Starting phenix.real_space_refine on Fri Mar 22 17:34:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo7_33339/03_2024/7xo7_33339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo7_33339/03_2024/7xo7_33339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo7_33339/03_2024/7xo7_33339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo7_33339/03_2024/7xo7_33339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo7_33339/03_2024/7xo7_33339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo7_33339/03_2024/7xo7_33339.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 163 5.16 5 Cl 2 4.86 5 C 21870 2.51 5 N 5627 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E ARG 559": "NH1" <-> "NH2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F ARG 559": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7943 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 55, 'TRANS': 969} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 17.75, per 1000 atoms: 0.52 Number of scatterers: 34209 At special positions: 0 Unit cell: (161.504, 138.432, 241.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 163 16.00 O 6545 8.00 N 5627 7.00 C 21870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 331 " " NAG E 903 " - " ASN E 322 " " NAG E 904 " - " ASN E 546 " " NAG E 905 " - " ASN E 90 " " NAG F 903 " - " ASN F 322 " " NAG F 904 " - " ASN F 546 " " NAG F 905 " - " ASN F 90 " Time building additional restraints: 13.61 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 902 " pdb="ZN ZN F 902 " - pdb=" NE2 HIS F 374 " 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 51 sheets defined 35.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.672A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.677A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.708A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.515A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.861A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.507A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.785A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.531A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.137A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) 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 removed outlier: 3.780A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.514A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.933A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.591A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 4.011A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.537A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.772A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.565A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.194A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (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 984 removed outlier: 3.735A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.538A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.982A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.703A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.568A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.513A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.598A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 778 removed outlier: 3.758A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.612A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.762A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.924A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 947 removed outlier: 3.684A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 946 " --> pdb=" O SER C 943 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 957 Processing helix chain 'C' and resid 960 through 965 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 removed outlier: 3.771A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.235A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.565A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.547A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.918A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.668A pdb=" N SER E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 3.525A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.794A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.532A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.860A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.547A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.699A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.531A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.198A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.523A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.585A pdb=" N VAL E 404 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.790A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.893A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 560 " --> pdb=" O ASN E 556 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.508A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.670A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.562A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 3.553A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.919A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 108 " --> pdb=" O SER F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.665A pdb=" N SER F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 194 removed outlier: 3.521A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.802A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.538A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 252 removed outlier: 3.863A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.566A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.721A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.520A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.175A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.509A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.596A pdb=" N VAL F 404 " --> pdb=" O PHE F 400 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 3.793A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 561 removed outlier: 3.883A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 560 " --> pdb=" O ASN F 556 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY F 561 " --> pdb=" O MET F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 removed outlier: 3.523A pdb=" N ASN F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.511A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.786A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 132 removed outlier: 4.063A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.666A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.702A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.932A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.543A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.065A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.175A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.842A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.836A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.980A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 94 removed outlier: 4.141A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 132 removed outlier: 4.102A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 316 removed outlier: 3.520A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.156A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 4.058A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.518A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.607A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.854A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.958A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.505A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.994A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.765A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 171 through 172 removed outlier: 4.387A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.516A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.786A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.541A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.598A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.826A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.875A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.028A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'E' and resid 131 through 134 removed outlier: 3.656A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN E 134 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU E 140 " --> pdb=" O ASN E 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.818A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.304A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 131 through 134 removed outlier: 3.663A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN F 134 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU F 140 " --> pdb=" O ASN F 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.836A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.340A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1343 hydrogen bonds defined for protein. 3702 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: 14.51 Time building geometry restraints manager: 14.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10768 1.34 - 1.46: 6241 1.46 - 1.58: 17812 1.58 - 1.70: 0 1.70 - 1.82: 229 Bond restraints: 35050 Sorted by residual: bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.22e-02 6.72e+03 1.25e+01 bond pdb=" C LEU C 216 " pdb=" N PRO C 217 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.44e-02 4.82e+03 8.96e+00 bond pdb=" N THR A 208 " pdb=" CA THR A 208 " ideal model delta sigma weight residual 1.453 1.476 -0.023 8.30e-03 1.45e+04 7.89e+00 bond pdb=" N HIS A 207 " pdb=" CA HIS A 207 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.73e+00 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.502 -0.029 1.40e-02 5.10e+03 4.29e+00 ... (remaining 35045 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 1146 107.04 - 113.78: 19112 113.78 - 120.51: 13629 120.51 - 127.24: 13421 127.24 - 133.98: 387 Bond angle restraints: 47695 Sorted by residual: angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 111.90 108.76 3.14 8.10e-01 1.52e+00 1.51e+01 angle pdb=" CA LEU C 216 " pdb=" C LEU C 216 " pdb=" N PRO C 217 " ideal model delta sigma weight residual 118.44 123.83 -5.39 1.59e+00 3.96e-01 1.15e+01 angle pdb=" CA LEU C 216 " pdb=" C LEU C 216 " pdb=" O LEU C 216 " ideal model delta sigma weight residual 120.16 115.93 4.23 1.37e+00 5.33e-01 9.52e+00 angle pdb=" C THR A 208 " pdb=" CA THR A 208 " pdb=" CB THR A 208 " ideal model delta sigma weight residual 109.22 104.57 4.65 1.52e+00 4.33e-01 9.37e+00 angle pdb=" CA PRO B 209 " pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.83e+00 ... (remaining 47690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 20563 17.26 - 34.51: 589 34.51 - 51.77: 110 51.77 - 69.02: 12 69.02 - 86.28: 5 Dihedral angle restraints: 21279 sinusoidal: 8826 harmonic: 12453 Sorted by residual: dihedral pdb=" CB GLU A 169 " pdb=" CG GLU A 169 " pdb=" CD GLU A 169 " pdb=" OE1 GLU A 169 " ideal model delta sinusoidal sigma weight residual 0.00 86.28 -86.28 1 3.00e+01 1.11e-03 9.97e+00 dihedral pdb=" N THR A 208 " pdb=" CA THR A 208 " pdb=" CB THR A 208 " pdb=" OG1 THR A 208 " ideal model delta sinusoidal sigma weight residual 60.00 115.94 -55.94 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB GLU E 110 " pdb=" CG GLU E 110 " pdb=" CD GLU E 110 " pdb=" OE1 GLU E 110 " ideal model delta sinusoidal sigma weight residual 0.00 -80.66 80.66 1 3.00e+01 1.11e-03 8.94e+00 ... (remaining 21276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5222 0.099 - 0.199: 175 0.199 - 0.298: 7 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 5405 Sorted by residual: chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C1 NAG F 903 " pdb=" ND2 ASN F 322 " pdb=" C2 NAG F 903 " pdb=" O5 NAG F 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 5402 not shown) Planarity restraints: 6154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.051 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" CG ASN B 122 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.236 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.433 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 209 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C PRO C 209 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO C 209 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 210 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 521 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.019 5.00e-02 4.00e+02 ... (remaining 6151 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 318 2.60 - 3.17: 28097 3.17 - 3.75: 51237 3.75 - 4.32: 70910 4.32 - 4.90: 117474 Nonbonded interactions: 268036 Sorted by model distance: nonbonded pdb=" CE1 PHE B 168 " pdb=" CD ARG C 357 " model vdw 2.025 3.740 nonbonded pdb=" ND2 ASN B 121 " pdb=" CD1 LEU B 176 " model vdw 2.127 3.540 nonbonded pdb=" O VAL B 130 " pdb=" OG1 THR B 167 " model vdw 2.147 2.440 nonbonded pdb=" OE1 GLU E 402 " pdb="ZN ZN E 902 " model vdw 2.185 2.230 nonbonded pdb=" OG1 THR B 124 " pdb=" O6 NAG B1310 " model vdw 2.199 2.440 ... (remaining 268031 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 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 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 resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 522 through 523 and (name N or name CA or nam \ e C or name O or name CB )) or resid 524 through 1146 or resid 1301 through 1311 \ )) selection = chain 'B' selection = (chain 'C' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 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 resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 522 through 523 and (name N or name CA or nam \ e C or name O or name CB )) or resid 524 through 1146 or resid 1301 through 1311 \ )) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 24.670 Check model and map are aligned: 0.620 Set scattering table: 0.340 Process input model: 98.750 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 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 : 0.002 0.043 35050 Z= 0.148 Angle : 0.449 6.308 47695 Z= 0.240 Chirality : 0.042 0.497 5405 Planarity : 0.003 0.034 6115 Dihedral : 8.030 86.275 13167 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.11), residues: 4213 helix: -1.66 (0.12), residues: 1331 sheet: -1.23 (0.19), residues: 627 loop : -2.77 (0.10), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP E 302 HIS 0.002 0.000 HIS A1058 PHE 0.009 0.001 PHE A 371 TYR 0.011 0.001 TYR A 369 ARG 0.003 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 859 time to evaluate : 3.785 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 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 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 REVERT: A 190 ARG cc_start: 0.6361 (mtt180) cc_final: 0.5829 (mtt180) REVERT: A 194 PHE cc_start: 0.8098 (m-10) cc_final: 0.7856 (m-10) REVERT: A 317 ASN cc_start: 0.7744 (m-40) cc_final: 0.7198 (m-40) REVERT: A 586 ASP cc_start: 0.6430 (m-30) cc_final: 0.6110 (m-30) REVERT: A 670 ILE cc_start: 0.8548 (mp) cc_final: 0.8334 (mt) REVERT: A 747 THR cc_start: 0.7548 (p) cc_final: 0.7346 (m) REVERT: A 759 PHE cc_start: 0.6096 (m-10) cc_final: 0.5862 (m-10) REVERT: A 772 VAL cc_start: 0.8416 (p) cc_final: 0.8191 (p) REVERT: A 774 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7024 (mm-40) REVERT: A 909 ILE cc_start: 0.5638 (pt) cc_final: 0.3347 (mt) REVERT: A 974 SER cc_start: 0.8346 (t) cc_final: 0.7966 (m) REVERT: A 1019 ARG cc_start: 0.6615 (ttm110) cc_final: 0.6218 (ttm170) REVERT: A 1110 TYR cc_start: 0.7923 (t80) cc_final: 0.7702 (t80) REVERT: B 88 ASP cc_start: 0.6779 (m-30) cc_final: 0.6553 (m-30) REVERT: B 276 LEU cc_start: 0.7806 (tp) cc_final: 0.7530 (tt) REVERT: B 317 ASN cc_start: 0.7250 (m110) cc_final: 0.6955 (m110) REVERT: B 599 THR cc_start: 0.8188 (t) cc_final: 0.7855 (p) REVERT: B 755 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 928 ASN cc_start: 0.7854 (m-40) cc_final: 0.7479 (m-40) REVERT: B 947 LYS cc_start: 0.8165 (mttt) cc_final: 0.7959 (mtpp) REVERT: B 969 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7618 (ptpp) REVERT: B 1017 GLU cc_start: 0.6776 (tp30) cc_final: 0.6449 (tp30) REVERT: B 1019 ARG cc_start: 0.6688 (ttm110) cc_final: 0.6285 (ttp80) REVERT: B 1072 GLU cc_start: 0.7664 (pm20) cc_final: 0.7203 (pm20) REVERT: B 1084 ASP cc_start: 0.7020 (t0) cc_final: 0.6610 (t0) REVERT: B 1123 SER cc_start: 0.7828 (t) cc_final: 0.7549 (t) REVERT: C 195 LYS cc_start: 0.6701 (mtmt) cc_final: 0.6483 (mtmt) REVERT: C 210 ILE cc_start: 0.4422 (OUTLIER) cc_final: 0.4168 (pt) REVERT: C 276 LEU cc_start: 0.7859 (tp) cc_final: 0.7611 (tp) REVERT: C 304 LYS cc_start: 0.8252 (ttmt) cc_final: 0.8017 (ttmm) REVERT: C 542 ASN cc_start: 0.7752 (t0) cc_final: 0.7533 (t0) REVERT: C 670 ILE cc_start: 0.8795 (mp) cc_final: 0.8556 (mt) REVERT: C 737 ASP cc_start: 0.6206 (t0) cc_final: 0.5883 (t0) REVERT: C 774 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7142 (mm110) REVERT: C 790 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7650 (mtmm) REVERT: C 881 THR cc_start: 0.8067 (t) cc_final: 0.7808 (t) REVERT: C 931 ILE cc_start: 0.7595 (mm) cc_final: 0.7232 (mm) REVERT: C 981 LEU cc_start: 0.7624 (mt) cc_final: 0.7364 (mt) REVERT: C 1017 GLU cc_start: 0.7342 (tp30) cc_final: 0.6555 (tp30) REVERT: C 1018 ILE cc_start: 0.7683 (mm) cc_final: 0.7363 (mm) REVERT: C 1072 GLU cc_start: 0.7645 (pm20) cc_final: 0.7310 (pm20) REVERT: C 1123 SER cc_start: 0.7853 (m) cc_final: 0.7528 (t) REVERT: E 39 LEU cc_start: 0.6080 (mt) cc_final: 0.5766 (mt) REVERT: E 72 PHE cc_start: 0.5324 (t80) cc_final: 0.4814 (t80) REVERT: E 521 TYR cc_start: 0.6044 (m-10) cc_final: 0.5484 (m-80) REVERT: F 323 MET cc_start: -0.2235 (mmt) cc_final: -0.3440 (mmt) outliers start: 3 outliers final: 2 residues processed: 861 average time/residue: 0.4706 time to fit residues: 662.2676 Evaluate side-chains 715 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 712 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 216 optimal weight: 0.0170 chunk 171 optimal weight: 0.4980 chunk 332 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 385 optimal weight: 40.0000 overall best weight: 0.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 360 ASN A 439 ASN A 474 GLN A 580 GLN A 607 GLN A 613 GLN A 755 GLN A 907 ASN A 949 GLN A 965 GLN A1010 GLN B 173 GLN B 394 ASN B 519 HIS B 606 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN B1119 ASN B1125 ASN C 66 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 607 GLN C 895 GLN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 960 ASN C 965 GLN C1106 GLN C1119 ASN E 33 ASN E 51 ASN E 58 ASN E 60 GLN E 63 ASN E 81 GLN E 239 HIS E 300 GLN E 325 GLN E 330 ASN E 340 GLN E 429 GLN ** E 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 81 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS F 300 GLN F 325 GLN F 340 GLN F 429 GLN F 493 HIS F 524 GLN F 552 GLN F 556 ASN ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35050 Z= 0.197 Angle : 0.536 9.894 47695 Z= 0.270 Chirality : 0.044 0.333 5405 Planarity : 0.004 0.048 6115 Dihedral : 4.933 56.664 5397 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.86 % Allowed : 9.31 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4213 helix: 0.25 (0.14), residues: 1352 sheet: -0.81 (0.19), residues: 632 loop : -2.17 (0.11), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.008 0.001 HIS A1064 PHE 0.025 0.002 PHE B 55 TYR 0.021 0.001 TYR B1138 ARG 0.006 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 750 time to evaluate : 3.387 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7941 (m) cc_final: 0.7618 (t) REVERT: A 574 ASP cc_start: 0.6238 (p0) cc_final: 0.6009 (p0) REVERT: A 737 ASP cc_start: 0.6743 (t0) cc_final: 0.6364 (t0) REVERT: A 772 VAL cc_start: 0.8603 (p) cc_final: 0.8391 (t) REVERT: A 774 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7396 (mm-40) REVERT: A 970 PHE cc_start: 0.8108 (m-80) cc_final: 0.7777 (m-10) REVERT: A 974 SER cc_start: 0.8394 (t) cc_final: 0.8115 (m) REVERT: A 979 ASP cc_start: 0.6405 (t0) cc_final: 0.5962 (t0) REVERT: A 1014 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7098 (ttm170) REVERT: A 1075 PHE cc_start: 0.8077 (m-80) cc_final: 0.7677 (m-80) REVERT: A 1110 TYR cc_start: 0.8059 (t80) cc_final: 0.7764 (t80) REVERT: B 88 ASP cc_start: 0.6925 (m-30) cc_final: 0.6618 (m-30) REVERT: B 198 ASP cc_start: 0.5663 (t0) cc_final: 0.5379 (t0) REVERT: B 203 ILE cc_start: 0.8714 (pt) cc_final: 0.8453 (mt) REVERT: B 233 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.6227 (mt) REVERT: B 276 LEU cc_start: 0.7870 (tp) cc_final: 0.7571 (tt) REVERT: B 599 THR cc_start: 0.8151 (t) cc_final: 0.7874 (p) REVERT: B 642 VAL cc_start: 0.8512 (t) cc_final: 0.8298 (t) REVERT: B 704 SER cc_start: 0.7960 (m) cc_final: 0.7577 (p) REVERT: B 928 ASN cc_start: 0.8143 (m-40) cc_final: 0.7793 (m-40) REVERT: B 947 LYS cc_start: 0.8194 (mttt) cc_final: 0.7984 (mtpp) REVERT: B 969 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7703 (ptpp) REVERT: B 970 PHE cc_start: 0.7605 (m-80) cc_final: 0.7203 (m-80) REVERT: B 1017 GLU cc_start: 0.6964 (tp30) cc_final: 0.6646 (tp30) REVERT: B 1019 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6111 (ttp80) REVERT: B 1072 GLU cc_start: 0.7896 (pm20) cc_final: 0.7433 (pm20) REVERT: B 1084 ASP cc_start: 0.7168 (t0) cc_final: 0.6766 (t0) REVERT: B 1123 SER cc_start: 0.7692 (t) cc_final: 0.7452 (t) REVERT: C 276 LEU cc_start: 0.7881 (tp) cc_final: 0.7659 (tp) REVERT: C 584 ILE cc_start: 0.7184 (mt) cc_final: 0.6916 (mm) REVERT: C 587 ILE cc_start: 0.8581 (mp) cc_final: 0.8330 (mp) REVERT: C 642 VAL cc_start: 0.8406 (t) cc_final: 0.8170 (p) REVERT: C 722 VAL cc_start: 0.7922 (m) cc_final: 0.7376 (p) REVERT: C 737 ASP cc_start: 0.7015 (t0) cc_final: 0.6748 (t0) REVERT: C 770 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8222 (tt) REVERT: C 774 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7407 (mm110) REVERT: C 776 LYS cc_start: 0.8241 (tttm) cc_final: 0.7928 (tttm) REVERT: C 868 GLU cc_start: 0.6738 (tp30) cc_final: 0.6495 (tp30) REVERT: C 981 LEU cc_start: 0.7479 (mt) cc_final: 0.7159 (mt) REVERT: C 1017 GLU cc_start: 0.7324 (tp30) cc_final: 0.6844 (tp30) REVERT: C 1038 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7618 (mmmm) REVERT: C 1072 GLU cc_start: 0.7840 (pm20) cc_final: 0.7637 (pm20) REVERT: C 1073 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7287 (mtpp) REVERT: E 22 GLU cc_start: 0.5440 (tt0) cc_final: 0.5049 (tt0) REVERT: E 31 LYS cc_start: 0.4800 (tptp) cc_final: 0.3691 (tptp) REVERT: E 60 GLN cc_start: 0.5997 (tp40) cc_final: 0.5757 (tp40) REVERT: E 64 ASN cc_start: 0.4754 (OUTLIER) cc_final: 0.3903 (p0) REVERT: E 358 ILE cc_start: 0.6891 (mt) cc_final: 0.6568 (mt) REVERT: F 323 MET cc_start: -0.2156 (mmt) cc_final: -0.3511 (mmt) outliers start: 69 outliers final: 29 residues processed: 793 average time/residue: 0.4411 time to fit residues: 571.6073 Evaluate side-chains 725 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 692 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 547 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 320 optimal weight: 8.9990 chunk 262 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 385 optimal weight: 50.0000 chunk 416 optimal weight: 30.0000 chunk 343 optimal weight: 0.0670 chunk 382 optimal weight: 50.0000 chunk 131 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 949 GLN B 30 ASN B 606 ASN B 613 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 804 GLN B 919 ASN B1106 GLN B1135 ASN C 658 ASN C 755 GLN C 895 GLN C 907 ASN C 925 ASN E 76 GLN E 81 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 35050 Z= 0.384 Angle : 0.638 10.102 47695 Z= 0.329 Chirality : 0.048 0.349 5405 Planarity : 0.004 0.043 6115 Dihedral : 5.080 58.887 5393 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.78 % Allowed : 12.14 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4213 helix: 0.55 (0.14), residues: 1377 sheet: -0.61 (0.20), residues: 587 loop : -1.96 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 461 HIS 0.018 0.001 HIS A1064 PHE 0.031 0.002 PHE C 970 TYR 0.031 0.002 TYR A 279 ARG 0.007 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 752 time to evaluate : 3.548 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7916 (m) cc_final: 0.7603 (t) REVERT: A 291 CYS cc_start: 0.4935 (m) cc_final: 0.4661 (m) REVERT: A 304 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7956 (mtpt) REVERT: A 543 PHE cc_start: 0.8421 (m-10) cc_final: 0.8169 (m-80) REVERT: A 574 ASP cc_start: 0.6459 (p0) cc_final: 0.6245 (p0) REVERT: A 577 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7675 (ttm-80) REVERT: A 606 ASN cc_start: 0.7535 (m-40) cc_final: 0.7306 (m-40) REVERT: A 615 VAL cc_start: 0.8345 (p) cc_final: 0.8108 (m) REVERT: A 710 ASN cc_start: 0.7794 (p0) cc_final: 0.7336 (p0) REVERT: A 781 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8209 (t) REVERT: A 821 LEU cc_start: 0.8449 (tt) cc_final: 0.8232 (tp) REVERT: A 950 ASP cc_start: 0.6746 (t0) cc_final: 0.6492 (t0) REVERT: A 957 GLN cc_start: 0.7343 (tt0) cc_final: 0.7125 (tt0) REVERT: A 1030 SER cc_start: 0.8473 (t) cc_final: 0.8193 (m) REVERT: A 1102 TRP cc_start: 0.8401 (m100) cc_final: 0.8051 (m100) REVERT: A 1105 THR cc_start: 0.8254 (t) cc_final: 0.7979 (p) REVERT: B 30 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7626 (p0) REVERT: B 58 PHE cc_start: 0.8298 (m-10) cc_final: 0.7984 (m-10) REVERT: B 198 ASP cc_start: 0.6812 (t0) cc_final: 0.6369 (t0) REVERT: B 203 ILE cc_start: 0.8764 (pt) cc_final: 0.8400 (mt) REVERT: B 233 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6941 (mp) REVERT: B 269 TYR cc_start: 0.7474 (m-80) cc_final: 0.7244 (m-80) REVERT: B 539 VAL cc_start: 0.7583 (p) cc_final: 0.7363 (p) REVERT: B 599 THR cc_start: 0.8112 (t) cc_final: 0.7811 (p) REVERT: B 603 ASN cc_start: 0.7006 (t0) cc_final: 0.6590 (t0) REVERT: B 642 VAL cc_start: 0.8772 (t) cc_final: 0.8507 (p) REVERT: B 651 ILE cc_start: 0.8204 (pt) cc_final: 0.7977 (mt) REVERT: B 656 VAL cc_start: 0.8096 (t) cc_final: 0.7862 (t) REVERT: B 658 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7677 (p0) REVERT: B 698 SER cc_start: 0.8396 (t) cc_final: 0.8058 (p) REVERT: B 704 SER cc_start: 0.8177 (m) cc_final: 0.7797 (p) REVERT: B 756 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6659 (t80) REVERT: B 790 LYS cc_start: 0.7601 (mttp) cc_final: 0.6787 (mttp) REVERT: B 907 ASN cc_start: 0.8011 (t0) cc_final: 0.7780 (t0) REVERT: B 963 VAL cc_start: 0.8749 (m) cc_final: 0.8354 (t) REVERT: B 964 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7814 (tttm) REVERT: B 969 LYS cc_start: 0.7966 (ptpt) cc_final: 0.7737 (ptpp) REVERT: B 1014 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7426 (ttm170) REVERT: B 1017 GLU cc_start: 0.6867 (tp30) cc_final: 0.6610 (tp30) REVERT: B 1084 ASP cc_start: 0.7202 (t0) cc_final: 0.6765 (t0) REVERT: B 1116 THR cc_start: 0.8003 (m) cc_final: 0.7650 (t) REVERT: B 1123 SER cc_start: 0.7549 (t) cc_final: 0.7272 (t) REVERT: C 104 TRP cc_start: 0.7549 (m-90) cc_final: 0.7282 (m-90) REVERT: C 276 LEU cc_start: 0.7933 (tp) cc_final: 0.7652 (tt) REVERT: C 541 PHE cc_start: 0.8274 (p90) cc_final: 0.8048 (p90) REVERT: C 559 PHE cc_start: 0.7768 (m-10) cc_final: 0.7398 (m-80) REVERT: C 642 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (p) REVERT: C 698 SER cc_start: 0.8479 (t) cc_final: 0.8253 (t) REVERT: C 1001 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8304 (tt) REVERT: C 1031 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7126 (mt-10) REVERT: C 1038 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7884 (mmmm) REVERT: E 22 GLU cc_start: 0.5406 (tt0) cc_final: 0.5151 (tt0) REVERT: E 208 GLU cc_start: 0.6066 (tm-30) cc_final: 0.5758 (tm-30) REVERT: E 358 ILE cc_start: 0.6981 (mt) cc_final: 0.6709 (mt) REVERT: E 380 GLN cc_start: 0.6527 (mm-40) cc_final: 0.6320 (tm-30) REVERT: E 457 GLU cc_start: 0.4934 (mm-30) cc_final: 0.4687 (mm-30) REVERT: F 366 MET cc_start: 0.1754 (tpt) cc_final: 0.1205 (tpt) outliers start: 103 outliers final: 49 residues processed: 810 average time/residue: 0.4337 time to fit residues: 574.2609 Evaluate side-chains 737 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 681 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 0.7980 chunk 290 optimal weight: 0.4980 chunk 200 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 184 optimal weight: 0.0970 chunk 259 optimal weight: 0.7980 chunk 387 optimal weight: 20.0000 chunk 409 optimal weight: 30.0000 chunk 202 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1106 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 606 ASN B 613 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 856 ASN C 360 ASN C 439 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 774 GLN C 949 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN E 524 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35050 Z= 0.193 Angle : 0.539 11.028 47695 Z= 0.273 Chirality : 0.044 0.329 5405 Planarity : 0.004 0.039 6115 Dihedral : 4.629 59.972 5392 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.48 % Allowed : 14.03 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4213 helix: 0.99 (0.14), residues: 1365 sheet: -0.46 (0.20), residues: 602 loop : -1.77 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 69 HIS 0.006 0.001 HIS A1064 PHE 0.026 0.001 PHE A1075 TYR 0.019 0.001 TYR A 655 ARG 0.009 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 705 time to evaluate : 3.549 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7875 (m) cc_final: 0.7632 (t) REVERT: A 304 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7975 (mtpt) REVERT: A 574 ASP cc_start: 0.6376 (p0) cc_final: 0.6162 (p0) REVERT: A 578 ASP cc_start: 0.7636 (t0) cc_final: 0.7071 (t0) REVERT: A 606 ASN cc_start: 0.7543 (m-40) cc_final: 0.7343 (m-40) REVERT: A 710 ASN cc_start: 0.7779 (p0) cc_final: 0.7286 (p0) REVERT: A 737 ASP cc_start: 0.6863 (t0) cc_final: 0.6471 (t0) REVERT: A 950 ASP cc_start: 0.6676 (t0) cc_final: 0.6461 (t0) REVERT: A 957 GLN cc_start: 0.7299 (tt0) cc_final: 0.6856 (tt0) REVERT: A 970 PHE cc_start: 0.8021 (m-10) cc_final: 0.7745 (m-80) REVERT: A 1030 SER cc_start: 0.8503 (t) cc_final: 0.8290 (m) REVERT: A 1105 THR cc_start: 0.8339 (t) cc_final: 0.7900 (p) REVERT: A 1110 TYR cc_start: 0.8396 (t80) cc_final: 0.8119 (t80) REVERT: B 58 PHE cc_start: 0.8259 (m-10) cc_final: 0.7957 (m-10) REVERT: B 198 ASP cc_start: 0.6832 (t0) cc_final: 0.6375 (t0) REVERT: B 203 ILE cc_start: 0.8814 (pt) cc_final: 0.8606 (mt) REVERT: B 233 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7042 (mp) REVERT: B 269 TYR cc_start: 0.7534 (m-80) cc_final: 0.7317 (m-80) REVERT: B 317 ASN cc_start: 0.7595 (m-40) cc_final: 0.7337 (m-40) REVERT: B 599 THR cc_start: 0.8089 (t) cc_final: 0.7796 (p) REVERT: B 603 ASN cc_start: 0.6829 (t0) cc_final: 0.6415 (t0) REVERT: B 642 VAL cc_start: 0.8735 (t) cc_final: 0.8469 (p) REVERT: B 656 VAL cc_start: 0.8056 (t) cc_final: 0.7837 (t) REVERT: B 658 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 703 ASN cc_start: 0.7886 (t0) cc_final: 0.7663 (t0) REVERT: B 704 SER cc_start: 0.8139 (m) cc_final: 0.7796 (p) REVERT: B 756 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6718 (t80) REVERT: B 790 LYS cc_start: 0.7372 (mttp) cc_final: 0.7141 (mttp) REVERT: B 907 ASN cc_start: 0.7959 (t0) cc_final: 0.7617 (t0) REVERT: B 969 LYS cc_start: 0.7941 (ptpt) cc_final: 0.7701 (ptpp) REVERT: B 996 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (mp) REVERT: B 1017 GLU cc_start: 0.6863 (tp30) cc_final: 0.6347 (tp30) REVERT: B 1019 ARG cc_start: 0.7253 (ttp80) cc_final: 0.6578 (ttp80) REVERT: B 1084 ASP cc_start: 0.7129 (t0) cc_final: 0.6697 (t0) REVERT: B 1123 SER cc_start: 0.7497 (t) cc_final: 0.7223 (t) REVERT: C 104 TRP cc_start: 0.7498 (m-90) cc_final: 0.7207 (m-90) REVERT: C 276 LEU cc_start: 0.7857 (tp) cc_final: 0.7636 (tt) REVERT: C 313 TYR cc_start: 0.7885 (m-80) cc_final: 0.7682 (m-80) REVERT: C 541 PHE cc_start: 0.8125 (p90) cc_final: 0.7889 (p90) REVERT: C 748 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: C 776 LYS cc_start: 0.8290 (tttm) cc_final: 0.8057 (tttp) REVERT: C 965 GLN cc_start: 0.7591 (mt0) cc_final: 0.7344 (tt0) REVERT: C 1017 GLU cc_start: 0.6796 (tp30) cc_final: 0.6192 (tp30) REVERT: C 1038 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7861 (mmmm) REVERT: C 1094 VAL cc_start: 0.8073 (m) cc_final: 0.7268 (t) REVERT: E 22 GLU cc_start: 0.5358 (tt0) cc_final: 0.4979 (tt0) REVERT: E 32 PHE cc_start: 0.6024 (t80) cc_final: 0.5803 (t80) REVERT: E 358 ILE cc_start: 0.6997 (mt) cc_final: 0.6555 (mt) REVERT: E 397 ASN cc_start: 0.3301 (p0) cc_final: 0.1655 (m110) REVERT: F 323 MET cc_start: -0.2390 (mmt) cc_final: -0.3329 (mmp) REVERT: F 366 MET cc_start: 0.1546 (tpt) cc_final: 0.0958 (tpt) outliers start: 92 outliers final: 51 residues processed: 756 average time/residue: 0.4585 time to fit residues: 564.0733 Evaluate side-chains 740 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 684 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 199 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 305 optimal weight: 0.4980 chunk 169 optimal weight: 0.6980 chunk 349 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 209 optimal weight: 0.3980 chunk 367 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1005 GLN A1119 ASN B 30 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 856 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 774 GLN C 895 GLN C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35050 Z= 0.227 Angle : 0.553 14.799 47695 Z= 0.276 Chirality : 0.046 0.954 5405 Planarity : 0.004 0.045 6115 Dihedral : 4.628 59.950 5392 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.83 % Allowed : 14.71 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4213 helix: 1.12 (0.14), residues: 1371 sheet: -0.39 (0.20), residues: 633 loop : -1.65 (0.12), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 566 HIS 0.008 0.001 HIS A1064 PHE 0.029 0.001 PHE E 327 TYR 0.017 0.001 TYR B1138 ARG 0.010 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 696 time to evaluate : 3.934 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7842 (m) cc_final: 0.7623 (t) REVERT: A 304 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7970 (mtpt) REVERT: A 468 ILE cc_start: 0.0087 (OUTLIER) cc_final: -0.0195 (mt) REVERT: A 578 ASP cc_start: 0.7780 (t0) cc_final: 0.7438 (t0) REVERT: A 710 ASN cc_start: 0.7819 (p0) cc_final: 0.7324 (p0) REVERT: A 737 ASP cc_start: 0.6928 (t0) cc_final: 0.6479 (t0) REVERT: A 950 ASP cc_start: 0.6658 (t0) cc_final: 0.6444 (t0) REVERT: A 957 GLN cc_start: 0.7196 (tt0) cc_final: 0.6880 (tt0) REVERT: A 970 PHE cc_start: 0.8022 (m-10) cc_final: 0.7782 (m-80) REVERT: A 979 ASP cc_start: 0.6274 (t0) cc_final: 0.5866 (t0) REVERT: A 1105 THR cc_start: 0.8368 (t) cc_final: 0.7960 (p) REVERT: A 1110 TYR cc_start: 0.8399 (t80) cc_final: 0.8055 (t80) REVERT: B 30 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7458 (p0) REVERT: B 58 PHE cc_start: 0.8271 (m-10) cc_final: 0.7984 (m-10) REVERT: B 87 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5630 (p0) REVERT: B 198 ASP cc_start: 0.7016 (t0) cc_final: 0.6563 (t0) REVERT: B 233 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7139 (mp) REVERT: B 269 TYR cc_start: 0.7659 (m-80) cc_final: 0.7410 (m-80) REVERT: B 317 ASN cc_start: 0.7620 (m-40) cc_final: 0.7308 (m-40) REVERT: B 599 THR cc_start: 0.8072 (t) cc_final: 0.7807 (p) REVERT: B 603 ASN cc_start: 0.6800 (t0) cc_final: 0.6360 (t0) REVERT: B 642 VAL cc_start: 0.8723 (t) cc_final: 0.8485 (p) REVERT: B 656 VAL cc_start: 0.8092 (t) cc_final: 0.7885 (t) REVERT: B 658 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7779 (p0) REVERT: B 704 SER cc_start: 0.8135 (m) cc_final: 0.7805 (p) REVERT: B 756 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6811 (t80) REVERT: B 907 ASN cc_start: 0.7985 (t0) cc_final: 0.7683 (t0) REVERT: B 969 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7680 (ptpp) REVERT: B 996 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8019 (mp) REVERT: B 1084 ASP cc_start: 0.7129 (t0) cc_final: 0.6700 (t0) REVERT: B 1123 SER cc_start: 0.7510 (t) cc_final: 0.7262 (t) REVERT: C 104 TRP cc_start: 0.7544 (m-90) cc_final: 0.7257 (m-90) REVERT: C 276 LEU cc_start: 0.7872 (tp) cc_final: 0.7653 (tt) REVERT: C 324 GLU cc_start: 0.8001 (pm20) cc_final: 0.7541 (pm20) REVERT: C 541 PHE cc_start: 0.8154 (p90) cc_final: 0.7920 (p90) REVERT: C 670 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8459 (mt) REVERT: C 765 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6781 (ttm170) REVERT: C 965 GLN cc_start: 0.7685 (mt0) cc_final: 0.7366 (tt0) REVERT: C 1001 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8245 (tt) REVERT: C 1038 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7885 (mmmm) REVERT: C 1094 VAL cc_start: 0.8029 (m) cc_final: 0.7348 (t) REVERT: E 32 PHE cc_start: 0.5965 (t80) cc_final: 0.5724 (t80) REVERT: E 327 PHE cc_start: 0.3035 (t80) cc_final: 0.2797 (t80) REVERT: E 358 ILE cc_start: 0.7033 (mt) cc_final: 0.6776 (mt) REVERT: E 397 ASN cc_start: 0.3277 (p0) cc_final: 0.1677 (m110) REVERT: F 323 MET cc_start: -0.2354 (mmt) cc_final: -0.3308 (mmp) REVERT: F 366 MET cc_start: 0.1462 (tpt) cc_final: 0.0901 (tpt) outliers start: 105 outliers final: 66 residues processed: 753 average time/residue: 0.4663 time to fit residues: 570.0209 Evaluate side-chains 753 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 678 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 376 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 0.2980 chunk 369 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 410 optimal weight: 30.0000 chunk 340 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A1005 GLN C 563 GLN C 751 ASN C 755 GLN C 895 GLN C 935 GLN C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 58 ASN F 305 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35050 Z= 0.208 Angle : 0.556 12.682 47695 Z= 0.280 Chirality : 0.045 0.538 5405 Planarity : 0.004 0.048 6115 Dihedral : 4.540 59.940 5392 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.10 % Allowed : 15.41 % Favored : 81.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4213 helix: 1.24 (0.14), residues: 1361 sheet: -0.31 (0.19), residues: 649 loop : -1.57 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 566 HIS 0.009 0.001 HIS E 241 PHE 0.023 0.001 PHE B 32 TYR 0.016 0.001 TYR B1138 ARG 0.009 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 697 time to evaluate : 3.556 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7835 (m) cc_final: 0.7624 (t) REVERT: A 304 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7986 (mtpt) REVERT: A 468 ILE cc_start: 0.0139 (OUTLIER) cc_final: -0.0135 (mt) REVERT: A 546 LEU cc_start: 0.8347 (tp) cc_final: 0.8051 (tp) REVERT: A 559 PHE cc_start: 0.7915 (m-10) cc_final: 0.7681 (m-10) REVERT: A 578 ASP cc_start: 0.7867 (t0) cc_final: 0.7485 (t0) REVERT: A 710 ASN cc_start: 0.7858 (p0) cc_final: 0.7338 (p0) REVERT: A 737 ASP cc_start: 0.6787 (t0) cc_final: 0.6564 (t0) REVERT: A 970 PHE cc_start: 0.8004 (m-10) cc_final: 0.7799 (m-10) REVERT: A 979 ASP cc_start: 0.6271 (t0) cc_final: 0.5865 (t0) REVERT: A 1105 THR cc_start: 0.8403 (t) cc_final: 0.7989 (p) REVERT: A 1110 TYR cc_start: 0.8398 (t80) cc_final: 0.8047 (t80) REVERT: A 1130 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 58 PHE cc_start: 0.8274 (m-10) cc_final: 0.8017 (m-10) REVERT: B 87 ASN cc_start: 0.6208 (OUTLIER) cc_final: 0.5623 (p0) REVERT: B 198 ASP cc_start: 0.7119 (t0) cc_final: 0.6683 (t0) REVERT: B 233 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7210 (mp) REVERT: B 269 TYR cc_start: 0.7688 (m-80) cc_final: 0.7439 (m-80) REVERT: B 599 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7740 (p) REVERT: B 603 ASN cc_start: 0.6765 (t0) cc_final: 0.6308 (t0) REVERT: B 642 VAL cc_start: 0.8756 (t) cc_final: 0.8555 (p) REVERT: B 704 SER cc_start: 0.8109 (m) cc_final: 0.7716 (p) REVERT: B 756 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6851 (t80) REVERT: B 790 LYS cc_start: 0.7467 (mttp) cc_final: 0.7244 (mttp) REVERT: B 907 ASN cc_start: 0.8040 (t0) cc_final: 0.7714 (t0) REVERT: B 969 LYS cc_start: 0.7872 (ptpt) cc_final: 0.7659 (ptpp) REVERT: B 996 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 1072 GLU cc_start: 0.8171 (pm20) cc_final: 0.7884 (pm20) REVERT: B 1084 ASP cc_start: 0.7111 (t0) cc_final: 0.6681 (t0) REVERT: B 1123 SER cc_start: 0.7479 (t) cc_final: 0.7228 (t) REVERT: C 104 TRP cc_start: 0.7547 (m-90) cc_final: 0.7267 (m-90) REVERT: C 276 LEU cc_start: 0.7863 (tp) cc_final: 0.7616 (tt) REVERT: C 309 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6295 (mm-30) REVERT: C 670 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8459 (mt) REVERT: C 765 ARG cc_start: 0.7116 (ttm170) cc_final: 0.6909 (ttm170) REVERT: C 1001 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8243 (tt) REVERT: C 1031 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7077 (mt-10) REVERT: C 1038 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7903 (mmmm) REVERT: C 1072 GLU cc_start: 0.7982 (pm20) cc_final: 0.7751 (pm20) REVERT: C 1094 VAL cc_start: 0.8001 (m) cc_final: 0.7370 (t) REVERT: E 32 PHE cc_start: 0.5926 (t80) cc_final: 0.5725 (t80) REVERT: E 208 GLU cc_start: 0.6180 (tm-30) cc_final: 0.5886 (tm-30) REVERT: E 297 MET cc_start: 0.5266 (tpp) cc_final: 0.5066 (tpp) REVERT: E 327 PHE cc_start: 0.3052 (t80) cc_final: 0.2832 (t80) REVERT: E 358 ILE cc_start: 0.7077 (mt) cc_final: 0.6835 (mt) REVERT: E 397 ASN cc_start: 0.3121 (p0) cc_final: 0.1379 (m110) REVERT: F 323 MET cc_start: -0.2467 (mmt) cc_final: -0.3295 (mmp) REVERT: F 366 MET cc_start: 0.1368 (tpt) cc_final: 0.0859 (tpt) outliers start: 115 outliers final: 69 residues processed: 756 average time/residue: 0.4671 time to fit residues: 574.4766 Evaluate side-chains 761 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 683 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 376 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 chunk 229 optimal weight: 0.7980 chunk 408 optimal weight: 30.0000 chunk 255 optimal weight: 0.0980 chunk 249 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 30 ASN B 856 ASN C 644 GLN C 755 GLN C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35050 Z= 0.195 Angle : 0.557 11.756 47695 Z= 0.280 Chirality : 0.044 0.420 5405 Planarity : 0.004 0.053 6115 Dihedral : 4.480 59.876 5392 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.91 % Allowed : 16.24 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4213 helix: 1.31 (0.14), residues: 1357 sheet: -0.23 (0.20), residues: 624 loop : -1.50 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP E 566 HIS 0.009 0.001 HIS E 241 PHE 0.038 0.001 PHE C 541 TYR 0.021 0.001 TYR F 50 ARG 0.008 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 701 time to evaluate : 3.777 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7857 (m) cc_final: 0.7648 (t) REVERT: A 304 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7970 (mtpt) REVERT: A 468 ILE cc_start: 0.0179 (OUTLIER) cc_final: -0.0092 (mt) REVERT: A 535 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7265 (mmtp) REVERT: A 546 LEU cc_start: 0.8305 (tp) cc_final: 0.8094 (tp) REVERT: A 559 PHE cc_start: 0.7880 (m-10) cc_final: 0.7626 (m-10) REVERT: A 578 ASP cc_start: 0.7902 (t0) cc_final: 0.7523 (t0) REVERT: A 656 VAL cc_start: 0.8675 (t) cc_final: 0.8461 (t) REVERT: A 710 ASN cc_start: 0.7887 (p0) cc_final: 0.7353 (p0) REVERT: A 796 TYR cc_start: 0.7950 (t80) cc_final: 0.7628 (t80) REVERT: A 979 ASP cc_start: 0.6264 (t0) cc_final: 0.5881 (t0) REVERT: A 1019 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6817 (ttp80) REVERT: A 1105 THR cc_start: 0.8415 (t) cc_final: 0.8019 (p) REVERT: A 1110 TYR cc_start: 0.8404 (t80) cc_final: 0.8064 (t80) REVERT: A 1130 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8300 (mt) REVERT: B 58 PHE cc_start: 0.8290 (m-10) cc_final: 0.8035 (m-10) REVERT: B 87 ASN cc_start: 0.6210 (OUTLIER) cc_final: 0.5568 (p0) REVERT: B 198 ASP cc_start: 0.7185 (t0) cc_final: 0.6734 (t0) REVERT: B 233 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7275 (mp) REVERT: B 549 THR cc_start: 0.8278 (p) cc_final: 0.7966 (m) REVERT: B 599 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7711 (p) REVERT: B 642 VAL cc_start: 0.8768 (t) cc_final: 0.8560 (p) REVERT: B 704 SER cc_start: 0.8131 (m) cc_final: 0.7685 (p) REVERT: B 756 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6913 (t80) REVERT: B 900 MET cc_start: 0.7822 (mtp) cc_final: 0.7519 (mtp) REVERT: B 907 ASN cc_start: 0.8019 (t0) cc_final: 0.7703 (t0) REVERT: B 963 VAL cc_start: 0.8710 (m) cc_final: 0.8332 (t) REVERT: B 969 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7633 (ptpp) REVERT: B 1072 GLU cc_start: 0.8161 (pm20) cc_final: 0.7893 (pm20) REVERT: B 1084 ASP cc_start: 0.7102 (t0) cc_final: 0.6682 (t0) REVERT: B 1123 SER cc_start: 0.7463 (t) cc_final: 0.7220 (t) REVERT: C 104 TRP cc_start: 0.7532 (m-90) cc_final: 0.7255 (m-90) REVERT: C 319 ARG cc_start: 0.6822 (ptm160) cc_final: 0.6568 (mtp85) REVERT: C 536 ASN cc_start: 0.7885 (m110) cc_final: 0.7518 (m-40) REVERT: C 538 CYS cc_start: 0.4836 (m) cc_final: 0.4525 (m) REVERT: C 650 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7877 (pt) REVERT: C 670 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8418 (mt) REVERT: C 1001 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8231 (tt) REVERT: E 358 ILE cc_start: 0.7101 (mt) cc_final: 0.6859 (mt) REVERT: F 474 MET cc_start: 0.2110 (mtp) cc_final: 0.1396 (mtp) outliers start: 108 outliers final: 76 residues processed: 755 average time/residue: 0.4550 time to fit residues: 559.2374 Evaluate side-chains 773 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 688 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 433 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 259 optimal weight: 0.0970 chunk 278 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 321 optimal weight: 10.0000 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 784 GLN C 755 GLN C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS E 101 GLN E 241 HIS ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35050 Z= 0.178 Angle : 0.555 11.250 47695 Z= 0.277 Chirality : 0.044 0.360 5405 Planarity : 0.004 0.048 6115 Dihedral : 4.435 59.410 5392 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.86 % Allowed : 16.54 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4213 helix: 1.42 (0.14), residues: 1355 sheet: -0.16 (0.20), residues: 639 loop : -1.40 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 566 HIS 0.005 0.001 HIS E 239 PHE 0.040 0.001 PHE A 643 TYR 0.025 0.001 TYR B 904 ARG 0.008 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 692 time to evaluate : 3.232 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7968 (mtpt) REVERT: A 468 ILE cc_start: 0.0204 (OUTLIER) cc_final: -0.0063 (mt) REVERT: A 559 PHE cc_start: 0.7832 (m-10) cc_final: 0.7609 (m-10) REVERT: A 578 ASP cc_start: 0.7912 (t0) cc_final: 0.7533 (t0) REVERT: A 710 ASN cc_start: 0.7905 (p0) cc_final: 0.7355 (p0) REVERT: A 796 TYR cc_start: 0.7922 (t80) cc_final: 0.7613 (t80) REVERT: A 979 ASP cc_start: 0.6233 (t0) cc_final: 0.5842 (t0) REVERT: A 1105 THR cc_start: 0.8441 (t) cc_final: 0.8071 (p) REVERT: A 1110 TYR cc_start: 0.8407 (t80) cc_final: 0.8097 (t80) REVERT: A 1130 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 58 PHE cc_start: 0.8299 (m-10) cc_final: 0.8057 (m-10) REVERT: B 87 ASN cc_start: 0.6184 (OUTLIER) cc_final: 0.5423 (p0) REVERT: B 175 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.4465 (p90) REVERT: B 198 ASP cc_start: 0.7202 (t0) cc_final: 0.6761 (t0) REVERT: B 233 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7288 (mp) REVERT: B 549 THR cc_start: 0.8263 (p) cc_final: 0.7944 (m) REVERT: B 599 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7690 (p) REVERT: B 704 SER cc_start: 0.8088 (m) cc_final: 0.7680 (p) REVERT: B 756 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 907 ASN cc_start: 0.8003 (t0) cc_final: 0.7686 (t0) REVERT: B 969 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7596 (ptpp) REVERT: B 1017 GLU cc_start: 0.6654 (tp30) cc_final: 0.6265 (tp30) REVERT: B 1072 GLU cc_start: 0.8160 (pm20) cc_final: 0.7894 (pm20) REVERT: B 1084 ASP cc_start: 0.7077 (t0) cc_final: 0.6659 (t0) REVERT: B 1123 SER cc_start: 0.7452 (t) cc_final: 0.7206 (t) REVERT: C 536 ASN cc_start: 0.7853 (m110) cc_final: 0.7494 (m-40) REVERT: C 538 CYS cc_start: 0.4835 (m) cc_final: 0.4474 (m) REVERT: C 670 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8402 (mt) REVERT: C 1001 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8216 (tt) REVERT: E 208 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5863 (tm-30) REVERT: E 358 ILE cc_start: 0.7054 (mt) cc_final: 0.6806 (mt) REVERT: F 323 MET cc_start: -0.1285 (mmt) cc_final: -0.2061 (mmt) REVERT: F 366 MET cc_start: 0.1242 (tpt) cc_final: 0.0971 (tpt) REVERT: F 474 MET cc_start: 0.2085 (mtp) cc_final: 0.1364 (mtp) outliers start: 106 outliers final: 77 residues processed: 747 average time/residue: 0.4628 time to fit residues: 559.6127 Evaluate side-chains 759 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 673 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 0.8980 chunk 391 optimal weight: 0.0370 chunk 357 optimal weight: 9.9990 chunk 380 optimal weight: 20.0000 chunk 229 optimal weight: 0.7980 chunk 165 optimal weight: 0.2980 chunk 299 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 344 optimal weight: 0.7980 chunk 360 optimal weight: 3.9990 chunk 379 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 925 ASN B1010 GLN C 755 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 241 HIS ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 58 ASN F 305 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35050 Z= 0.200 Angle : 0.578 11.238 47695 Z= 0.291 Chirality : 0.045 0.328 5405 Planarity : 0.004 0.048 6115 Dihedral : 4.643 59.221 5392 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.62 % Allowed : 17.05 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4213 helix: 1.45 (0.15), residues: 1349 sheet: -0.18 (0.19), residues: 658 loop : -1.37 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP E 566 HIS 0.006 0.001 HIS A1064 PHE 0.029 0.001 PHE C 541 TYR 0.034 0.001 TYR B 904 ARG 0.008 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 681 time to evaluate : 3.770 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 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: A 304 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7971 (mtpt) REVERT: A 468 ILE cc_start: 0.0183 (OUTLIER) cc_final: -0.0082 (mt) REVERT: A 578 ASP cc_start: 0.7933 (t0) cc_final: 0.7563 (t0) REVERT: A 710 ASN cc_start: 0.7938 (p0) cc_final: 0.7396 (p0) REVERT: A 796 TYR cc_start: 0.7959 (t80) cc_final: 0.7686 (t80) REVERT: A 974 SER cc_start: 0.8525 (t) cc_final: 0.8252 (m) REVERT: A 979 ASP cc_start: 0.6251 (t0) cc_final: 0.5969 (t0) REVERT: A 983 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6916 (ttm-80) REVERT: A 1105 THR cc_start: 0.8477 (t) cc_final: 0.8109 (p) REVERT: A 1110 TYR cc_start: 0.8400 (t80) cc_final: 0.8083 (t80) REVERT: A 1130 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 58 PHE cc_start: 0.8316 (m-10) cc_final: 0.8066 (m-10) REVERT: B 87 ASN cc_start: 0.6252 (OUTLIER) cc_final: 0.5506 (p0) REVERT: B 175 PHE cc_start: 0.4882 (OUTLIER) cc_final: 0.4435 (p90) REVERT: B 198 ASP cc_start: 0.7237 (t0) cc_final: 0.6787 (t0) REVERT: B 233 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7325 (mp) REVERT: B 549 THR cc_start: 0.8295 (p) cc_final: 0.7966 (m) REVERT: B 599 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7686 (p) REVERT: B 719 THR cc_start: 0.8475 (t) cc_final: 0.8222 (p) REVERT: B 756 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 907 ASN cc_start: 0.8010 (t0) cc_final: 0.7680 (t0) REVERT: B 969 LYS cc_start: 0.7819 (ptpt) cc_final: 0.7592 (ptpp) REVERT: B 1072 GLU cc_start: 0.8157 (pm20) cc_final: 0.7898 (pm20) REVERT: B 1084 ASP cc_start: 0.7091 (t0) cc_final: 0.6665 (t0) REVERT: B 1123 SER cc_start: 0.7494 (t) cc_final: 0.7258 (t) REVERT: C 536 ASN cc_start: 0.7862 (m110) cc_final: 0.7545 (m-40) REVERT: C 615 VAL cc_start: 0.8391 (p) cc_final: 0.8189 (p) REVERT: C 670 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 1001 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8216 (tt) REVERT: E 208 GLU cc_start: 0.6098 (tm-30) cc_final: 0.5703 (tm-30) REVERT: E 358 ILE cc_start: 0.7056 (mt) cc_final: 0.6802 (mt) REVERT: E 521 TYR cc_start: 0.6085 (m-10) cc_final: 0.5624 (m-80) REVERT: F 323 MET cc_start: -0.1277 (mmt) cc_final: -0.2152 (mmt) REVERT: F 366 MET cc_start: 0.1227 (tpt) cc_final: 0.0998 (tpt) outliers start: 97 outliers final: 77 residues processed: 729 average time/residue: 0.4522 time to fit residues: 536.1193 Evaluate side-chains 754 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 668 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.5980 chunk 402 optimal weight: 0.0000 chunk 245 optimal weight: 20.0000 chunk 191 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 chunk 422 optimal weight: 20.0000 chunk 388 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 259 optimal weight: 0.0570 chunk 206 optimal weight: 2.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 607 GLN B 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35050 Z= 0.186 Angle : 0.587 11.933 47695 Z= 0.292 Chirality : 0.044 0.323 5405 Planarity : 0.004 0.048 6115 Dihedral : 4.714 58.424 5392 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.24 % Allowed : 17.51 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4213 helix: 1.47 (0.15), residues: 1350 sheet: -0.16 (0.19), residues: 660 loop : -1.32 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 566 HIS 0.008 0.001 HIS E 241 PHE 0.028 0.001 PHE C 541 TYR 0.033 0.001 TYR B 904 ARG 0.008 0.000 ARG A1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 668 time to evaluate : 3.537 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.0076 (OUTLIER) cc_final: -0.0210 (mt) REVERT: A 546 LEU cc_start: 0.8195 (mt) cc_final: 0.7846 (mp) REVERT: A 565 PHE cc_start: 0.7195 (m-10) cc_final: 0.6876 (m-10) REVERT: A 578 ASP cc_start: 0.7899 (t0) cc_final: 0.7544 (t0) REVERT: A 710 ASN cc_start: 0.7936 (p0) cc_final: 0.7385 (p0) REVERT: A 796 TYR cc_start: 0.7951 (t80) cc_final: 0.7669 (t80) REVERT: A 974 SER cc_start: 0.8529 (t) cc_final: 0.8249 (m) REVERT: A 979 ASP cc_start: 0.6229 (t0) cc_final: 0.5951 (t0) REVERT: A 983 ARG cc_start: 0.7244 (ttp-170) cc_final: 0.6880 (ttm-80) REVERT: A 1094 VAL cc_start: 0.7738 (m) cc_final: 0.7001 (t) REVERT: A 1105 THR cc_start: 0.8472 (t) cc_final: 0.8098 (p) REVERT: A 1110 TYR cc_start: 0.8402 (t80) cc_final: 0.8131 (t80) REVERT: A 1130 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 58 PHE cc_start: 0.8323 (m-10) cc_final: 0.8071 (m-10) REVERT: B 87 ASN cc_start: 0.6222 (OUTLIER) cc_final: 0.5473 (p0) REVERT: B 175 PHE cc_start: 0.4814 (OUTLIER) cc_final: 0.4376 (p90) REVERT: B 198 ASP cc_start: 0.7246 (t0) cc_final: 0.6805 (t0) REVERT: B 233 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7340 (mp) REVERT: B 549 THR cc_start: 0.8294 (p) cc_final: 0.7965 (m) REVERT: B 599 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7687 (p) REVERT: B 719 THR cc_start: 0.8477 (t) cc_final: 0.8222 (p) REVERT: B 756 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.6883 (t80) REVERT: B 785 VAL cc_start: 0.8701 (p) cc_final: 0.8469 (m) REVERT: B 907 ASN cc_start: 0.8007 (t0) cc_final: 0.7686 (t0) REVERT: B 969 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7588 (ptpp) REVERT: B 1072 GLU cc_start: 0.8157 (pm20) cc_final: 0.7899 (pm20) REVERT: B 1084 ASP cc_start: 0.7079 (t0) cc_final: 0.6655 (t0) REVERT: B 1123 SER cc_start: 0.7488 (t) cc_final: 0.7238 (t) REVERT: C 513 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6745 (mt) REVERT: C 536 ASN cc_start: 0.7855 (m110) cc_final: 0.7548 (m-40) REVERT: C 615 VAL cc_start: 0.8381 (p) cc_final: 0.8151 (p) REVERT: C 670 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8406 (mt) REVERT: C 1130 ILE cc_start: 0.8608 (pt) cc_final: 0.8332 (mt) REVERT: E 208 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5751 (tm-30) REVERT: E 358 ILE cc_start: 0.7050 (mt) cc_final: 0.6794 (mt) REVERT: E 478 TRP cc_start: 0.3315 (m100) cc_final: 0.2538 (m100) REVERT: E 521 TYR cc_start: 0.5951 (m-10) cc_final: 0.5704 (m-80) REVERT: F 323 MET cc_start: -0.1252 (mmt) cc_final: -0.2144 (mmt) REVERT: F 366 MET cc_start: 0.1210 (tpt) cc_final: 0.0979 (tpt) outliers start: 83 outliers final: 71 residues processed: 712 average time/residue: 0.4591 time to fit residues: 529.9177 Evaluate side-chains 744 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 664 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 0.5980 chunk 358 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 310 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 336 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 345 optimal weight: 0.9980 chunk 42 optimal weight: 40.0000 chunk 62 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.220915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156015 restraints weight = 53517.708| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.15 r_work: 0.3467 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35050 Z= 0.228 Angle : 0.595 12.192 47695 Z= 0.297 Chirality : 0.045 0.323 5405 Planarity : 0.004 0.048 6115 Dihedral : 4.593 58.244 5392 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.62 % Allowed : 17.30 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4213 helix: 1.45 (0.14), residues: 1349 sheet: -0.16 (0.19), residues: 657 loop : -1.29 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP E 566 HIS 0.009 0.001 HIS E 241 PHE 0.031 0.001 PHE E 230 TYR 0.034 0.001 TYR B 904 ARG 0.008 0.000 ARG B1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11070.08 seconds wall clock time: 197 minutes 52.16 seconds (11872.16 seconds total)