904 removed outlier: 4.024A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.673A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.529A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 961 removed outlier: 3.644A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.664A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 979 " --> pdb=" O ASN C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.692A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1143 removed outlier: 3.563A pdb=" N ASP C1143 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.604A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.466A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.564A pdb=" N GLY A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 118 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 125 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 124 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A 165 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 126 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 163 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 128 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N CYS A 161 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN A 132 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 157 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.547A pdb=" N THR A 312 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.183A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 508 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 428 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 573 removed outlier: 7.004A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.111A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 701 removed outlier: 5.911A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 787 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 725 removed outlier: 7.059A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 725 removed outlier: 7.059A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.619A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 786 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.486A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.791A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 190 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.751A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.794A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.273A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 7.621A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.511A pdb=" N ILE B 355 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.511A pdb=" N ILE B 355 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 397 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 570 through 573 Processing sheet with id=AC8, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.874A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 688 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 698 through 700 removed outlier: 6.398A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.445A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.445A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.394A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 6.071A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.052A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.794A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 53 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.794A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR C 271 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP C 287 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.720A pdb=" N LEU C 82 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 235 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 105 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 116 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 127 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.751A pdb=" N TYR C 195 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 316 removed outlier: 3.524A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 645 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.863A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.863A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 396 through 399 Processing sheet with id=AE5, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AE6, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE7, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE8, first strand: chain 'C' and resid 535 through 540 removed outlier: 3.606A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 545 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 543 " --> pdb=" O PHE C 540 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 582 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 573 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.045A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 710 through 725 removed outlier: 6.853A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C1067 " --> pdb=" O ASN C 714 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.469A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1073 through 1075 removed outlier: 3.652A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 795 hydrogen bonds defined for protein. 2166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.55 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4180 1.32 - 1.45: 7114 1.45 - 1.57: 14208 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25640 Sorted by residual: bond pdb=" C ALA C 369 " pdb=" N PRO C 370 " ideal model delta sigma weight residual 1.335 1.387 -0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C PRO B 983 " pdb=" O PRO B 983 " ideal model delta sigma weight residual 1.240 1.199 0.042 1.12e-02 7.97e+03 1.38e+01 bond pdb=" C PRO A 983 " pdb=" O PRO A 983 " ideal model delta sigma weight residual 1.240 1.203 0.037 1.12e-02 7.97e+03 1.09e+01 bond pdb=" N ASP C 982 " pdb=" CA ASP C 982 " ideal model delta sigma weight residual 1.453 1.480 -0.027 8.30e-03 1.45e+04 1.08e+01 bond pdb=" N LEU B 981 " pdb=" CA LEU B 981 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.27e-02 6.20e+03 7.87e+00 ... (remaining 25635 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.83: 765 106.83 - 113.62: 13940 113.62 - 120.41: 9264 120.41 - 127.20: 10666 127.20 - 133.99: 227 Bond angle restraints: 34862 Sorted by residual: angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 121.54 -10.84 1.22e+00 6.72e-01 7.90e+01 angle pdb=" N PRO C 983 " pdb=" CA PRO C 983 " pdb=" C PRO C 983 " ideal model delta sigma weight residual 110.70 119.24 -8.54 1.22e+00 6.72e-01 4.90e+01 angle pdb=" N ILE B 831 " pdb=" CA ILE B 831 " pdb=" C ILE B 831 " ideal model delta sigma weight residual 113.53 106.82 6.71 9.80e-01 1.04e+00 4.69e+01 angle pdb=" N GLU A 985 " pdb=" CA GLU A 985 " pdb=" C GLU A 985 " ideal model delta sigma weight residual 114.39 105.62 8.77 1.45e+00 4.76e-01 3.65e+01 angle pdb=" C ILE B 192 " pdb=" N ASP B 193 " pdb=" CA ASP B 193 " ideal model delta sigma weight residual 122.46 130.68 -8.22 1.41e+00 5.03e-01 3.40e+01 ... (remaining 34857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13688 17.65 - 35.30: 1243 35.30 - 52.95: 255 52.95 - 70.59: 51 70.59 - 88.24: 20 Dihedral angle restraints: 15257 sinusoidal: 6087 harmonic: 9170 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -169.71 83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 376 " pdb=" SG CYS A 376 " pdb=" SG CYS A 429 " pdb=" CB CYS A 429 " ideal model delta sinusoidal sigma weight residual -86.00 -139.37 53.37 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A 535 " pdb=" SG CYS A 535 " pdb=" SG CYS A 587 " pdb=" CB CYS A 587 " ideal model delta sinusoidal sigma weight residual -86.00 -35.21 -50.79 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 15254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3972 0.131 - 0.261: 64 0.261 - 0.392: 3 0.392 - 0.523: 1 0.523 - 0.653: 1 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CA PRO B 983 " pdb=" N PRO B 983 " pdb=" C PRO B 983 " pdb=" CB PRO B 983 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PRO C 983 " pdb=" N PRO C 983 " pdb=" C PRO C 983 " pdb=" CB PRO C 983 " both_signs ideal model delta sigma weight residual False 2.72 2.21 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CA PRO A 983 " pdb=" N PRO A 983 " pdb=" C PRO A 983 " pdb=" CB PRO A 983 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4038 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 983 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PRO A 983 " 0.064 2.00e-02 2.50e+03 pdb=" O PRO A 983 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 984 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " -0.053 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO A 984 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 209 " 0.048 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO C 210 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " 0.040 5.00e-02 4.00e+02 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 7241 2.82 - 3.34: 19606 3.34 - 3.86: 41003 3.86 - 4.38: 45139 4.38 - 4.90: 79393 Nonbonded interactions: 192382 Sorted by model distance: nonbonded pdb=" OE1 GLU A 295 " pdb=" OH TYR A 633 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.319 2.440 nonbonded pdb=" O GLY A 877 " pdb=" OG SER A 881 " model vdw 2.323 2.440 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.336 2.440 nonbonded pdb=" O ALA B 876 " pdb=" OG1 THR B 880 " model vdw 2.343 2.440 ... (remaining 192377 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 17 through 23 or resid 25 through 401 or resid 403 through \ 407 or resid 414 through 415 or resid 417 through 419 or resid 421 through 464 \ or resid 468 through 495 or resid 503 through 1144 or resid 1301 through 1304)) selection = (chain 'B' and (resid 17 through 368 or resid 374 through 1144 or resid 1301 thr \ ough 1304)) selection = (chain 'C' and (resid 17 through 23 or resid 25 through 368 or resid 374 through \ 401 or resid 403 through 407 or resid 414 through 415 or resid 417 through 419 \ or resid 421 through 464 or resid 468 through 495 or resid 503 through 1144 or r \ esid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16028 2.51 5 N 4136 2.21 5 O 4802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 24.650 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.220 Process input model: 64.200 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 25640 Z= 0.223 Angle : 0.759 11.949 34862 Z= 0.461 Chirality : 0.051 0.653 4041 Planarity : 0.006 0.077 4467 Dihedral : 14.221 88.243 9243 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.12), residues: 3077 helix: -2.77 (0.15), residues: 589 sheet: -1.72 (0.20), residues: 593 loop : -3.11 (0.11), residues: 1895 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 486 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 495 average time/residue: 1.2346 time to fit residues: 714.6109 Evaluate side-chains 356 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 353 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.3106 time to fit residues: 4.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 283 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 202 HIS A 268 GLN A 318 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 529 ASN A 553 ASN A 610 GLN A 641 GLN A 672 GLN A 687 GLN A 774 ASN A 850 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 49 HIS B 700 ASN B 707 ASN B 759 GLN B 771 GLN B 781 GLN B 898 GLN B 916 ASN B 932 GLN B 952 ASN B 954 GLN B 962 GLN B 999 GLN B1098 HIS B1132 ASN C 183 ASN C 311 GLN C 318 GLN C 367 ASN C 447 ASN C 560 GLN C 672 GLN C 687 GLN C 898 GLN C 952 ASN C 975 ASN C1002 GLN C1020 ASN C1045 HIS C1051 GLN C1071 ASN C1110 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 25640 Z= 0.378 Angle : 0.624 7.544 34862 Z= 0.330 Chirality : 0.047 0.305 4041 Planarity : 0.005 0.098 4467 Dihedral : 5.075 26.313 3528 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.13), residues: 3077 helix: -0.82 (0.20), residues: 578 sheet: -1.13 (0.20), residues: 631 loop : -2.62 (0.12), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 409 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 32 residues processed: 455 average time/residue: 1.2752 time to fit residues: 681.4811 Evaluate side-chains 404 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 372 time to evaluate : 2.761 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 10 average time/residue: 0.6424 time to fit residues: 12.3538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 235 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 283 optimal weight: 0.0970 chunk 306 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 281 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 529 ASN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN A 952 ASN A 962 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN A1132 ASN B 30 ASN B 202 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 436 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 700 ASN B 999 GLN B1071 ASN C 655 ASN C 975 ASN C1071 ASN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25640 Z= 0.208 Angle : 0.539 7.680 34862 Z= 0.281 Chirality : 0.044 0.263 4041 Planarity : 0.005 0.136 4467 Dihedral : 4.782 25.064 3528 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 3077 helix: 0.00 (0.21), residues: 598 sheet: -0.89 (0.20), residues: 641 loop : -2.46 (0.13), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 397 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 41 residues processed: 452 average time/residue: 1.2309 time to fit residues: 656.2072 Evaluate side-chains 425 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 384 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 26 residues processed: 16 average time/residue: 0.6359 time to fit residues: 17.7373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 301 optimal weight: 0.0770 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN A 610 GLN A 687 GLN A 952 ASN A 962 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 17 ASN B 30 ASN B 79 ASN B 97 ASN B 236 GLN B 700 ASN B 776 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN C 916 ASN C 954 GLN C 975 ASN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 25640 Z= 0.309 Angle : 0.573 10.997 34862 Z= 0.298 Chirality : 0.045 0.296 4041 Planarity : 0.005 0.101 4467 Dihedral : 4.884 26.143 3528 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3077 helix: 0.25 (0.21), residues: 603 sheet: -0.86 (0.20), residues: 638 loop : -2.30 (0.13), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 406 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 62 residues processed: 462 average time/residue: 1.1651 time to fit residues: 634.0818 Evaluate side-chains 451 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 389 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 33 residues processed: 31 average time/residue: 0.6686 time to fit residues: 30.5046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 9.9990 chunk 171 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 257 optimal weight: 0.0670 chunk 208 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN B 97 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 776 GLN B 916 ASN B 954 GLN C 340 ASN C 447 ASN C 603 ASN C 781 GLN C 975 ASN C1071 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 25640 Z= 0.195 Angle : 0.530 9.762 34862 Z= 0.275 Chirality : 0.043 0.286 4041 Planarity : 0.004 0.075 4467 Dihedral : 4.698 33.482 3528 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3077 helix: 0.70 (0.22), residues: 602 sheet: -0.71 (0.20), residues: 621 loop : -2.20 (0.13), residues: 1854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 396 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 46 residues processed: 447 average time/residue: 1.1706 time to fit residues: 618.9702 Evaluate side-chains 429 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 383 time to evaluate : 2.804 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 34 residues processed: 14 average time/residue: 0.5381 time to fit residues: 14.3966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.3980 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 139 optimal weight: 40.0000 chunk 25 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN B 79 ASN B 97 ASN B 700 ASN B 776 GLN B 869 GLN B 954 GLN C 603 ASN C 975 ASN C1071 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.124 25640 Z= 0.220 Angle : 0.536 10.961 34862 Z= 0.279 Chirality : 0.044 0.299 4041 Planarity : 0.004 0.063 4467 Dihedral : 4.674 38.010 3528 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3077 helix: 0.91 (0.22), residues: 601 sheet: -0.64 (0.20), residues: 615 loop : -2.10 (0.13), residues: 1861 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 389 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 50 residues processed: 449 average time/residue: 1.2237 time to fit residues: 646.9936 Evaluate side-chains 422 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 372 time to evaluate : 2.746 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 40 residues processed: 11 average time/residue: 0.7110 time to fit residues: 14.0521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 254 optimal weight: 0.7980 chunk 168 optimal weight: 0.0270 chunk 300 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 138 optimal weight: 40.0000 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 17 ASN B 30 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 707 ASN B 776 GLN B 932 GLN B 954 GLN C 603 ASN C 975 ASN C1071 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.134 25640 Z= 0.221 Angle : 0.537 10.800 34862 Z= 0.279 Chirality : 0.044 0.304 4041 Planarity : 0.004 0.082 4467 Dihedral : 4.644 37.358 3528 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3077 helix: 1.05 (0.22), residues: 601 sheet: -0.62 (0.20), residues: 617 loop : -2.04 (0.13), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 378 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 53 residues processed: 432 average time/residue: 1.2570 time to fit residues: 642.6264 Evaluate side-chains 428 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 375 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 41 residues processed: 14 average time/residue: 0.4385 time to fit residues: 12.9839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 191 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 28 optimal weight: 30.0000 chunk 236 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1071 ASN B 30 ASN B 231 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 776 GLN B 954 GLN C 603 ASN C 975 ASN C1071 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.145 25640 Z= 0.253 Angle : 0.551 12.376 34862 Z= 0.285 Chirality : 0.044 0.313 4041 Planarity : 0.004 0.073 4467 Dihedral : 4.696 38.438 3528 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 3077 helix: 0.99 (0.22), residues: 609 sheet: -0.59 (0.20), residues: 613 loop : -2.03 (0.13), residues: 1855 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 378 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 56 residues processed: 439 average time/residue: 1.2221 time to fit residues: 632.2491 Evaluate side-chains 425 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 369 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 45 residues processed: 12 average time/residue: 0.4854 time to fit residues: 12.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.1980 chunk 288 optimal weight: 0.0770 chunk 262 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 122 optimal weight: 0.0060 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 279 optimal weight: 0.4980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 776 GLN B 954 GLN C 268 GLN C 603 ASN C 962 GLN C 975 ASN C1071 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.168 25640 Z= 0.182 Angle : 0.543 13.766 34862 Z= 0.280 Chirality : 0.044 0.306 4041 Planarity : 0.004 0.074 4467 Dihedral : 4.557 37.604 3528 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3077 helix: 1.19 (0.22), residues: 612 sheet: -0.61 (0.20), residues: 612 loop : -1.96 (0.13), residues: 1853 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 371 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 49 residues processed: 423 average time/residue: 1.3185 time to fit residues: 660.1274 Evaluate side-chains 413 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 364 time to evaluate : 2.773 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 7 average time/residue: 0.6021 time to fit residues: 9.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.8980 chunk 296 optimal weight: 0.0870 chunk 180 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 205 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 191 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 954 GLN C 268 GLN C 603 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN C1071 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.112 25640 Z= 0.260 Angle : 0.569 14.578 34862 Z= 0.294 Chirality : 0.045 0.318 4041 Planarity : 0.005 0.176 4467 Dihedral : 4.650 36.916 3528 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3077 helix: 1.07 (0.22), residues: 613 sheet: -0.61 (0.20), residues: 614 loop : -1.96 (0.13), residues: 1850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 373 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 50 residues processed: 422 average time/residue: 1.2448 time to fit residues: 618.5096 Evaluate side-chains 421 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 371 time to evaluate : 2.735 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 45 residues processed: 6 average time/residue: 0.6204 time to fit residues: 8.9245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 603 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN C1071 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.199573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151730 restraints weight = 33216.373| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.55 r_work: 0.3801 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.3765 rms_B_bonded: 2.37 restraints_weight: 0.1250 r_work: 0.3746 rms_B_bonded: 2.48 restraints_weight: 0.0625 r_work: 0.3724 rms_B_bonded: 2.64 restraints_weight: 0.0312 r_work: 0.3699 rms_B_bonded: 2.86 restraints_weight: 0.0156 r_work: 0.3671 rms_B_bonded: 3.16 restraints_weight: 0.0078 r_work: 0.3639 rms_B_bonded: 3.52 restraints_weight: 0.0039 r_work: 0.3602 rms_B_bonded: 3.98 restraints_weight: 0.0020 r_work: 0.3559 rms_B_bonded: 4.55 restraints_weight: 0.0010 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 25640 Z= 0.288 Angle : 0.580 15.410 34862 Z= 0.301 Chirality : 0.045 0.325 4041 Planarity : 0.005 0.139 4467 Dihedral : 4.744 38.261 3528 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3077 helix: 0.98 (0.21), residues: 619 sheet: -0.61 (0.20), residues: 614 loop : -1.95 (0.14), residues: 1844 =============================================================================== Job complete usr+sys time: 9586.89 seconds wall clock time: 171 minutes 0.69 seconds (10260.69 seconds total)