Starting phenix.real_space_refine (version: dev) on Sun May 15 16:53:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcm_22127/05_2022/6xcm_22127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcm_22127/05_2022/6xcm_22127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcm_22127/05_2022/6xcm_22127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcm_22127/05_2022/6xcm_22127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcm_22127/05_2022/6xcm_22127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcm_22127/05_2022/6xcm_22127.pdb" } resolution = 3.42 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= 0.004 sd= 0.022 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 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 26772 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7393 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 12 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7587 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7735 Chain: "C" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "N" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1, 'FUC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2, 'FUC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "M" 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: "O" 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: "P" 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2, 'FUC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER B 459 " occ=0.40 Time building chain proxies: 22.68, per 1000 atoms: 0.85 Number of scatterers: 26772 At special positions: 0 Unit cell: (132.924, 136.268, 219.868, 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 114 16.00 O 5235 8.00 N 4375 7.00 C 17048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.07 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG F 1 " - " FUC F 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG T 1 " - " FUC T 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG B1303 " - " ASN B 709 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 343 " " NAG B1312 " - " ASN B 603 " " NAG B1313 " - " ASN B 616 " " NAG B1314 " - " ASN B 657 " " NAG B1319 " - " ASN B1074 " " NAG B1320 " - " ASN B1098 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 709 " " NAG C1321 " - " ASN C1098 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG O 1 " - " ASN C 331 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 5.9 seconds 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6308 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 66 sheets defined 23.3% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.217A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.181A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.639A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.150A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.445A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.569A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.877A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.855A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.702A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.901A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.552A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.314A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.692A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.598A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.880A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.803A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.981A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.579A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.025A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.233A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.908A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.880A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.483A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'S' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.534A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.833A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.001A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.179A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.629A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.720A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.818A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.525A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.681A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.005A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.822A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.188A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.750A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.640A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.836A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.705A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.510A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.768A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.825A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.689A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.560A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.560A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.571A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.792A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.679A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.069A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.569A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.725A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.163A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 49 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 52 through 55 removed outlier: 4.418A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 104 through 106 removed outlier: 4.005A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.653A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.521A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.556A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.628A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.628A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 539 through 542 Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.308A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 719 removed outlier: 3.562A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AG1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.854A pdb=" N ILE H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.793A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.954A pdb=" N VAL N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET N 82 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU N 80 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.708A pdb=" N THR N 110 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 45 through 47 removed outlier: 3.564A pdb=" N ARG N 38 " --> pdb=" O GLU N 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 49 through 51 removed outlier: 3.619A pdb=" N VAL N 50 " --> pdb=" O TYR N 58 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AH1, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AH2, first strand: chain 'S' and resid 19 through 24 removed outlier: 3.992A pdb=" N THR S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER S 67 " --> pdb=" O THR S 70 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 44 through 49 removed outlier: 6.530A pdb=" N TRP S 35 " --> pdb=" O MET S 47 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR S 49 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER S 90 " --> pdb=" O VAL S 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL S 97 " --> pdb=" O SER S 90 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.66 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 8460 1.35 - 1.48: 7529 1.48 - 1.62: 11219 1.62 - 1.75: 0 1.75 - 1.89: 144 Bond restraints: 27352 Sorted by residual: bond pdb=" CA LEU A1034 " pdb=" C LEU A1034 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.07e+01 bond pdb=" CA CYS B 291 " pdb=" C CYS B 291 " ideal model delta sigma weight residual 1.523 1.469 0.055 1.34e-02 5.57e+03 1.66e+01 bond pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " ideal model delta sigma weight residual 1.808 1.888 -0.080 3.30e-02 9.18e+02 5.93e+00 bond pdb=" C PHE B1095 " pdb=" N VAL B1096 " ideal model delta sigma weight residual 1.334 1.311 0.023 1.29e-02 6.01e+03 3.28e+00 bond pdb=" CA ARG A 190 " pdb=" CB ARG A 190 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.33e-02 5.65e+03 2.83e+00 ... (remaining 27347 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.71: 575 105.71 - 112.83: 14981 112.83 - 119.94: 8767 119.94 - 127.05: 12671 127.05 - 134.16: 244 Bond angle restraints: 37238 Sorted by residual: angle pdb=" CA CYS C 166 " pdb=" CB CYS C 166 " pdb=" SG CYS C 166 " ideal model delta sigma weight residual 114.40 128.43 -14.03 2.30e+00 1.89e-01 3.72e+01 angle pdb=" C2 NAG I 2 " pdb=" N2 NAG I 2 " pdb=" C7 NAG I 2 " ideal model delta sigma weight residual 123.12 129.13 -6.01 1.28e+00 6.08e-01 2.20e+01 angle pdb=" C2 NAG B1308 " pdb=" N2 NAG B1308 " pdb=" C7 NAG B1308 " ideal model delta sigma weight residual 123.12 129.00 -5.88 1.28e+00 6.08e-01 2.10e+01 angle pdb=" C2 NAG K 1 " pdb=" N2 NAG K 1 " pdb=" C7 NAG K 1 " ideal model delta sigma weight residual 123.12 128.88 -5.76 1.28e+00 6.08e-01 2.02e+01 angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 124.71 -10.31 2.30e+00 1.89e-01 2.01e+01 ... (remaining 37233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.25: 14180 18.25 - 36.50: 1498 36.50 - 54.76: 325 54.76 - 73.01: 51 73.01 - 91.26: 36 Dihedral angle restraints: 16090 sinusoidal: 6269 harmonic: 9821 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.54 -87.46 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 1.13 -87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 7.63 85.37 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 16087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3458 0.054 - 0.109: 852 0.109 - 0.163: 110 0.163 - 0.217: 15 0.217 - 0.272: 2 Chirality restraints: 4437 Sorted by residual: chirality pdb=" CA CYS C 166 " pdb=" N CYS C 166 " pdb=" C CYS C 166 " pdb=" CB CYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB THR C 95 " pdb=" CA THR C 95 " pdb=" OG1 THR C 95 " pdb=" CG2 THR C 95 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 4434 not shown) Planarity restraints: 4757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO A 85 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO C 85 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO B 986 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.025 5.00e-02 4.00e+02 ... (remaining 4754 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 647 2.63 - 3.20: 25701 3.20 - 3.77: 40481 3.77 - 4.33: 55343 4.33 - 4.90: 92006 Nonbonded interactions: 214178 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.068 2.440 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.118 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.119 2.440 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.139 2.440 nonbonded pdb=" O VAL S 51 " pdb=" OG SER S 63 " model vdw 2.155 2.440 ... (remaining 214173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) or \ resid 116 through 124 or (resid 125 and (name N or name CA or name C or name O o \ r name CB )) or resid 126 through 131 or (resid 132 and (name N or name CA or na \ me C or name O or name CB )) or resid 133 or (resid 134 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 66 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB )) or resid 186 through 196 or resid 200 through 211 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 308 or (resid 309 and (name N or name CA or \ name C or name O or name CB )) or resid 310 through 332 or (resid 333 and (name \ N or name CA or name C or name O or name CB )) or resid 334 through 458 or resid \ 460 through 518 or resid 520 through 528 or (resid 529 and (name N or name CA o \ r name C or name O or name CB )) or resid 530 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 through 793 or (re \ sid 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or \ (resid 796 and (name N or name CA or name C or name O or name CB )) or resid 79 \ 7 through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 1311) \ ) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 166 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 339 or (resid 340 and (name N or name CA or name C or name O or \ name CB )) or resid 341 through 344 or (resid 345 and (name N or name CA or name \ C or name O or name CB )) or resid 346 through 404 or (resid 405 through 406 an \ d (name N or name CA or name C or name O or name CB )) or resid 407 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 419 or (resid 420 and (name N or name CA or name C or name O or name \ CB )) or resid 421 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 through 439 or (resid 440 and (name N or nam \ e CA or name C or name O or name CB )) or resid 441 or (resid 442 and (name N or \ name CA or name C or name O or name CB )) or resid 448 through 457 or (resid 45 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 460 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or re \ sid 466 through 470 or resid 490 through 501 or resid 503 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throug \ h 517 or (resid 518 through 520 and (name N or name CA or name C or name O or na \ me CB )) or resid 521 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 or \ (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 2 through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA o \ r name C or name O or name CB )) or resid 587 through 613 or (resid 614 and (nam \ e N or name CA or name C or name O or name CB )) or resid 615 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 th \ rough 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name \ C or name O or name CB )) or resid 746 through 827 or (resid 855 and (name N or \ name CA or name C or name O or name CB )) or resid 856 through 920 or (resid 921 \ and (name N or name CA or name C or name O or name CB )) or resid 922 through 1 \ 072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or r \ esid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name O \ or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 or resid 1303 throu \ gh 1314)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 166 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 339 or (resid 340 and (name N or name CA or name C or name O or \ name CB )) or resid 341 through 344 or (resid 345 and (name N or name CA or name \ C or name O or name CB )) or resid 346 through 404 or (resid 405 through 406 an \ d (name N or name CA or name C or name O or name CB )) or resid 407 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 419 or (resid 420 and (name N or name CA or name C or name O or name \ CB )) or resid 421 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 through 439 or (resid 440 and (name N or nam \ e CA or name C or name O or name CB )) or resid 441 or (resid 442 and (name N or \ name CA or name C or name O or name CB )) or resid 448 through 457 or (resid 45 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 460 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or re \ sid 466 through 470 or resid 490 through 501 or resid 503 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throug \ h 517 or (resid 518 through 520 and (name N or name CA or name C or name O or na \ me CB )) or resid 521 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 or \ (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 2 through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA o \ r name C or name O or name CB )) or resid 587 through 613 or (resid 614 and (nam \ e N or name CA or name C or name O or name CB )) or resid 615 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 th \ rough 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name \ C or name O or name CB )) or resid 746 through 827 or (resid 855 and (name N or \ name CA or name C or name O or name CB )) or resid 856 through 920 or (resid 921 \ and (name N or name CA or name C or name O or name CB )) or resid 922 through 1 \ 072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or r \ esid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name O \ or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 or resid 1305 throu \ gh 1321)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'N' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) } ncs_group { reference = chain 'L' selection = chain 'S' } 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 114 5.16 5 C 17048 2.51 5 N 4375 2.21 5 O 5235 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=0.33 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: 2.280 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: 0.030 Extract box with map and model: 11.180 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.270 Process input model: 82.270 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.008 0.080 27352 Z= 0.510 Angle : 0.733 14.027 37238 Z= 0.414 Chirality : 0.047 0.272 4437 Planarity : 0.004 0.073 4714 Dihedral : 15.640 91.262 9662 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.64 % Favored : 88.27 % Rotamer Outliers : 8.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.31 (0.12), residues: 3313 helix: -1.00 (0.17), residues: 679 sheet: -3.34 (0.17), residues: 708 loop : -3.53 (0.11), residues: 1926 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 204 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 174 residues processed: 437 average time/residue: 0.3614 time to fit residues: 256.9581 Evaluate side-chains 320 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 146 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 174 outliers final: 0 residues processed: 174 average time/residue: 0.2358 time to fit residues: 81.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 305 optimal weight: 30.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 804 GLN A 901 GLN A 935 GLN A1005 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 955 ASN B1071 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 949 GLN C 953 ASN C 965 GLN C1071 GLN C1106 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN N 39 GLN N 81 GLN ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95AASN ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 27352 Z= 0.211 Angle : 0.637 12.845 37238 Z= 0.341 Chirality : 0.046 0.408 4437 Planarity : 0.004 0.096 4714 Dihedral : 5.830 90.683 3987 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.13), residues: 3313 helix: 0.72 (0.19), residues: 690 sheet: -2.61 (0.18), residues: 703 loop : -2.81 (0.12), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 168 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 29 residues processed: 239 average time/residue: 0.3819 time to fit residues: 147.4787 Evaluate side-chains 167 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 2.940 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2531 time to fit residues: 18.0396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 20.0000 chunk 330 optimal weight: 30.0000 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 50.0000 chunk 104 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.107 27352 Z= 0.418 Angle : 0.670 10.710 37238 Z= 0.356 Chirality : 0.047 0.446 4437 Planarity : 0.004 0.056 4714 Dihedral : 5.918 91.286 3987 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.77 % Favored : 91.17 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.14), residues: 3313 helix: 0.90 (0.19), residues: 695 sheet: -2.53 (0.18), residues: 736 loop : -2.66 (0.12), residues: 1882 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 147 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 32 residues processed: 207 average time/residue: 0.3890 time to fit residues: 130.0811 Evaluate side-chains 162 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 3.124 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2391 time to fit residues: 18.4210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 158 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.124 27352 Z= 0.272 Angle : 0.601 10.964 37238 Z= 0.320 Chirality : 0.045 0.393 4437 Planarity : 0.004 0.048 4714 Dihedral : 5.741 91.584 3987 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.50 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.34 (0.14), residues: 3313 helix: 1.29 (0.20), residues: 693 sheet: -2.33 (0.18), residues: 746 loop : -2.42 (0.13), residues: 1874 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 19 residues processed: 198 average time/residue: 0.3872 time to fit residues: 124.2098 Evaluate side-chains 153 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 3.192 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2597 time to fit residues: 13.2012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 27352 Z= 0.420 Angle : 0.651 12.241 37238 Z= 0.343 Chirality : 0.046 0.278 4437 Planarity : 0.004 0.096 4714 Dihedral : 5.866 92.107 3987 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.83 % Favored : 91.11 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.34 (0.14), residues: 3313 helix: 1.20 (0.19), residues: 696 sheet: -2.24 (0.18), residues: 753 loop : -2.43 (0.13), residues: 1864 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 147 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 27 residues processed: 199 average time/residue: 0.3940 time to fit residues: 127.8072 Evaluate side-chains 162 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 3.117 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3106 time to fit residues: 19.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.7980 chunk 292 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 chunk 325 optimal weight: 0.0070 chunk 269 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.9616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 27352 Z= 0.186 Angle : 0.572 9.123 37238 Z= 0.301 Chirality : 0.044 0.258 4437 Planarity : 0.004 0.066 4714 Dihedral : 5.589 91.715 3987 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.96 (0.14), residues: 3313 helix: 1.55 (0.20), residues: 696 sheet: -2.12 (0.18), residues: 764 loop : -2.14 (0.13), residues: 1853 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 178 average time/residue: 0.3806 time to fit residues: 111.2740 Evaluate side-chains 151 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 3.021 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2326 time to fit residues: 8.7906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 185 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 323 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 207 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1048 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 27352 Z= 0.399 Angle : 0.633 9.698 37238 Z= 0.333 Chirality : 0.046 0.274 4437 Planarity : 0.004 0.054 4714 Dihedral : 5.739 92.624 3987 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.04 % Favored : 91.93 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3313 helix: 1.43 (0.20), residues: 695 sheet: -2.02 (0.18), residues: 764 loop : -2.21 (0.13), residues: 1854 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 174 average time/residue: 0.3912 time to fit residues: 110.9148 Evaluate side-chains 160 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2417 time to fit residues: 13.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 160 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 27352 Z= 0.241 Angle : 0.575 10.796 37238 Z= 0.302 Chirality : 0.044 0.251 4437 Planarity : 0.004 0.061 4714 Dihedral : 5.607 92.499 3987 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.83 (0.14), residues: 3313 helix: 1.62 (0.20), residues: 693 sheet: -1.98 (0.18), residues: 770 loop : -2.06 (0.13), residues: 1850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 160 average time/residue: 0.4157 time to fit residues: 107.5183 Evaluate side-chains 144 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2623 time to fit residues: 7.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 50.0000 chunk 310 optimal weight: 30.0000 chunk 283 optimal weight: 0.9990 chunk 301 optimal weight: 50.0000 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 27352 Z= 0.346 Angle : 0.618 13.864 37238 Z= 0.324 Chirality : 0.045 0.328 4437 Planarity : 0.004 0.050 4714 Dihedral : 5.706 92.949 3987 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.92 % Favored : 92.05 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.88 (0.14), residues: 3313 helix: 1.51 (0.20), residues: 696 sheet: -1.90 (0.18), residues: 759 loop : -2.12 (0.13), residues: 1858 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 148 average time/residue: 0.4067 time to fit residues: 97.8866 Evaluate side-chains 140 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2320 time to fit residues: 7.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.6980 chunk 319 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 334 optimal weight: 40.0000 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 27352 Z= 0.214 Angle : 0.572 10.897 37238 Z= 0.300 Chirality : 0.044 0.244 4437 Planarity : 0.004 0.044 4714 Dihedral : 5.595 92.699 3987 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3313 helix: 1.70 (0.20), residues: 693 sheet: -1.83 (0.18), residues: 750 loop : -1.98 (0.13), residues: 1870 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 143 average time/residue: 0.4069 time to fit residues: 95.5340 Evaluate side-chains 134 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 3.125 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3096 time to fit residues: 4.7393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 8.9990 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 274 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075014 restraints weight = 96654.977| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.27 r_work: 0.3153 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work: 0.3121 rms_B_bonded: 3.94 restraints_weight: 0.1250 r_work: 0.3104 rms_B_bonded: 4.00 restraints_weight: 0.0625 r_work: 0.3087 rms_B_bonded: 4.11 restraints_weight: 0.0312 r_work: 0.3069 rms_B_bonded: 4.25 restraints_weight: 0.0156 r_work: 0.3050 rms_B_bonded: 4.43 restraints_weight: 0.0078 r_work: 0.3031 rms_B_bonded: 4.66 restraints_weight: 0.0039 r_work: 0.3010 rms_B_bonded: 4.92 restraints_weight: 0.0020 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 27352 Z= 0.254 Angle : 0.584 11.302 37238 Z= 0.304 Chirality : 0.044 0.243 4437 Planarity : 0.004 0.047 4714 Dihedral : 5.636 93.045 3987 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.71 % Favored : 93.26 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.66 (0.14), residues: 3313 helix: 1.69 (0.20), residues: 697 sheet: -1.79 (0.18), residues: 734 loop : -1.98 (0.13), residues: 1882 =============================================================================== Job complete usr+sys time: 4924.03 seconds wall clock time: 91 minutes 27.21 seconds (5487.21 seconds total)