Starting phenix.real_space_refine on Wed Feb 21 17:54:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wou_32659/02_2024/7wou_32659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wou_32659/02_2024/7wou_32659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wou_32659/02_2024/7wou_32659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wou_32659/02_2024/7wou_32659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wou_32659/02_2024/7wou_32659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wou_32659/02_2024/7wou_32659.pdb" } resolution = 3.47 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 19974 2.51 5 N 5206 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31397 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8005 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 970} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.15, per 1000 atoms: 0.51 Number of scatterers: 31397 At special positions: 0 Unit cell: (142.576, 163.856, 207.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 6076 8.00 N 5206 7.00 C 19974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 220 " 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 A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 6.6 seconds 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 67 sheets defined 17.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.847A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.098A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.503A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.712A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.535A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.069A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.798A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.536A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.644A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.205A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.936A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.901A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.200A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.872A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.603A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 Processing helix chain 'B' and resid 761 through 782 removed outlier: 3.516A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.901A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.364A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.532A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.263A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.729A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.818A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.583A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.657A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.853A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.512A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.599A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.557A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 4.378A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.211A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.590A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.037A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.496A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.526A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 7.546A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.983A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.231A pdb=" N PHE A 392 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.551A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.443A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.756A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.664A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.933A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 89 through 92 removed outlier: 3.610A pdb=" N TYR B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 229 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 201 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.551A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC9, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD2, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.479A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.641A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.938A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 718 removed outlier: 7.016A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.181A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD8, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.543A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.645A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.892A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 192 through 194 removed outlier: 7.359A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.960A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.690A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.371A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.791A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AF2, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AF3, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.700A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.591A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.758A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.826A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 88 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR D 106 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.704A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 172 through 176 removed outlier: 5.981A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AG2, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AG5, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.608A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.137A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.697A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 172 through 176 removed outlier: 5.979A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AH1, first strand: chain 'G' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR G 87 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.564A pdb=" N SER G 131 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 182 through 184 removed outlier: 6.631A pdb=" N TRP G 160 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL G 174 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2271 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: 12.43 Time building geometry restraints manager: 13.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5791 1.33 - 1.45: 8620 1.45 - 1.57: 17537 1.57 - 1.69: 0 1.69 - 1.82: 182 Bond restraints: 32130 Sorted by residual: bond pdb=" CA TYR A 707 " pdb=" C TYR A 707 " ideal model delta sigma weight residual 1.526 1.435 0.091 1.20e-02 6.94e+03 5.74e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.21e-02 6.83e+03 3.75e+01 bond pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 1.457 1.385 0.072 1.29e-02 6.01e+03 3.12e+01 bond pdb=" CA ASN B 801 " pdb=" C ASN B 801 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.21e-02 6.83e+03 2.91e+01 bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.23e-02 6.61e+03 2.86e+01 ... (remaining 32125 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.10: 1025 107.10 - 113.83: 17577 113.83 - 120.56: 11951 120.56 - 127.29: 12878 127.29 - 134.02: 294 Bond angle restraints: 43725 Sorted by residual: angle pdb=" O ALA A 706 " pdb=" C ALA A 706 " pdb=" N TYR A 707 " ideal model delta sigma weight residual 122.89 115.64 7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" O VAL B 615 " pdb=" C VAL B 615 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 123.03 128.29 -5.26 1.05e+00 9.07e-01 2.51e+01 angle pdb=" CA ALA A 706 " pdb=" C ALA A 706 " pdb=" N TYR A 707 " ideal model delta sigma weight residual 115.88 122.23 -6.35 1.28e+00 6.10e-01 2.46e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 111.34 117.79 -6.45 1.55e+00 4.16e-01 1.73e+01 angle pdb=" CA VAL B 615 " pdb=" C VAL B 615 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 115.61 109.92 5.69 1.38e+00 5.25e-01 1.70e+01 ... (remaining 43720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 18438 17.89 - 35.78: 772 35.78 - 53.67: 116 53.67 - 71.55: 28 71.55 - 89.44: 4 Dihedral angle restraints: 19358 sinusoidal: 7726 harmonic: 11632 Sorted by residual: dihedral pdb=" CA ASN B 709 " pdb=" C ASN B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C ASN B1134 " pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" CB ASN B1134 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" CA ILE A 332 " pdb=" C ILE A 332 " pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta harmonic sigma weight residual 180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 19355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4490 0.076 - 0.151: 463 0.151 - 0.227: 6 0.227 - 0.302: 3 0.302 - 0.378: 3 Chirality restraints: 4965 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 4962 not shown) Planarity restraints: 5671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG B1302 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.341 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG C1307 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.343 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B1301 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.112 2.00e-02 2.50e+03 ... (remaining 5668 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2831 2.75 - 3.28: 31430 3.28 - 3.82: 51427 3.82 - 4.36: 59480 4.36 - 4.90: 103071 Nonbonded interactions: 248239 Sorted by model distance: nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.208 2.440 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.217 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.219 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.231 2.440 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.231 2.440 ... (remaining 248234 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 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 516 or resid 522 throu \ gh 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 26 through 516 or resid 522 through 1147 or resid 1301 thr \ ough 1307)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.400 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 82.650 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.220 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 32130 Z= 0.203 Angle : 0.574 7.250 43725 Z= 0.335 Chirality : 0.043 0.378 4965 Planarity : 0.014 0.301 5648 Dihedral : 9.568 89.442 11777 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.97 % Favored : 92.00 % Rotamer: Outliers : 5.49 % Allowed : 8.37 % Favored : 86.14 % 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: -4.25 (0.11), residues: 3963 helix: -0.88 (0.19), residues: 632 sheet: -2.70 (0.16), residues: 762 loop : -3.62 (0.10), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 98 HIS 0.002 0.000 HIS G 159 PHE 0.007 0.001 PHE B 92 TYR 0.016 0.001 TYR C 28 ARG 0.002 0.000 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 725 time to evaluate : 3.334 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: A 51 THR cc_start: 0.8199 (t) cc_final: 0.7804 (p) REVERT: A 53 ASP cc_start: 0.6577 (t0) cc_final: 0.6367 (t0) REVERT: A 63 THR cc_start: 0.7714 (m) cc_final: 0.6559 (t) REVERT: A 102 ARG cc_start: 0.5330 (mtm110) cc_final: 0.5080 (mtm110) REVERT: A 117 LEU cc_start: 0.7888 (mt) cc_final: 0.7590 (mp) REVERT: A 201 ILE cc_start: 0.8187 (mt) cc_final: 0.7751 (tt) REVERT: A 541 PHE cc_start: 0.7934 (p90) cc_final: 0.7525 (p90) REVERT: A 549 THR cc_start: 0.8288 (p) cc_final: 0.8044 (m) REVERT: A 596 SER cc_start: 0.8379 (m) cc_final: 0.8094 (p) REVERT: A 644 GLN cc_start: 0.7864 (tp40) cc_final: 0.7435 (tp40) REVERT: A 714 ILE cc_start: 0.7974 (mm) cc_final: 0.7350 (mt) REVERT: A 733 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7434 (mtpt) REVERT: A 743 CYS cc_start: 0.5736 (m) cc_final: 0.5341 (m) REVERT: A 746 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 776 LYS cc_start: 0.8103 (tmmt) cc_final: 0.7892 (tmmt) REVERT: A 854 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7000 (ttpp) REVERT: A 950 ASP cc_start: 0.6531 (t70) cc_final: 0.6080 (t0) REVERT: A 953 ASN cc_start: 0.7552 (m-40) cc_final: 0.7290 (m-40) REVERT: A 981 PHE cc_start: 0.7512 (m-10) cc_final: 0.7262 (m-80) REVERT: A 1028 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7843 (ttmm) REVERT: A 1081 ILE cc_start: 0.8151 (pt) cc_final: 0.7918 (mt) REVERT: A 1138 TYR cc_start: 0.6389 (t80) cc_final: 0.6160 (t80) REVERT: B 95 ILE cc_start: 0.7390 (mt) cc_final: 0.7110 (mt) REVERT: B 105 ILE cc_start: 0.7903 (mm) cc_final: 0.7684 (mm) REVERT: B 121 ASN cc_start: 0.7007 (t0) cc_final: 0.6196 (t0) REVERT: B 126 VAL cc_start: 0.7106 (t) cc_final: 0.6892 (m) REVERT: B 130 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7126 (p) REVERT: B 193 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7500 (ttpt) REVERT: B 203 SER cc_start: 0.8309 (p) cc_final: 0.8053 (t) REVERT: B 227 VAL cc_start: 0.7934 (m) cc_final: 0.7713 (m) REVERT: B 265 TYR cc_start: 0.7272 (p90) cc_final: 0.6774 (p90) REVERT: B 275 PHE cc_start: 0.8096 (m-80) cc_final: 0.7842 (m-80) REVERT: B 281 GLU cc_start: 0.6681 (pp20) cc_final: 0.6460 (pp20) REVERT: B 355 ARG cc_start: 0.4706 (OUTLIER) cc_final: 0.4247 (tmt90) REVERT: B 483 VAL cc_start: 0.5192 (OUTLIER) cc_final: 0.4897 (p) REVERT: B 542 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7242 (t0) REVERT: B 547 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7555 (mttm) REVERT: B 619 GLU cc_start: 0.6908 (tt0) cc_final: 0.6646 (tt0) REVERT: B 656 VAL cc_start: 0.8338 (p) cc_final: 0.8026 (m) REVERT: B 751 ASN cc_start: 0.8232 (m-40) cc_final: 0.7854 (m110) REVERT: B 765 ARG cc_start: 0.6857 (ttp-170) cc_final: 0.6532 (mtm110) REVERT: B 884 SER cc_start: 0.8601 (t) cc_final: 0.8289 (p) REVERT: B 918 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 933 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7448 (mtpp) REVERT: B 957 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6184 (tm130) REVERT: B 964 LYS cc_start: 0.7957 (ttpp) cc_final: 0.7724 (mtpp) REVERT: B 1014 ARG cc_start: 0.7367 (ttm170) cc_final: 0.7147 (mtm-85) REVERT: B 1073 LYS cc_start: 0.8094 (mtpm) cc_final: 0.7763 (ttmt) REVERT: B 1097 SER cc_start: 0.8797 (t) cc_final: 0.8436 (p) REVERT: B 1107 ARG cc_start: 0.6802 (mtt90) cc_final: 0.4936 (mtt180) REVERT: B 1111 GLU cc_start: 0.7262 (tt0) cc_final: 0.7014 (tt0) REVERT: B 1113 GLN cc_start: 0.7784 (mt0) cc_final: 0.7571 (mt0) REVERT: B 1138 TYR cc_start: 0.6693 (t80) cc_final: 0.6366 (t80) REVERT: B 1144 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6789 (mm-30) REVERT: C 51 THR cc_start: 0.8422 (t) cc_final: 0.8170 (p) REVERT: C 83 VAL cc_start: 0.7869 (t) cc_final: 0.7635 (p) REVERT: C 105 ILE cc_start: 0.7342 (mt) cc_final: 0.7098 (mt) REVERT: C 187 LEU cc_start: 0.7017 (tp) cc_final: 0.6269 (mt) REVERT: C 269 TYR cc_start: 0.7396 (m-10) cc_final: 0.7141 (m-10) REVERT: C 302 THR cc_start: 0.8129 (t) cc_final: 0.7734 (p) REVERT: C 537 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7668 (ttmm) REVERT: C 542 ASN cc_start: 0.7783 (t0) cc_final: 0.7405 (t0) REVERT: C 546 LEU cc_start: 0.7251 (tt) cc_final: 0.6903 (tp) REVERT: C 564 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6722 (mm110) REVERT: C 578 ASP cc_start: 0.7619 (t0) cc_final: 0.7368 (t0) REVERT: C 586 ASP cc_start: 0.7149 (t0) cc_final: 0.6934 (t0) REVERT: C 603 ASN cc_start: 0.7673 (t0) cc_final: 0.7297 (t0) REVERT: C 619 GLU cc_start: 0.7023 (tt0) cc_final: 0.6763 (tt0) REVERT: C 778 THR cc_start: 0.7990 (p) cc_final: 0.7658 (p) REVERT: C 821 LEU cc_start: 0.7890 (tp) cc_final: 0.7510 (tt) REVERT: C 867 ASP cc_start: 0.7781 (m-30) cc_final: 0.7511 (m-30) REVERT: C 868 GLU cc_start: 0.7006 (tp30) cc_final: 0.6780 (tp30) REVERT: C 914 ASN cc_start: 0.7933 (p0) cc_final: 0.7566 (p0) REVERT: C 933 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7486 (mtmm) REVERT: C 953 ASN cc_start: 0.8139 (m-40) cc_final: 0.7863 (m-40) REVERT: C 979 ASP cc_start: 0.6589 (m-30) cc_final: 0.6015 (m-30) REVERT: C 994 ASP cc_start: 0.7188 (m-30) cc_final: 0.6766 (t70) REVERT: C 1014 ARG cc_start: 0.7498 (tpp80) cc_final: 0.7276 (mtm-85) REVERT: C 1038 LYS cc_start: 0.8080 (mtmp) cc_final: 0.7783 (mtmm) REVERT: C 1097 SER cc_start: 0.8746 (t) cc_final: 0.8416 (p) REVERT: C 1111 GLU cc_start: 0.7322 (tt0) cc_final: 0.7016 (tt0) REVERT: C 1123 SER cc_start: 0.6962 (t) cc_final: 0.6617 (p) REVERT: C 1129 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 1136 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 1141 LEU cc_start: 0.8241 (tp) cc_final: 0.7988 (tp) REVERT: D 111 LEU cc_start: -0.1551 (OUTLIER) cc_final: -0.2478 (tm) REVERT: E 207 MET cc_start: 0.6149 (mtp) cc_final: 0.5492 (mtp) REVERT: F 144 LEU cc_start: 0.1831 (OUTLIER) cc_final: 0.1614 (tm) REVERT: F 148 CYS cc_start: 0.3721 (OUTLIER) cc_final: 0.3034 (p) REVERT: G 67 LYS cc_start: 0.4831 (OUTLIER) cc_final: 0.4330 (tmmm) outliers start: 188 outliers final: 73 residues processed: 881 average time/residue: 0.4410 time to fit residues: 611.2092 Evaluate side-chains 636 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 551 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 40.0000 chunk 302 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 203 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 312 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 232 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 81 ASN A 121 ASN A 173 GLN A 186 ASN A 271 GLN A 370 ASN A 388 ASN A 409 GLN A 448 ASN A 481 ASN A 487 ASN A 506 GLN A 540 ASN A 762 GLN A 784 GLN A 787 GLN A 804 GLN A 872 GLN A 901 GLN A1010 GLN A1011 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 181 GLN B 205 HIS B 245 HIS B 317 ASN B 354 ASN B 370 ASN B 388 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 540 ASN B 544 ASN B 563 GLN B 606 ASN B 613 GLN B 853 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 49 HIS C 81 ASN C 164 ASN C 205 HIS C 321 GLN C 354 ASN C 370 ASN C 388 ASN C 409 GLN C 448 ASN C 477 ASN C 540 ASN C 901 GLN C 914 ASN C 955 ASN C1005 GLN C1048 HIS C1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN D 129 GLN D 165 GLN E 6 GLN E 16 GLN E 52 ASN E 80 GLN E 97 ASN E 127 GLN E 137 GLN E 201 ASN E 206 GLN E 233 ASN F 33 ASN F 39 GLN F 40 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN G 6 GLN G 16 GLN G 52 ASN G 80 GLN G 97 ASN G 127 GLN G 137 GLN G 159 HIS G 201 ASN G 206 GLN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32130 Z= 0.192 Angle : 0.567 11.576 43725 Z= 0.280 Chirality : 0.045 0.397 4965 Planarity : 0.005 0.119 5648 Dihedral : 7.380 80.607 5011 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.87 % Allowed : 13.34 % Favored : 81.79 % 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: -3.46 (0.12), residues: 3963 helix: 0.21 (0.21), residues: 660 sheet: -2.20 (0.16), residues: 813 loop : -3.24 (0.10), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 37 HIS 0.006 0.001 HIS A 66 PHE 0.027 0.001 PHE C 541 TYR 0.023 0.001 TYR A 674 ARG 0.011 0.000 ARG G 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 561 time to evaluate : 3.604 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 43 PHE cc_start: 0.8509 (t80) cc_final: 0.8275 (t80) REVERT: A 51 THR cc_start: 0.8182 (t) cc_final: 0.7706 (p) REVERT: A 63 THR cc_start: 0.7889 (m) cc_final: 0.6593 (t) REVERT: A 102 ARG cc_start: 0.6331 (mtm110) cc_final: 0.6021 (mtm110) REVERT: A 281 GLU cc_start: 0.6601 (pp20) cc_final: 0.6362 (pp20) REVERT: A 290 ASP cc_start: 0.7327 (p0) cc_final: 0.7097 (p0) REVERT: A 541 PHE cc_start: 0.7793 (p90) cc_final: 0.7471 (p90) REVERT: A 574 ASP cc_start: 0.6873 (t70) cc_final: 0.6585 (t0) REVERT: A 596 SER cc_start: 0.8559 (m) cc_final: 0.8241 (p) REVERT: A 644 GLN cc_start: 0.7964 (tp40) cc_final: 0.7738 (tp40) REVERT: A 714 ILE cc_start: 0.8065 (mm) cc_final: 0.7391 (mt) REVERT: A 746 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8087 (t) REVERT: A 854 LYS cc_start: 0.7625 (ttpp) cc_final: 0.7227 (tptp) REVERT: A 914 ASN cc_start: 0.7257 (p0) cc_final: 0.6931 (p0) REVERT: A 950 ASP cc_start: 0.6801 (t70) cc_final: 0.6358 (t0) REVERT: A 964 LYS cc_start: 0.8220 (tmtm) cc_final: 0.7959 (ttmm) REVERT: A 984 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7917 (tt) REVERT: A 1029 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7626 (ttm) REVERT: A 1072 GLU cc_start: 0.7553 (pm20) cc_final: 0.7297 (pm20) REVERT: A 1091 ARG cc_start: 0.7393 (ttm170) cc_final: 0.7062 (ttp-170) REVERT: B 126 VAL cc_start: 0.7311 (t) cc_final: 0.7077 (m) REVERT: B 130 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7111 (p) REVERT: B 193 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7586 (ttpt) REVERT: B 281 GLU cc_start: 0.6744 (pp20) cc_final: 0.6499 (pp20) REVERT: B 355 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.4236 (tmt90) REVERT: B 406 GLU cc_start: 0.5243 (pt0) cc_final: 0.4958 (pt0) REVERT: B 591 SER cc_start: 0.8204 (t) cc_final: 0.7823 (m) REVERT: B 603 ASN cc_start: 0.7930 (t0) cc_final: 0.7723 (t0) REVERT: B 747 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (m) REVERT: B 751 ASN cc_start: 0.8249 (m-40) cc_final: 0.7872 (m110) REVERT: B 774 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7080 (mm-40) REVERT: B 902 MET cc_start: 0.7596 (tpp) cc_final: 0.7308 (tpp) REVERT: B 933 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7438 (mtpp) REVERT: B 964 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7761 (ttmm) REVERT: B 1097 SER cc_start: 0.8708 (t) cc_final: 0.8191 (p) REVERT: B 1118 ASP cc_start: 0.6643 (t70) cc_final: 0.6301 (t0) REVERT: B 1144 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6744 (mm-30) REVERT: C 51 THR cc_start: 0.8356 (t) cc_final: 0.8152 (p) REVERT: C 59 PHE cc_start: 0.8101 (m-10) cc_final: 0.7739 (m-80) REVERT: C 85 PRO cc_start: 0.7442 (Cg_endo) cc_final: 0.6189 (Cg_exo) REVERT: C 95 ILE cc_start: 0.8260 (mt) cc_final: 0.7866 (mt) REVERT: C 105 ILE cc_start: 0.7594 (mt) cc_final: 0.7282 (mt) REVERT: C 190 PHE cc_start: 0.6752 (m-80) cc_final: 0.6529 (m-80) REVERT: C 269 TYR cc_start: 0.7598 (m-10) cc_final: 0.7034 (m-10) REVERT: C 281 GLU cc_start: 0.6879 (pp20) cc_final: 0.6607 (pp20) REVERT: C 287 ASP cc_start: 0.7044 (p0) cc_final: 0.6792 (p0) REVERT: C 298 GLU cc_start: 0.7280 (tp30) cc_final: 0.6997 (tp30) REVERT: C 319 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7614 (ttp-110) REVERT: C 327 VAL cc_start: 0.8423 (t) cc_final: 0.8156 (m) REVERT: C 537 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7896 (ttmm) REVERT: C 541 PHE cc_start: 0.7407 (p90) cc_final: 0.6952 (p90) REVERT: C 542 ASN cc_start: 0.7919 (t0) cc_final: 0.7615 (t0) REVERT: C 547 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7679 (mtmm) REVERT: C 564 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6896 (mm110) REVERT: C 574 ASP cc_start: 0.7341 (p0) cc_final: 0.6918 (t0) REVERT: C 578 ASP cc_start: 0.7661 (t0) cc_final: 0.7258 (t0) REVERT: C 586 ASP cc_start: 0.7029 (t0) cc_final: 0.6734 (t0) REVERT: C 603 ASN cc_start: 0.7767 (t0) cc_final: 0.7385 (t0) REVERT: C 619 GLU cc_start: 0.7093 (tt0) cc_final: 0.6735 (tt0) REVERT: C 779 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7070 (mm-40) REVERT: C 821 LEU cc_start: 0.7767 (tp) cc_final: 0.7473 (tt) REVERT: C 904 TYR cc_start: 0.7249 (m-10) cc_final: 0.7025 (m-10) REVERT: C 914 ASN cc_start: 0.7891 (p0) cc_final: 0.7575 (p0) REVERT: C 935 GLN cc_start: 0.7562 (tt0) cc_final: 0.7338 (mt0) REVERT: C 979 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.6389 (m-30) REVERT: C 994 ASP cc_start: 0.7220 (m-30) cc_final: 0.6846 (t0) REVERT: C 1014 ARG cc_start: 0.7468 (tpp80) cc_final: 0.7203 (mtm-85) REVERT: C 1031 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7292 (mt-10) REVERT: C 1081 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7982 (mt) REVERT: C 1097 SER cc_start: 0.8711 (t) cc_final: 0.8395 (p) REVERT: C 1111 GLU cc_start: 0.7349 (tt0) cc_final: 0.7114 (tt0) REVERT: C 1129 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8012 (p) REVERT: D 111 LEU cc_start: -0.1582 (OUTLIER) cc_final: -0.2550 (tm) REVERT: E 207 MET cc_start: 0.6185 (mtp) cc_final: 0.5511 (mtp) REVERT: F 148 CYS cc_start: 0.3643 (OUTLIER) cc_final: 0.2416 (p) REVERT: G 67 LYS cc_start: 0.4781 (OUTLIER) cc_final: 0.4278 (tmmm) outliers start: 167 outliers final: 86 residues processed: 692 average time/residue: 0.4674 time to fit residues: 515.9583 Evaluate side-chains 602 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 504 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 246 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 362 optimal weight: 20.0000 chunk 392 optimal weight: 0.0470 chunk 323 optimal weight: 20.0000 chunk 359 optimal weight: 50.0000 chunk 123 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 955 ASN B 30 ASN B 66 HIS B 121 ASN B 186 ASN B 239 GLN B 334 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 901 GLN B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 239 GLN C 955 ASN C1011 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 159 HIS E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32130 Z= 0.282 Angle : 0.601 13.998 43725 Z= 0.300 Chirality : 0.046 0.271 4965 Planarity : 0.005 0.064 5648 Dihedral : 7.298 81.032 4975 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 5.14 % Allowed : 15.00 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.12), residues: 3963 helix: 0.67 (0.21), residues: 652 sheet: -1.97 (0.17), residues: 823 loop : -2.97 (0.11), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 37 HIS 0.009 0.001 HIS A1048 PHE 0.020 0.002 PHE A1121 TYR 0.030 0.001 TYR B1067 ARG 0.006 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 551 time to evaluate : 3.407 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: A 51 THR cc_start: 0.8151 (t) cc_final: 0.7646 (p) REVERT: A 63 THR cc_start: 0.8015 (m) cc_final: 0.6000 (t) REVERT: A 102 ARG cc_start: 0.6677 (mtm110) cc_final: 0.6291 (mtm110) REVERT: A 117 LEU cc_start: 0.7602 (mt) cc_final: 0.7384 (mt) REVERT: A 129 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7215 (ttmm) REVERT: A 228 ASP cc_start: 0.7305 (m-30) cc_final: 0.6812 (t0) REVERT: A 290 ASP cc_start: 0.7254 (p0) cc_final: 0.6982 (p0) REVERT: A 318 PHE cc_start: 0.7798 (t80) cc_final: 0.7567 (t80) REVERT: A 541 PHE cc_start: 0.7866 (p90) cc_final: 0.7500 (p90) REVERT: A 574 ASP cc_start: 0.6910 (t70) cc_final: 0.6677 (t0) REVERT: A 589 PRO cc_start: 0.8565 (Cg_endo) cc_final: 0.8337 (Cg_exo) REVERT: A 596 SER cc_start: 0.8591 (m) cc_final: 0.8167 (p) REVERT: A 644 GLN cc_start: 0.7874 (tp40) cc_final: 0.7627 (tp40) REVERT: A 740 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6918 (tpp) REVERT: A 746 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8176 (t) REVERT: A 749 CYS cc_start: 0.5677 (t) cc_final: 0.5297 (t) REVERT: A 765 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6774 (ttp80) REVERT: A 854 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7536 (tttp) REVERT: A 914 ASN cc_start: 0.7475 (p0) cc_final: 0.7252 (p0) REVERT: A 916 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7734 (tt) REVERT: A 950 ASP cc_start: 0.7033 (t70) cc_final: 0.6329 (t70) REVERT: A 954 HIS cc_start: 0.7463 (m-70) cc_final: 0.6947 (m170) REVERT: A 964 LYS cc_start: 0.8298 (tmtm) cc_final: 0.8046 (ttmm) REVERT: A 984 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 1001 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8012 (mt) REVERT: A 1002 GLN cc_start: 0.7452 (tp-100) cc_final: 0.7176 (tp-100) REVERT: A 1072 GLU cc_start: 0.7528 (pm20) cc_final: 0.7252 (pm20) REVERT: A 1091 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7161 (ttm-80) REVERT: B 95 ILE cc_start: 0.7530 (mt) cc_final: 0.7330 (mt) REVERT: B 126 VAL cc_start: 0.7341 (t) cc_final: 0.7028 (m) REVERT: B 129 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7918 (ptpp) REVERT: B 130 VAL cc_start: 0.7445 (t) cc_final: 0.7038 (p) REVERT: B 193 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7636 (ttpt) REVERT: B 227 VAL cc_start: 0.8145 (m) cc_final: 0.7866 (t) REVERT: B 281 GLU cc_start: 0.6729 (pp20) cc_final: 0.6504 (pp20) REVERT: B 319 ARG cc_start: 0.7523 (ptp-110) cc_final: 0.6577 (mtp85) REVERT: B 355 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4291 (tmt90) REVERT: B 406 GLU cc_start: 0.5235 (OUTLIER) cc_final: 0.4954 (pt0) REVERT: B 537 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7737 (ptmt) REVERT: B 591 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.7925 (p) REVERT: B 675 GLN cc_start: 0.6152 (tm-30) cc_final: 0.5911 (tm-30) REVERT: B 726 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.7441 (mt) REVERT: B 751 ASN cc_start: 0.8264 (m-40) cc_final: 0.7792 (m110) REVERT: B 774 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7423 (mm-40) REVERT: B 933 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7576 (mtpp) REVERT: B 963 VAL cc_start: 0.8756 (p) cc_final: 0.8540 (t) REVERT: B 964 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7826 (mtpp) REVERT: B 980 ILE cc_start: 0.8580 (mt) cc_final: 0.8283 (mm) REVERT: B 1107 ARG cc_start: 0.6897 (mtt90) cc_final: 0.6645 (mtt180) REVERT: B 1118 ASP cc_start: 0.6866 (t70) cc_final: 0.6486 (t0) REVERT: B 1138 TYR cc_start: 0.7372 (t80) cc_final: 0.7104 (t80) REVERT: B 1139 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7091 (p0) REVERT: B 1144 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6773 (mm-30) REVERT: C 51 THR cc_start: 0.8367 (t) cc_final: 0.8094 (p) REVERT: C 59 PHE cc_start: 0.8464 (m-10) cc_final: 0.8189 (m-80) REVERT: C 85 PRO cc_start: 0.7373 (Cg_endo) cc_final: 0.6867 (Cg_exo) REVERT: C 95 ILE cc_start: 0.8456 (mt) cc_final: 0.8032 (mt) REVERT: C 105 ILE cc_start: 0.7743 (mt) cc_final: 0.7500 (mt) REVERT: C 240 THR cc_start: 0.6786 (t) cc_final: 0.6114 (p) REVERT: C 269 TYR cc_start: 0.7761 (m-10) cc_final: 0.7457 (m-10) REVERT: C 281 GLU cc_start: 0.7058 (pp20) cc_final: 0.6720 (pp20) REVERT: C 298 GLU cc_start: 0.7306 (tp30) cc_final: 0.6965 (tp30) REVERT: C 319 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7532 (ttp-110) REVERT: C 327 VAL cc_start: 0.8427 (t) cc_final: 0.8194 (m) REVERT: C 537 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7899 (ttmm) REVERT: C 541 PHE cc_start: 0.7574 (p90) cc_final: 0.7181 (p90) REVERT: C 542 ASN cc_start: 0.8040 (t0) cc_final: 0.7710 (t0) REVERT: C 547 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7626 (mtmm) REVERT: C 564 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7349 (mm110) REVERT: C 578 ASP cc_start: 0.7392 (t0) cc_final: 0.7033 (t0) REVERT: C 586 ASP cc_start: 0.7147 (t0) cc_final: 0.6788 (t0) REVERT: C 592 PHE cc_start: 0.7986 (p90) cc_final: 0.7647 (p90) REVERT: C 603 ASN cc_start: 0.7972 (t0) cc_final: 0.7552 (t0) REVERT: C 619 GLU cc_start: 0.7137 (tt0) cc_final: 0.6860 (tt0) REVERT: C 773 GLU cc_start: 0.7196 (tt0) cc_final: 0.6783 (tt0) REVERT: C 821 LEU cc_start: 0.7790 (tp) cc_final: 0.7470 (tt) REVERT: C 900 MET cc_start: 0.7577 (ttm) cc_final: 0.7359 (ttm) REVERT: C 979 ASP cc_start: 0.6729 (m-30) cc_final: 0.6111 (m-30) REVERT: C 983 ARG cc_start: 0.7038 (ptp-110) cc_final: 0.6799 (ptp-110) REVERT: C 990 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: C 993 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7645 (tt) REVERT: C 994 ASP cc_start: 0.7230 (m-30) cc_final: 0.6943 (t0) REVERT: C 1014 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7206 (mtm-85) REVERT: C 1017 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6975 (tm-30) REVERT: C 1081 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7788 (mt) REVERT: C 1097 SER cc_start: 0.8714 (t) cc_final: 0.8347 (p) REVERT: C 1111 GLU cc_start: 0.7328 (tt0) cc_final: 0.7118 (tt0) REVERT: C 1125 ASN cc_start: 0.7725 (p0) cc_final: 0.7213 (p0) REVERT: C 1129 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8033 (p) REVERT: E 207 MET cc_start: 0.6207 (mtp) cc_final: 0.5499 (mtp) REVERT: F 148 CYS cc_start: 0.3417 (OUTLIER) cc_final: 0.2956 (p) REVERT: G 67 LYS cc_start: 0.4854 (OUTLIER) cc_final: 0.4337 (tmmm) outliers start: 176 outliers final: 111 residues processed: 684 average time/residue: 0.4452 time to fit residues: 482.6080 Evaluate side-chains 646 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 519 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 0.0970 chunk 272 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 40 optimal weight: 50.0000 chunk 173 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 364 optimal weight: 50.0000 chunk 385 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 955 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS B 121 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 544 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 321 GLN C 901 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 127 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 32130 Z= 0.341 Angle : 0.613 14.293 43725 Z= 0.308 Chirality : 0.046 0.288 4965 Planarity : 0.005 0.087 5648 Dihedral : 7.356 81.747 4963 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.46 % Allowed : 16.05 % Favored : 78.49 % 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: -2.86 (0.12), residues: 3963 helix: 0.74 (0.21), residues: 657 sheet: -1.87 (0.17), residues: 816 loop : -2.82 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.007 0.001 HIS A1048 PHE 0.027 0.002 PHE A 65 TYR 0.032 0.001 TYR B1067 ARG 0.012 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 532 time to evaluate : 4.408 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: A 51 THR cc_start: 0.8160 (t) cc_final: 0.7633 (p) REVERT: A 63 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7704 (m) REVERT: A 117 LEU cc_start: 0.7678 (mt) cc_final: 0.7470 (mt) REVERT: A 129 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7274 (ttmm) REVERT: A 186 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.5842 (p0) REVERT: A 204 LYS cc_start: 0.7858 (tptm) cc_final: 0.7624 (tptm) REVERT: A 224 GLU cc_start: 0.7961 (pm20) cc_final: 0.6985 (mp0) REVERT: A 290 ASP cc_start: 0.7299 (p0) cc_final: 0.7026 (p0) REVERT: A 324 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6741 (mt-10) REVERT: A 537 LYS cc_start: 0.7979 (tttp) cc_final: 0.7490 (tttt) REVERT: A 541 PHE cc_start: 0.8010 (p90) cc_final: 0.7677 (p90) REVERT: A 574 ASP cc_start: 0.7042 (t70) cc_final: 0.6736 (t0) REVERT: A 596 SER cc_start: 0.8622 (m) cc_final: 0.8204 (p) REVERT: A 607 GLN cc_start: 0.7910 (mt0) cc_final: 0.7704 (mt0) REVERT: A 644 GLN cc_start: 0.7939 (tp40) cc_final: 0.7603 (tp40) REVERT: A 656 VAL cc_start: 0.8439 (t) cc_final: 0.8175 (t) REVERT: A 740 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7086 (mmm) REVERT: A 749 CYS cc_start: 0.5646 (t) cc_final: 0.5227 (t) REVERT: A 765 ARG cc_start: 0.7343 (ttp-110) cc_final: 0.6838 (ttp80) REVERT: A 854 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7573 (tttp) REVERT: A 904 TYR cc_start: 0.6872 (m-10) cc_final: 0.6135 (m-10) REVERT: A 916 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7744 (tt) REVERT: A 933 LYS cc_start: 0.8221 (mttm) cc_final: 0.7993 (mttp) REVERT: A 950 ASP cc_start: 0.7184 (t70) cc_final: 0.6718 (t0) REVERT: A 964 LYS cc_start: 0.8265 (tmtm) cc_final: 0.8008 (ttmm) REVERT: A 970 PHE cc_start: 0.8225 (m-10) cc_final: 0.8025 (m-10) REVERT: A 984 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 1002 GLN cc_start: 0.7526 (tp-100) cc_final: 0.7198 (tp-100) REVERT: A 1097 SER cc_start: 0.8506 (t) cc_final: 0.8162 (p) REVERT: B 33 THR cc_start: 0.8616 (m) cc_final: 0.8319 (t) REVERT: B 102 ARG cc_start: 0.7659 (mtm110) cc_final: 0.7392 (ptp90) REVERT: B 126 VAL cc_start: 0.7455 (t) cc_final: 0.7230 (t) REVERT: B 129 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7963 (ptpp) REVERT: B 130 VAL cc_start: 0.7532 (t) cc_final: 0.7075 (p) REVERT: B 193 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7661 (ttpt) REVERT: B 200 LYS cc_start: 0.8207 (mttm) cc_final: 0.7949 (mtmt) REVERT: B 319 ARG cc_start: 0.7549 (ptp-110) cc_final: 0.7200 (mtp85) REVERT: B 328 ARG cc_start: 0.7254 (mmm160) cc_final: 0.6970 (mtt-85) REVERT: B 355 ARG cc_start: 0.4784 (OUTLIER) cc_final: 0.4250 (tmt90) REVERT: B 362 VAL cc_start: 0.6368 (OUTLIER) cc_final: 0.6108 (p) REVERT: B 406 GLU cc_start: 0.5249 (pt0) cc_final: 0.4702 (pt0) REVERT: B 537 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7812 (ptmm) REVERT: B 544 ASN cc_start: 0.7576 (t0) cc_final: 0.7108 (t0) REVERT: B 547 LYS cc_start: 0.7884 (mttp) cc_final: 0.7624 (mtmm) REVERT: B 558 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7460 (mtpp) REVERT: B 591 SER cc_start: 0.8454 (t) cc_final: 0.7842 (p) REVERT: B 603 ASN cc_start: 0.8137 (t0) cc_final: 0.7899 (t0) REVERT: B 619 GLU cc_start: 0.7083 (tt0) cc_final: 0.6403 (tp30) REVERT: B 747 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7475 (p) REVERT: B 751 ASN cc_start: 0.8252 (m-40) cc_final: 0.7849 (m110) REVERT: B 774 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7527 (mm-40) REVERT: B 902 MET cc_start: 0.7773 (tpp) cc_final: 0.7316 (tpp) REVERT: B 933 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7559 (mtpp) REVERT: B 963 VAL cc_start: 0.8777 (p) cc_final: 0.8555 (t) REVERT: B 964 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7814 (ttmm) REVERT: B 974 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7515 (m) REVERT: B 980 ILE cc_start: 0.8627 (mt) cc_final: 0.8372 (mm) REVERT: B 1097 SER cc_start: 0.8627 (t) cc_final: 0.8123 (p) REVERT: B 1107 ARG cc_start: 0.6933 (mtt90) cc_final: 0.5961 (mtt180) REVERT: B 1118 ASP cc_start: 0.7006 (t70) cc_final: 0.6536 (t0) REVERT: B 1127 ASP cc_start: 0.6649 (p0) cc_final: 0.6299 (p0) REVERT: B 1138 TYR cc_start: 0.7452 (t80) cc_final: 0.7129 (t80) REVERT: B 1139 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6994 (p0) REVERT: C 51 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8025 (p) REVERT: C 62 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7908 (m) REVERT: C 81 ASN cc_start: 0.8302 (m-40) cc_final: 0.8020 (m-40) REVERT: C 95 ILE cc_start: 0.8584 (mt) cc_final: 0.8118 (mt) REVERT: C 189 GLU cc_start: 0.7078 (mp0) cc_final: 0.6850 (mm-30) REVERT: C 190 PHE cc_start: 0.7401 (m-80) cc_final: 0.7142 (m-80) REVERT: C 239 GLN cc_start: 0.6896 (tp-100) cc_final: 0.6530 (tm-30) REVERT: C 298 GLU cc_start: 0.7373 (tp30) cc_final: 0.6938 (tp30) REVERT: C 314 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7362 (mt0) REVERT: C 319 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7729 (ttp-110) REVERT: C 541 PHE cc_start: 0.7631 (p90) cc_final: 0.7253 (p90) REVERT: C 542 ASN cc_start: 0.8074 (t0) cc_final: 0.7794 (t0) REVERT: C 547 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7717 (mtpp) REVERT: C 564 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7486 (mm110) REVERT: C 568 ASP cc_start: 0.6891 (p0) cc_final: 0.5960 (p0) REVERT: C 578 ASP cc_start: 0.7593 (t0) cc_final: 0.7272 (t0) REVERT: C 603 ASN cc_start: 0.8025 (t0) cc_final: 0.7610 (t0) REVERT: C 725 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7004 (tm-30) REVERT: C 742 ILE cc_start: 0.8592 (mt) cc_final: 0.8291 (mm) REVERT: C 745 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6322 (m-30) REVERT: C 773 GLU cc_start: 0.7273 (tt0) cc_final: 0.6848 (tt0) REVERT: C 790 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7931 (mtmm) REVERT: C 821 LEU cc_start: 0.7790 (tp) cc_final: 0.7506 (tt) REVERT: C 902 MET cc_start: 0.7634 (mmm) cc_final: 0.6958 (mmm) REVERT: C 979 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.5961 (m-30) REVERT: C 983 ARG cc_start: 0.7104 (ptp-110) cc_final: 0.6882 (ptp-110) REVERT: C 990 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 993 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7793 (tt) REVERT: C 994 ASP cc_start: 0.7229 (m-30) cc_final: 0.6876 (t0) REVERT: C 1014 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7243 (mtm-85) REVERT: C 1017 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 1097 SER cc_start: 0.8687 (t) cc_final: 0.8271 (p) REVERT: C 1111 GLU cc_start: 0.7331 (tt0) cc_final: 0.7125 (tt0) REVERT: C 1129 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8055 (p) REVERT: E 207 MET cc_start: 0.6262 (mtp) cc_final: 0.6041 (mtp) REVERT: F 148 CYS cc_start: 0.3453 (OUTLIER) cc_final: 0.2944 (p) REVERT: G 67 LYS cc_start: 0.4868 (OUTLIER) cc_final: 0.4369 (tmmm) outliers start: 187 outliers final: 116 residues processed: 675 average time/residue: 0.4544 time to fit residues: 490.4623 Evaluate side-chains 649 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 514 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 329 optimal weight: 40.0000 chunk 266 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 346 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 641 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS B 121 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 755 GLN C1106 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN F 209 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32130 Z= 0.211 Angle : 0.569 14.369 43725 Z= 0.282 Chirality : 0.045 0.276 4965 Planarity : 0.004 0.054 5648 Dihedral : 7.191 81.715 4962 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 5.54 % Allowed : 16.81 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.13), residues: 3963 helix: 1.01 (0.21), residues: 662 sheet: -1.71 (0.17), residues: 802 loop : -2.70 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 37 HIS 0.006 0.001 HIS A1048 PHE 0.029 0.001 PHE A 168 TYR 0.021 0.001 TYR C 91 ARG 0.005 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 532 time to evaluate : 3.564 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: A 51 THR cc_start: 0.8165 (t) cc_final: 0.7660 (p) REVERT: A 129 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7169 (ttmm) REVERT: A 220 PHE cc_start: 0.7308 (t80) cc_final: 0.6918 (t80) REVERT: A 290 ASP cc_start: 0.7306 (p0) cc_final: 0.7031 (p0) REVERT: A 324 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6684 (mt-10) REVERT: A 537 LYS cc_start: 0.7895 (tttp) cc_final: 0.7499 (tttt) REVERT: A 541 PHE cc_start: 0.8017 (p90) cc_final: 0.7727 (p90) REVERT: A 574 ASP cc_start: 0.7085 (t70) cc_final: 0.6770 (t0) REVERT: A 596 SER cc_start: 0.8559 (m) cc_final: 0.8135 (p) REVERT: A 602 THR cc_start: 0.7881 (m) cc_final: 0.7662 (p) REVERT: A 607 GLN cc_start: 0.7920 (mt0) cc_final: 0.7652 (mt0) REVERT: A 644 GLN cc_start: 0.7757 (tp40) cc_final: 0.7539 (tp40) REVERT: A 655 TYR cc_start: 0.7515 (t80) cc_final: 0.7283 (t80) REVERT: A 656 VAL cc_start: 0.8439 (t) cc_final: 0.8111 (t) REVERT: A 711 SER cc_start: 0.8249 (m) cc_final: 0.8043 (p) REVERT: A 740 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6961 (mmm) REVERT: A 749 CYS cc_start: 0.5544 (t) cc_final: 0.5149 (t) REVERT: A 765 ARG cc_start: 0.7251 (ttp-110) cc_final: 0.6862 (ttp-170) REVERT: A 854 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7526 (tttp) REVERT: A 904 TYR cc_start: 0.6845 (m-10) cc_final: 0.6136 (m-10) REVERT: A 914 ASN cc_start: 0.7466 (p0) cc_final: 0.7250 (p0) REVERT: A 916 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 933 LYS cc_start: 0.8214 (mttm) cc_final: 0.7984 (mttp) REVERT: A 950 ASP cc_start: 0.7195 (t70) cc_final: 0.6781 (t0) REVERT: A 964 LYS cc_start: 0.8240 (tmtm) cc_final: 0.7980 (ttmm) REVERT: A 965 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: A 970 PHE cc_start: 0.8170 (m-10) cc_final: 0.7933 (m-10) REVERT: A 984 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 1002 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7109 (tp-100) REVERT: B 41 LYS cc_start: 0.7876 (mtpp) cc_final: 0.7630 (mtpp) REVERT: B 105 ILE cc_start: 0.8226 (mp) cc_final: 0.7882 (mt) REVERT: B 129 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7897 (ptpp) REVERT: B 130 VAL cc_start: 0.7466 (t) cc_final: 0.6999 (p) REVERT: B 187 LEU cc_start: 0.8188 (tp) cc_final: 0.7956 (tp) REVERT: B 188 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7585 (mtt-85) REVERT: B 193 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7658 (ttpt) REVERT: B 200 LYS cc_start: 0.8281 (mttm) cc_final: 0.8065 (mttt) REVERT: B 355 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.4310 (tmt90) REVERT: B 362 VAL cc_start: 0.6434 (OUTLIER) cc_final: 0.6182 (p) REVERT: B 537 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7675 (ptmm) REVERT: B 544 ASN cc_start: 0.7502 (t0) cc_final: 0.7020 (t0) REVERT: B 558 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7434 (mtpp) REVERT: B 591 SER cc_start: 0.8421 (t) cc_final: 0.7750 (p) REVERT: B 603 ASN cc_start: 0.8033 (t0) cc_final: 0.7780 (t0) REVERT: B 619 GLU cc_start: 0.6905 (tt0) cc_final: 0.6237 (tp30) REVERT: B 725 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 726 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 747 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7243 (p) REVERT: B 751 ASN cc_start: 0.8194 (m-40) cc_final: 0.7820 (m110) REVERT: B 902 MET cc_start: 0.7689 (tpp) cc_final: 0.7275 (tpp) REVERT: B 933 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7449 (mtpp) REVERT: B 963 VAL cc_start: 0.8748 (p) cc_final: 0.8497 (t) REVERT: B 964 LYS cc_start: 0.8112 (ttpp) cc_final: 0.7782 (ttmm) REVERT: B 974 SER cc_start: 0.7677 (p) cc_final: 0.7405 (m) REVERT: B 980 ILE cc_start: 0.8620 (mt) cc_final: 0.8387 (mm) REVERT: B 1107 ARG cc_start: 0.6908 (mtt90) cc_final: 0.5898 (mtt180) REVERT: B 1113 GLN cc_start: 0.7739 (mt0) cc_final: 0.7503 (mt0) REVERT: B 1118 ASP cc_start: 0.6973 (t70) cc_final: 0.6546 (t0) REVERT: B 1127 ASP cc_start: 0.6672 (p0) cc_final: 0.6333 (p0) REVERT: C 51 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7946 (p) REVERT: C 81 ASN cc_start: 0.8343 (m-40) cc_final: 0.8025 (m-40) REVERT: C 168 PHE cc_start: 0.8539 (t80) cc_final: 0.7986 (t80) REVERT: C 190 PHE cc_start: 0.7499 (m-80) cc_final: 0.7260 (m-80) REVERT: C 239 GLN cc_start: 0.6906 (tp-100) cc_final: 0.6619 (tm-30) REVERT: C 269 TYR cc_start: 0.7814 (m-10) cc_final: 0.7386 (m-10) REVERT: C 314 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7386 (mt0) REVERT: C 319 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7808 (ttp-110) REVERT: C 541 PHE cc_start: 0.7571 (p90) cc_final: 0.7193 (p90) REVERT: C 542 ASN cc_start: 0.8044 (t0) cc_final: 0.7772 (t0) REVERT: C 564 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7440 (mm110) REVERT: C 568 ASP cc_start: 0.6654 (p0) cc_final: 0.5821 (p0) REVERT: C 590 CYS cc_start: 0.5636 (m) cc_final: 0.5402 (m) REVERT: C 603 ASN cc_start: 0.7977 (t0) cc_final: 0.7561 (t0) REVERT: C 725 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6913 (tm-30) REVERT: C 727 LEU cc_start: 0.8693 (mt) cc_final: 0.8431 (mt) REVERT: C 773 GLU cc_start: 0.7260 (tt0) cc_final: 0.6852 (tt0) REVERT: C 821 LEU cc_start: 0.7789 (tp) cc_final: 0.7498 (tt) REVERT: C 902 MET cc_start: 0.7680 (mmm) cc_final: 0.7227 (tpt) REVERT: C 934 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 979 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.5947 (m-30) REVERT: C 983 ARG cc_start: 0.7101 (ptp-110) cc_final: 0.6858 (ptp-110) REVERT: C 990 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: C 993 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7777 (tt) REVERT: C 994 ASP cc_start: 0.7198 (m-30) cc_final: 0.6831 (t0) REVERT: C 1014 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7268 (mtm-85) REVERT: C 1017 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 1097 SER cc_start: 0.8700 (t) cc_final: 0.8247 (p) REVERT: C 1111 GLU cc_start: 0.7205 (tt0) cc_final: 0.6925 (tt0) REVERT: C 1129 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (p) REVERT: E 207 MET cc_start: 0.6274 (mtp) cc_final: 0.6046 (mtp) REVERT: F 148 CYS cc_start: 0.3509 (OUTLIER) cc_final: 0.2969 (p) REVERT: G 67 LYS cc_start: 0.4883 (OUTLIER) cc_final: 0.4383 (tmmm) outliers start: 190 outliers final: 135 residues processed: 662 average time/residue: 0.4316 time to fit residues: 455.2037 Evaluate side-chains 664 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 513 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 0.6980 chunk 347 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 386 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 202 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 542 ASN B 824 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 32130 Z= 0.195 Angle : 0.562 14.564 43725 Z= 0.278 Chirality : 0.044 0.272 4965 Planarity : 0.004 0.050 5648 Dihedral : 7.150 81.578 4961 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 5.37 % Allowed : 17.25 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3963 helix: 1.17 (0.21), residues: 663 sheet: -1.65 (0.17), residues: 809 loop : -2.61 (0.11), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 PHE 0.024 0.001 PHE A 592 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 535 time to evaluate : 3.273 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 51 THR cc_start: 0.8146 (t) cc_final: 0.7636 (p) REVERT: A 52 GLN cc_start: 0.8048 (tp40) cc_final: 0.7804 (tp40) REVERT: A 129 LYS cc_start: 0.7539 (ttmm) cc_final: 0.7074 (ttmm) REVERT: A 220 PHE cc_start: 0.7355 (t80) cc_final: 0.6932 (t80) REVERT: A 324 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6785 (mt-10) REVERT: A 537 LYS cc_start: 0.7965 (tttp) cc_final: 0.7505 (tttt) REVERT: A 541 PHE cc_start: 0.8047 (p90) cc_final: 0.7758 (p90) REVERT: A 589 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8353 (Cg_exo) REVERT: A 596 SER cc_start: 0.8554 (m) cc_final: 0.8101 (p) REVERT: A 602 THR cc_start: 0.7918 (m) cc_final: 0.7681 (p) REVERT: A 607 GLN cc_start: 0.7923 (mt0) cc_final: 0.7632 (mp10) REVERT: A 644 GLN cc_start: 0.7966 (tp40) cc_final: 0.7520 (tp40) REVERT: A 656 VAL cc_start: 0.8441 (t) cc_final: 0.8085 (t) REVERT: A 711 SER cc_start: 0.8237 (m) cc_final: 0.8030 (p) REVERT: A 740 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6981 (mmm) REVERT: A 765 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6805 (ttp-170) REVERT: A 854 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7628 (tttm) REVERT: A 904 TYR cc_start: 0.6826 (m-10) cc_final: 0.5749 (m-10) REVERT: A 914 ASN cc_start: 0.7500 (p0) cc_final: 0.7268 (p0) REVERT: A 916 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 933 LYS cc_start: 0.8208 (mttm) cc_final: 0.7981 (mttp) REVERT: A 950 ASP cc_start: 0.7180 (t70) cc_final: 0.6778 (t0) REVERT: A 964 LYS cc_start: 0.8231 (tmtm) cc_final: 0.7985 (ttmm) REVERT: A 965 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: A 970 PHE cc_start: 0.8159 (m-10) cc_final: 0.7914 (m-10) REVERT: A 984 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7837 (tt) REVERT: A 1002 GLN cc_start: 0.7372 (tp-100) cc_final: 0.7088 (tp-100) REVERT: A 1097 SER cc_start: 0.8495 (t) cc_final: 0.8145 (p) REVERT: B 41 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7658 (mtpt) REVERT: B 129 LYS cc_start: 0.8176 (ptpt) cc_final: 0.7897 (ptpp) REVERT: B 130 VAL cc_start: 0.7459 (t) cc_final: 0.7001 (p) REVERT: B 193 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7652 (ttpt) REVERT: B 200 LYS cc_start: 0.8281 (mttm) cc_final: 0.8055 (mttt) REVERT: B 319 ARG cc_start: 0.7618 (ptp-110) cc_final: 0.6975 (mtp85) REVERT: B 328 ARG cc_start: 0.7089 (mmm160) cc_final: 0.6882 (mtt-85) REVERT: B 355 ARG cc_start: 0.4808 (OUTLIER) cc_final: 0.4251 (tmt90) REVERT: B 362 VAL cc_start: 0.6472 (OUTLIER) cc_final: 0.6225 (p) REVERT: B 406 GLU cc_start: 0.5626 (pt0) cc_final: 0.5300 (pt0) REVERT: B 537 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7713 (ptmm) REVERT: B 544 ASN cc_start: 0.7524 (t0) cc_final: 0.7018 (t0) REVERT: B 558 LYS cc_start: 0.7692 (mtpp) cc_final: 0.7422 (mtpp) REVERT: B 591 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.7773 (p) REVERT: B 619 GLU cc_start: 0.6863 (tt0) cc_final: 0.6197 (tp30) REVERT: B 725 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6792 (tm-30) REVERT: B 726 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 747 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7113 (p) REVERT: B 751 ASN cc_start: 0.8187 (m-40) cc_final: 0.7806 (m110) REVERT: B 773 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6109 (tm-30) REVERT: B 820 ASP cc_start: 0.7433 (t0) cc_final: 0.7229 (t0) REVERT: B 902 MET cc_start: 0.7709 (tpp) cc_final: 0.7201 (tpp) REVERT: B 933 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7415 (mtpp) REVERT: B 963 VAL cc_start: 0.8750 (p) cc_final: 0.8467 (t) REVERT: B 964 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7800 (ttmm) REVERT: B 974 SER cc_start: 0.7636 (p) cc_final: 0.7429 (m) REVERT: B 980 ILE cc_start: 0.8648 (mt) cc_final: 0.8399 (mm) REVERT: B 1107 ARG cc_start: 0.6916 (mtt90) cc_final: 0.5646 (mtt180) REVERT: B 1113 GLN cc_start: 0.7740 (mt0) cc_final: 0.7497 (mt0) REVERT: B 1118 ASP cc_start: 0.7007 (t70) cc_final: 0.6536 (t0) REVERT: C 51 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7928 (p) REVERT: C 81 ASN cc_start: 0.8369 (m-40) cc_final: 0.8060 (m-40) REVERT: C 168 PHE cc_start: 0.8486 (t80) cc_final: 0.7922 (t80) REVERT: C 190 PHE cc_start: 0.7464 (m-80) cc_final: 0.7219 (m-80) REVERT: C 239 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6606 (tm-30) REVERT: C 269 TYR cc_start: 0.7771 (m-10) cc_final: 0.7358 (m-80) REVERT: C 298 GLU cc_start: 0.7334 (tp30) cc_final: 0.7023 (tp30) REVERT: C 319 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7902 (ttm170) REVERT: C 541 PHE cc_start: 0.7574 (p90) cc_final: 0.7215 (p90) REVERT: C 542 ASN cc_start: 0.8078 (t0) cc_final: 0.7740 (t0) REVERT: C 564 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7410 (mm110) REVERT: C 568 ASP cc_start: 0.6528 (p0) cc_final: 0.5716 (p0) REVERT: C 603 ASN cc_start: 0.7974 (t0) cc_final: 0.7553 (t0) REVERT: C 725 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6935 (tm-30) REVERT: C 727 LEU cc_start: 0.8619 (mt) cc_final: 0.8330 (mt) REVERT: C 752 LEU cc_start: 0.8463 (tp) cc_final: 0.8102 (tt) REVERT: C 773 GLU cc_start: 0.7254 (tt0) cc_final: 0.6897 (tt0) REVERT: C 821 LEU cc_start: 0.7790 (tp) cc_final: 0.7503 (tt) REVERT: C 902 MET cc_start: 0.7682 (mmm) cc_final: 0.7200 (tpt) REVERT: C 934 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7752 (tt) REVERT: C 979 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6013 (m-30) REVERT: C 990 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 994 ASP cc_start: 0.7176 (m-30) cc_final: 0.6889 (t0) REVERT: C 1014 ARG cc_start: 0.7694 (tpp80) cc_final: 0.7267 (mtm-85) REVERT: C 1097 SER cc_start: 0.8684 (t) cc_final: 0.8242 (p) REVERT: C 1129 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 1137 VAL cc_start: 0.8798 (t) cc_final: 0.8411 (m) REVERT: E 207 MET cc_start: 0.6245 (mtp) cc_final: 0.6027 (mtp) REVERT: F 148 CYS cc_start: 0.3549 (OUTLIER) cc_final: 0.2979 (p) REVERT: G 67 LYS cc_start: 0.4819 (OUTLIER) cc_final: 0.4341 (tmmm) outliers start: 184 outliers final: 136 residues processed: 667 average time/residue: 0.4232 time to fit residues: 450.1228 Evaluate side-chains 675 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 523 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 219 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 215 optimal weight: 0.0370 chunk 384 optimal weight: 50.0000 chunk 240 optimal weight: 1.9990 chunk 234 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32130 Z= 0.243 Angle : 0.583 14.953 43725 Z= 0.290 Chirality : 0.045 0.274 4965 Planarity : 0.004 0.052 5648 Dihedral : 7.167 81.448 4958 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 5.57 % Allowed : 17.74 % Favored : 76.69 % 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: -2.40 (0.13), residues: 3963 helix: 1.19 (0.21), residues: 663 sheet: -1.57 (0.18), residues: 789 loop : -2.55 (0.11), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 PHE 0.027 0.001 PHE C 106 TYR 0.024 0.001 TYR B1067 ARG 0.008 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 531 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: A 51 THR cc_start: 0.8124 (t) cc_final: 0.7610 (p) REVERT: A 52 GLN cc_start: 0.8048 (tp40) cc_final: 0.7800 (tp40) REVERT: A 105 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 129 LYS cc_start: 0.7457 (ttmm) cc_final: 0.6974 (ttmm) REVERT: A 186 ASN cc_start: 0.6535 (OUTLIER) cc_final: 0.6096 (p0) REVERT: A 220 PHE cc_start: 0.7408 (t80) cc_final: 0.6991 (t80) REVERT: A 315 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8290 (p) REVERT: A 319 ARG cc_start: 0.6954 (ttm110) cc_final: 0.6198 (mtm-85) REVERT: A 324 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6695 (mt-10) REVERT: A 537 LYS cc_start: 0.7929 (tttp) cc_final: 0.7433 (tttt) REVERT: A 541 PHE cc_start: 0.8054 (p90) cc_final: 0.7768 (p90) REVERT: A 596 SER cc_start: 0.8587 (m) cc_final: 0.8146 (p) REVERT: A 602 THR cc_start: 0.7969 (m) cc_final: 0.7695 (p) REVERT: A 607 GLN cc_start: 0.7951 (mt0) cc_final: 0.7628 (mp10) REVERT: A 656 VAL cc_start: 0.8413 (t) cc_final: 0.8071 (t) REVERT: A 740 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7040 (mmm) REVERT: A 749 CYS cc_start: 0.5456 (t) cc_final: 0.5097 (t) REVERT: A 765 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6876 (ttp-170) REVERT: A 854 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7694 (tttm) REVERT: A 904 TYR cc_start: 0.6876 (m-10) cc_final: 0.5769 (m-10) REVERT: A 916 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7669 (tt) REVERT: A 933 LYS cc_start: 0.8217 (mttm) cc_final: 0.7995 (mttp) REVERT: A 950 ASP cc_start: 0.7214 (t70) cc_final: 0.6733 (t70) REVERT: A 964 LYS cc_start: 0.8264 (tmtm) cc_final: 0.8014 (ttmm) REVERT: A 965 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: A 984 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 1002 GLN cc_start: 0.7375 (tp-100) cc_final: 0.7056 (tp-100) REVERT: A 1097 SER cc_start: 0.8495 (t) cc_final: 0.8144 (p) REVERT: B 33 THR cc_start: 0.8423 (m) cc_final: 0.8135 (t) REVERT: B 41 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7612 (mtpp) REVERT: B 129 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7895 (ptpp) REVERT: B 130 VAL cc_start: 0.7473 (t) cc_final: 0.6999 (p) REVERT: B 193 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7662 (ttpt) REVERT: B 200 LYS cc_start: 0.8252 (mttm) cc_final: 0.7958 (mtmt) REVERT: B 319 ARG cc_start: 0.7629 (ptp-110) cc_final: 0.6998 (mtp85) REVERT: B 355 ARG cc_start: 0.4803 (OUTLIER) cc_final: 0.4272 (tmt90) REVERT: B 362 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.6206 (p) REVERT: B 406 GLU cc_start: 0.5705 (pt0) cc_final: 0.5417 (pt0) REVERT: B 537 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7710 (ptmm) REVERT: B 544 ASN cc_start: 0.7600 (t0) cc_final: 0.7084 (t0) REVERT: B 558 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7423 (mtpp) REVERT: B 591 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.7818 (p) REVERT: B 619 GLU cc_start: 0.6883 (tt0) cc_final: 0.6197 (tp30) REVERT: B 725 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6756 (tm-30) REVERT: B 726 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (mt) REVERT: B 747 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7047 (p) REVERT: B 751 ASN cc_start: 0.8176 (m-40) cc_final: 0.7796 (m110) REVERT: B 765 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7529 (mtm110) REVERT: B 773 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6098 (tm-30) REVERT: B 820 ASP cc_start: 0.7470 (t0) cc_final: 0.7253 (t0) REVERT: B 902 MET cc_start: 0.7765 (tpp) cc_final: 0.7162 (tpp) REVERT: B 933 LYS cc_start: 0.7712 (mtmt) cc_final: 0.7439 (mtpp) REVERT: B 963 VAL cc_start: 0.8745 (p) cc_final: 0.8473 (t) REVERT: B 964 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7866 (ttmm) REVERT: B 974 SER cc_start: 0.7661 (p) cc_final: 0.7453 (m) REVERT: B 980 ILE cc_start: 0.8653 (mt) cc_final: 0.8412 (mm) REVERT: B 1107 ARG cc_start: 0.6942 (mtt90) cc_final: 0.5649 (mtt180) REVERT: B 1113 GLN cc_start: 0.7764 (mt0) cc_final: 0.7535 (mt0) REVERT: B 1118 ASP cc_start: 0.7015 (t70) cc_final: 0.6562 (t0) REVERT: C 81 ASN cc_start: 0.8389 (m-40) cc_final: 0.8063 (m-40) REVERT: C 168 PHE cc_start: 0.8519 (t80) cc_final: 0.7905 (t80) REVERT: C 190 PHE cc_start: 0.7533 (m-80) cc_final: 0.7301 (m-80) REVERT: C 239 GLN cc_start: 0.6792 (tp-100) cc_final: 0.6529 (tm-30) REVERT: C 266 TYR cc_start: 0.6449 (m-10) cc_final: 0.6198 (m-10) REVERT: C 269 TYR cc_start: 0.7782 (m-10) cc_final: 0.7384 (m-80) REVERT: C 298 GLU cc_start: 0.7341 (tp30) cc_final: 0.7034 (tp30) REVERT: C 541 PHE cc_start: 0.7551 (p90) cc_final: 0.7250 (p90) REVERT: C 542 ASN cc_start: 0.8088 (t0) cc_final: 0.7766 (t0) REVERT: C 568 ASP cc_start: 0.6453 (p0) cc_final: 0.5643 (p0) REVERT: C 603 ASN cc_start: 0.8014 (t0) cc_final: 0.7596 (t0) REVERT: C 725 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6992 (tm-30) REVERT: C 727 LEU cc_start: 0.8673 (mt) cc_final: 0.8355 (mt) REVERT: C 745 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: C 752 LEU cc_start: 0.8491 (tp) cc_final: 0.8137 (tt) REVERT: C 773 GLU cc_start: 0.7276 (tt0) cc_final: 0.6896 (tt0) REVERT: C 821 LEU cc_start: 0.7801 (tp) cc_final: 0.7516 (tt) REVERT: C 934 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7742 (tt) REVERT: C 979 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6162 (m-30) REVERT: C 990 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: C 994 ASP cc_start: 0.7262 (m-30) cc_final: 0.6961 (t0) REVERT: C 1014 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7266 (mtm-85) REVERT: C 1084 ASP cc_start: 0.7630 (m-30) cc_final: 0.7374 (t70) REVERT: C 1097 SER cc_start: 0.8678 (t) cc_final: 0.8205 (p) REVERT: C 1129 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.8031 (p) REVERT: C 1137 VAL cc_start: 0.8813 (t) cc_final: 0.8430 (m) REVERT: D 49 MET cc_start: 0.2700 (ppp) cc_final: 0.1625 (ppp) REVERT: E 207 MET cc_start: 0.6230 (mtp) cc_final: 0.6025 (mtp) REVERT: F 148 CYS cc_start: 0.3687 (OUTLIER) cc_final: 0.3090 (p) REVERT: G 67 LYS cc_start: 0.4838 (OUTLIER) cc_final: 0.4325 (tmmm) outliers start: 191 outliers final: 139 residues processed: 666 average time/residue: 0.4354 time to fit residues: 459.7144 Evaluate side-chains 684 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 525 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 229 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 262 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 302 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 613 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN G 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32130 Z= 0.177 Angle : 0.577 15.162 43725 Z= 0.284 Chirality : 0.044 0.262 4965 Planarity : 0.004 0.050 5648 Dihedral : 7.116 81.285 4956 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.81 % Allowed : 18.59 % Favored : 76.60 % 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: -2.30 (0.13), residues: 3963 helix: 1.33 (0.22), residues: 664 sheet: -1.47 (0.18), residues: 794 loop : -2.51 (0.11), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 241 HIS 0.004 0.001 HIS B1083 PHE 0.032 0.001 PHE A 592 TYR 0.017 0.001 TYR B 265 ARG 0.006 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 535 time to evaluate : 3.520 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 52 GLN cc_start: 0.8031 (tp40) cc_final: 0.7781 (tp40) REVERT: A 105 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7743 (mt) REVERT: A 129 LYS cc_start: 0.7425 (ttmm) cc_final: 0.6898 (ttmm) REVERT: A 220 PHE cc_start: 0.7435 (t80) cc_final: 0.7036 (t80) REVERT: A 324 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6864 (mt-10) REVERT: A 537 LYS cc_start: 0.8014 (tttp) cc_final: 0.7491 (tttt) REVERT: A 541 PHE cc_start: 0.8062 (p90) cc_final: 0.7764 (p90) REVERT: A 596 SER cc_start: 0.8575 (m) cc_final: 0.8118 (p) REVERT: A 602 THR cc_start: 0.7967 (m) cc_final: 0.7671 (p) REVERT: A 607 GLN cc_start: 0.7951 (mt0) cc_final: 0.7607 (mp10) REVERT: A 656 VAL cc_start: 0.8275 (t) cc_final: 0.7990 (t) REVERT: A 697 MET cc_start: 0.7836 (ptp) cc_final: 0.7625 (ptm) REVERT: A 740 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6940 (mmm) REVERT: A 749 CYS cc_start: 0.5444 (t) cc_final: 0.5084 (t) REVERT: A 765 ARG cc_start: 0.7188 (ttp-110) cc_final: 0.6775 (ttp-170) REVERT: A 854 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7609 (tttp) REVERT: A 904 TYR cc_start: 0.6811 (m-10) cc_final: 0.5765 (m-10) REVERT: A 950 ASP cc_start: 0.7135 (t70) cc_final: 0.6738 (t70) REVERT: A 964 LYS cc_start: 0.8249 (tmtm) cc_final: 0.8006 (ttmm) REVERT: A 965 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: A 984 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 1002 GLN cc_start: 0.7307 (tp-100) cc_final: 0.7024 (tp-100) REVERT: A 1038 LYS cc_start: 0.8169 (mtmp) cc_final: 0.7901 (mtmm) REVERT: A 1097 SER cc_start: 0.8490 (t) cc_final: 0.8140 (p) REVERT: B 33 THR cc_start: 0.8355 (m) cc_final: 0.8053 (t) REVERT: B 41 LYS cc_start: 0.7848 (mtpp) cc_final: 0.7602 (mtpp) REVERT: B 105 ILE cc_start: 0.8180 (mm) cc_final: 0.7975 (mp) REVERT: B 129 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7837 (ptpp) REVERT: B 130 VAL cc_start: 0.7417 (t) cc_final: 0.6974 (p) REVERT: B 187 LEU cc_start: 0.8190 (tp) cc_final: 0.7972 (tp) REVERT: B 193 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7629 (ttpt) REVERT: B 200 LYS cc_start: 0.8244 (mttm) cc_final: 0.7933 (mtmt) REVERT: B 228 ASP cc_start: 0.7394 (t70) cc_final: 0.6887 (t0) REVERT: B 319 ARG cc_start: 0.7637 (ptp-110) cc_final: 0.7015 (mtp85) REVERT: B 355 ARG cc_start: 0.4818 (OUTLIER) cc_final: 0.4297 (tmt90) REVERT: B 362 VAL cc_start: 0.6482 (OUTLIER) cc_final: 0.6241 (p) REVERT: B 537 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7682 (ptmm) REVERT: B 544 ASN cc_start: 0.7562 (t0) cc_final: 0.7052 (t0) REVERT: B 558 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7419 (mtpp) REVERT: B 591 SER cc_start: 0.8505 (t) cc_final: 0.7890 (p) REVERT: B 619 GLU cc_start: 0.6784 (tt0) cc_final: 0.5959 (tp30) REVERT: B 725 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6782 (tm-30) REVERT: B 726 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8115 (mt) REVERT: B 747 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6953 (p) REVERT: B 751 ASN cc_start: 0.8159 (m-40) cc_final: 0.7783 (m110) REVERT: B 765 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7483 (mtm110) REVERT: B 902 MET cc_start: 0.7651 (tpp) cc_final: 0.7015 (tpp) REVERT: B 933 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7340 (mtpp) REVERT: B 963 VAL cc_start: 0.8743 (p) cc_final: 0.8442 (t) REVERT: B 964 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7876 (ttmm) REVERT: B 974 SER cc_start: 0.7602 (p) cc_final: 0.7387 (m) REVERT: B 980 ILE cc_start: 0.8661 (mt) cc_final: 0.8430 (mm) REVERT: B 1084 ASP cc_start: 0.7307 (p0) cc_final: 0.6763 (p0) REVERT: B 1107 ARG cc_start: 0.6925 (mtt90) cc_final: 0.5548 (mtt180) REVERT: B 1113 GLN cc_start: 0.7754 (mt0) cc_final: 0.7516 (mt0) REVERT: B 1118 ASP cc_start: 0.7028 (t70) cc_final: 0.6687 (t0) REVERT: C 51 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7838 (p) REVERT: C 81 ASN cc_start: 0.8376 (m-40) cc_final: 0.8040 (m-40) REVERT: C 129 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7629 (ttmt) REVERT: C 168 PHE cc_start: 0.8391 (t80) cc_final: 0.7799 (t80) REVERT: C 190 PHE cc_start: 0.7454 (m-80) cc_final: 0.7223 (m-80) REVERT: C 239 GLN cc_start: 0.6888 (tp-100) cc_final: 0.6634 (tm-30) REVERT: C 269 TYR cc_start: 0.7740 (m-10) cc_final: 0.7298 (m-80) REVERT: C 298 GLU cc_start: 0.7368 (tp30) cc_final: 0.7105 (tp30) REVERT: C 541 PHE cc_start: 0.7552 (p90) cc_final: 0.7231 (p90) REVERT: C 542 ASN cc_start: 0.8075 (t0) cc_final: 0.7774 (t0) REVERT: C 568 ASP cc_start: 0.6401 (p0) cc_final: 0.5641 (p0) REVERT: C 603 ASN cc_start: 0.7958 (t0) cc_final: 0.7539 (t0) REVERT: C 616 ASN cc_start: 0.7151 (t0) cc_final: 0.6879 (t0) REVERT: C 643 PHE cc_start: 0.6713 (t80) cc_final: 0.6325 (t80) REVERT: C 645 THR cc_start: 0.8347 (t) cc_final: 0.7961 (p) REVERT: C 725 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6837 (tm-30) REVERT: C 727 LEU cc_start: 0.8591 (mt) cc_final: 0.8293 (mt) REVERT: C 752 LEU cc_start: 0.8454 (tp) cc_final: 0.8126 (tp) REVERT: C 773 GLU cc_start: 0.7225 (tt0) cc_final: 0.6840 (tt0) REVERT: C 821 LEU cc_start: 0.7766 (tp) cc_final: 0.7468 (tt) REVERT: C 934 ILE cc_start: 0.7873 (tp) cc_final: 0.7636 (tt) REVERT: C 979 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.6188 (m-30) REVERT: C 990 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: C 1014 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7270 (mtm-85) REVERT: C 1097 SER cc_start: 0.8664 (t) cc_final: 0.8205 (p) REVERT: C 1129 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8002 (p) REVERT: C 1137 VAL cc_start: 0.8774 (t) cc_final: 0.8376 (m) REVERT: D 49 MET cc_start: 0.2676 (ppp) cc_final: 0.1692 (ppp) REVERT: F 148 CYS cc_start: 0.3828 (OUTLIER) cc_final: 0.3142 (p) REVERT: G 67 LYS cc_start: 0.4833 (OUTLIER) cc_final: 0.4347 (tmmm) outliers start: 165 outliers final: 126 residues processed: 656 average time/residue: 0.4850 time to fit residues: 514.2063 Evaluate side-chains 659 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 518 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 50.0000 chunk 368 optimal weight: 9.9990 chunk 336 optimal weight: 50.0000 chunk 358 optimal weight: 0.4980 chunk 215 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 66 HIS B 121 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1048 HIS ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 580 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.157 32130 Z= 0.592 Angle : 0.769 16.400 43725 Z= 0.391 Chirality : 0.053 0.301 4965 Planarity : 0.005 0.057 5648 Dihedral : 7.732 81.055 4954 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 4.96 % Allowed : 19.03 % Favored : 76.01 % 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: -2.66 (0.13), residues: 3963 helix: 0.51 (0.20), residues: 671 sheet: -1.64 (0.18), residues: 769 loop : -2.61 (0.11), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 64 HIS 0.013 0.001 HIS B1064 PHE 0.034 0.003 PHE B 86 TYR 0.048 0.002 TYR B1067 ARG 0.009 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 560 time to evaluate : 3.296 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 41 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7607 (mttt) REVERT: A 95 ILE cc_start: 0.7539 (mt) cc_final: 0.7331 (tt) REVERT: A 96 GLU cc_start: 0.6473 (pt0) cc_final: 0.6012 (pt0) REVERT: A 105 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 117 LEU cc_start: 0.7792 (mt) cc_final: 0.7473 (mp) REVERT: A 129 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7195 (ttmm) REVERT: A 186 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6185 (p0) REVERT: A 188 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7642 (ptp-170) REVERT: A 220 PHE cc_start: 0.7591 (t80) cc_final: 0.7072 (t80) REVERT: A 290 ASP cc_start: 0.7330 (p0) cc_final: 0.7073 (p0) REVERT: A 304 LYS cc_start: 0.8026 (mptt) cc_final: 0.7825 (mptt) REVERT: A 319 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6403 (mtm-85) REVERT: A 324 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 537 LYS cc_start: 0.8093 (tttp) cc_final: 0.7853 (tttt) REVERT: A 541 PHE cc_start: 0.8173 (p90) cc_final: 0.7943 (p90) REVERT: A 574 ASP cc_start: 0.7610 (t70) cc_final: 0.7124 (t0) REVERT: A 602 THR cc_start: 0.8172 (m) cc_final: 0.7765 (p) REVERT: A 607 GLN cc_start: 0.7999 (mt0) cc_final: 0.7713 (mp10) REVERT: A 656 VAL cc_start: 0.8359 (t) cc_final: 0.8142 (t) REVERT: A 670 ILE cc_start: 0.8547 (mm) cc_final: 0.8263 (mt) REVERT: A 749 CYS cc_start: 0.5535 (t) cc_final: 0.5133 (t) REVERT: A 765 ARG cc_start: 0.7496 (ttp-110) cc_final: 0.7120 (ttp-170) REVERT: A 854 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7992 (tttp) REVERT: A 904 TYR cc_start: 0.7152 (m-10) cc_final: 0.6520 (m-10) REVERT: A 950 ASP cc_start: 0.7162 (t70) cc_final: 0.6846 (t0) REVERT: A 964 LYS cc_start: 0.8237 (tmtm) cc_final: 0.7929 (ttmm) REVERT: A 965 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: A 984 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7956 (tt) REVERT: A 1002 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7277 (tp-100) REVERT: A 1086 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7297 (mtmm) REVERT: A 1091 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7256 (ttm-80) REVERT: A 1097 SER cc_start: 0.8497 (t) cc_final: 0.8095 (p) REVERT: B 41 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7650 (mtpp) REVERT: B 105 ILE cc_start: 0.8251 (mm) cc_final: 0.8047 (mt) REVERT: B 129 LYS cc_start: 0.8258 (ptpt) cc_final: 0.7953 (ptpp) REVERT: B 130 VAL cc_start: 0.7704 (t) cc_final: 0.7137 (p) REVERT: B 193 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7693 (ttpt) REVERT: B 200 LYS cc_start: 0.8264 (mttm) cc_final: 0.8064 (mttt) REVERT: B 228 ASP cc_start: 0.7530 (t70) cc_final: 0.7066 (t0) REVERT: B 236 THR cc_start: 0.7985 (p) cc_final: 0.7733 (m) REVERT: B 355 ARG cc_start: 0.4716 (OUTLIER) cc_final: 0.4077 (tmt90) REVERT: B 536 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 537 LYS cc_start: 0.8381 (ttpt) cc_final: 0.7948 (ptmm) REVERT: B 544 ASN cc_start: 0.7747 (t0) cc_final: 0.7295 (t0) REVERT: B 558 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7449 (mtpp) REVERT: B 560 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7384 (mt) REVERT: B 591 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8117 (m) REVERT: B 619 GLU cc_start: 0.7188 (tt0) cc_final: 0.6543 (tp30) REVERT: B 725 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 726 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 737 ASP cc_start: 0.6983 (m-30) cc_final: 0.6742 (m-30) REVERT: B 751 ASN cc_start: 0.8183 (m-40) cc_final: 0.7685 (m110) REVERT: B 765 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7501 (mtm110) REVERT: B 803 SER cc_start: 0.8394 (m) cc_final: 0.8089 (p) REVERT: B 933 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7653 (mtpp) REVERT: B 963 VAL cc_start: 0.8774 (p) cc_final: 0.8535 (t) REVERT: B 964 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7956 (ttmm) REVERT: B 1002 GLN cc_start: 0.7734 (tp40) cc_final: 0.7101 (tp40) REVERT: B 1097 SER cc_start: 0.8580 (t) cc_final: 0.8046 (p) REVERT: B 1107 ARG cc_start: 0.6953 (mtt90) cc_final: 0.6228 (mtt180) REVERT: B 1113 GLN cc_start: 0.7859 (mt0) cc_final: 0.7633 (mt0) REVERT: B 1118 ASP cc_start: 0.7059 (t70) cc_final: 0.6664 (t0) REVERT: C 81 ASN cc_start: 0.8440 (m-40) cc_final: 0.8226 (m-40) REVERT: C 129 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7622 (ttmt) REVERT: C 269 TYR cc_start: 0.7941 (m-10) cc_final: 0.7729 (m-10) REVERT: C 537 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7909 (mtpp) REVERT: C 541 PHE cc_start: 0.7663 (p90) cc_final: 0.7204 (p90) REVERT: C 542 ASN cc_start: 0.8261 (t0) cc_final: 0.7809 (t0) REVERT: C 603 ASN cc_start: 0.8156 (t0) cc_final: 0.7688 (t0) REVERT: C 604 THR cc_start: 0.8190 (p) cc_final: 0.7932 (m) REVERT: C 616 ASN cc_start: 0.7678 (t0) cc_final: 0.7363 (t0) REVERT: C 619 GLU cc_start: 0.7315 (tt0) cc_final: 0.7107 (tt0) REVERT: C 725 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6929 (tm-30) REVERT: C 752 LEU cc_start: 0.8622 (tp) cc_final: 0.8399 (tt) REVERT: C 772 VAL cc_start: 0.8580 (t) cc_final: 0.8299 (p) REVERT: C 773 GLU cc_start: 0.7346 (tt0) cc_final: 0.6993 (tt0) REVERT: C 821 LEU cc_start: 0.7789 (tp) cc_final: 0.7478 (tt) REVERT: C 979 ASP cc_start: 0.6466 (OUTLIER) cc_final: 0.6243 (m-30) REVERT: C 990 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: C 994 ASP cc_start: 0.7113 (t0) cc_final: 0.6906 (t0) REVERT: C 1014 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7320 (mtm-85) REVERT: C 1084 ASP cc_start: 0.7767 (m-30) cc_final: 0.7498 (t70) REVERT: C 1097 SER cc_start: 0.8632 (t) cc_final: 0.8149 (p) REVERT: C 1129 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 1137 VAL cc_start: 0.8835 (t) cc_final: 0.8468 (m) REVERT: E 238 MET cc_start: -0.2774 (mtm) cc_final: -0.2985 (mtm) REVERT: F 148 CYS cc_start: 0.3794 (OUTLIER) cc_final: 0.3182 (p) REVERT: G 67 LYS cc_start: 0.4918 (OUTLIER) cc_final: 0.4423 (tmmm) outliers start: 170 outliers final: 128 residues processed: 680 average time/residue: 0.4417 time to fit residues: 475.5486 Evaluate side-chains 684 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 541 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 10.0000 chunk 378 optimal weight: 30.0000 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 263 optimal weight: 3.9990 chunk 397 optimal weight: 6.9990 chunk 365 optimal weight: 0.0980 chunk 316 optimal weight: 50.0000 chunk 32 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 949 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32130 Z= 0.325 Angle : 0.657 15.962 43725 Z= 0.328 Chirality : 0.047 0.335 4965 Planarity : 0.005 0.053 5648 Dihedral : 7.435 80.923 4951 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 4.03 % Allowed : 20.34 % Favored : 75.63 % 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: -2.47 (0.13), residues: 3963 helix: 0.87 (0.21), residues: 667 sheet: -1.49 (0.18), residues: 772 loop : -2.56 (0.11), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1102 HIS 0.018 0.001 HIS A 66 PHE 0.028 0.002 PHE A 981 TYR 0.031 0.001 TYR B1067 ARG 0.006 0.000 ARG B 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 535 time to evaluate : 3.566 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 41 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7509 (mtpt) REVERT: A 95 ILE cc_start: 0.7505 (mt) cc_final: 0.7291 (tt) REVERT: A 96 GLU cc_start: 0.6656 (pt0) cc_final: 0.6151 (pt0) REVERT: A 105 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7780 (mt) REVERT: A 117 LEU cc_start: 0.7569 (mt) cc_final: 0.7274 (mp) REVERT: A 129 LYS cc_start: 0.7578 (ttmm) cc_final: 0.6998 (ttmm) REVERT: A 188 ARG cc_start: 0.7755 (ptp-170) cc_final: 0.7390 (ptp90) REVERT: A 220 PHE cc_start: 0.7585 (t80) cc_final: 0.7183 (t80) REVERT: A 228 ASP cc_start: 0.7375 (m-30) cc_final: 0.6981 (p0) REVERT: A 290 ASP cc_start: 0.7139 (p0) cc_final: 0.6845 (p0) REVERT: A 319 ARG cc_start: 0.7075 (ttm110) cc_final: 0.6606 (mtm-85) REVERT: A 324 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 537 LYS cc_start: 0.8125 (tttp) cc_final: 0.7659 (mtpt) REVERT: A 596 SER cc_start: 0.8597 (m) cc_final: 0.8144 (p) REVERT: A 602 THR cc_start: 0.8120 (m) cc_final: 0.7740 (p) REVERT: A 607 GLN cc_start: 0.7992 (mt0) cc_final: 0.7636 (mp10) REVERT: A 670 ILE cc_start: 0.8491 (mm) cc_final: 0.8195 (mt) REVERT: A 749 CYS cc_start: 0.5494 (t) cc_final: 0.5085 (t) REVERT: A 765 ARG cc_start: 0.7336 (ttp-110) cc_final: 0.6945 (ttp-170) REVERT: A 854 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7931 (tttp) REVERT: A 904 TYR cc_start: 0.7046 (m-10) cc_final: 0.6287 (m-10) REVERT: A 950 ASP cc_start: 0.7101 (t70) cc_final: 0.6572 (t0) REVERT: A 964 LYS cc_start: 0.8217 (tmtm) cc_final: 0.7964 (ttmm) REVERT: A 965 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: A 984 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7949 (tt) REVERT: A 994 ASP cc_start: 0.7552 (t70) cc_final: 0.7260 (t0) REVERT: A 1002 GLN cc_start: 0.7387 (tp-100) cc_final: 0.7116 (tp-100) REVERT: A 1086 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7345 (ttmm) REVERT: A 1091 ARG cc_start: 0.7642 (ttm170) cc_final: 0.7256 (ttm-80) REVERT: A 1097 SER cc_start: 0.8481 (t) cc_final: 0.8087 (p) REVERT: A 1139 ASP cc_start: 0.7379 (t0) cc_final: 0.7176 (t0) REVERT: B 41 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7643 (mtpp) REVERT: B 129 LYS cc_start: 0.8198 (ptpt) cc_final: 0.7868 (ptpp) REVERT: B 130 VAL cc_start: 0.7574 (t) cc_final: 0.7029 (p) REVERT: B 168 PHE cc_start: 0.7791 (t80) cc_final: 0.7580 (t80) REVERT: B 189 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7257 (mt-10) REVERT: B 193 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7667 (ttpt) REVERT: B 200 LYS cc_start: 0.8272 (mttm) cc_final: 0.8068 (mttt) REVERT: B 228 ASP cc_start: 0.7508 (t70) cc_final: 0.7048 (t0) REVERT: B 236 THR cc_start: 0.7849 (p) cc_final: 0.7628 (m) REVERT: B 319 ARG cc_start: 0.7748 (ptp-110) cc_final: 0.6985 (mtp85) REVERT: B 355 ARG cc_start: 0.4725 (OUTLIER) cc_final: 0.4204 (tmt90) REVERT: B 537 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7776 (ptmm) REVERT: B 544 ASN cc_start: 0.7653 (t0) cc_final: 0.7231 (t0) REVERT: B 558 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7438 (mtpp) REVERT: B 591 SER cc_start: 0.8421 (t) cc_final: 0.8088 (m) REVERT: B 619 GLU cc_start: 0.7031 (tt0) cc_final: 0.6311 (tp30) REVERT: B 725 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6637 (tm-30) REVERT: B 726 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8174 (mt) REVERT: B 737 ASP cc_start: 0.6853 (m-30) cc_final: 0.6536 (m-30) REVERT: B 751 ASN cc_start: 0.8145 (m-40) cc_final: 0.7673 (m110) REVERT: B 765 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7468 (mtm110) REVERT: B 803 SER cc_start: 0.8325 (m) cc_final: 0.8041 (p) REVERT: B 933 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7514 (mtpp) REVERT: B 963 VAL cc_start: 0.8772 (p) cc_final: 0.8506 (t) REVERT: B 964 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7933 (ttmm) REVERT: B 1107 ARG cc_start: 0.6938 (mtt90) cc_final: 0.6053 (mtt180) REVERT: B 1113 GLN cc_start: 0.7797 (mt0) cc_final: 0.7528 (mt0) REVERT: B 1118 ASP cc_start: 0.7094 (t70) cc_final: 0.6680 (t0) REVERT: C 121 ASN cc_start: 0.6647 (m-40) cc_final: 0.6337 (t0) REVERT: C 168 PHE cc_start: 0.8570 (t80) cc_final: 0.8110 (t80) REVERT: C 269 TYR cc_start: 0.7916 (m-10) cc_final: 0.7584 (m-10) REVERT: C 537 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7877 (mtpp) REVERT: C 541 PHE cc_start: 0.7605 (p90) cc_final: 0.7137 (p90) REVERT: C 542 ASN cc_start: 0.8234 (t0) cc_final: 0.7793 (t0) REVERT: C 568 ASP cc_start: 0.6350 (p0) cc_final: 0.5632 (p0) REVERT: C 603 ASN cc_start: 0.8063 (t0) cc_final: 0.7634 (t0) REVERT: C 616 ASN cc_start: 0.7542 (t0) cc_final: 0.7284 (t0) REVERT: C 619 GLU cc_start: 0.7186 (tt0) cc_final: 0.6939 (tt0) REVERT: C 723 THR cc_start: 0.8382 (t) cc_final: 0.8134 (p) REVERT: C 725 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7012 (tm-30) REVERT: C 742 ILE cc_start: 0.8609 (mm) cc_final: 0.8382 (mt) REVERT: C 761 THR cc_start: 0.8270 (t) cc_final: 0.8006 (p) REVERT: C 765 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7475 (ttp80) REVERT: C 772 VAL cc_start: 0.8559 (t) cc_final: 0.8259 (p) REVERT: C 773 GLU cc_start: 0.7306 (tt0) cc_final: 0.6932 (tt0) REVERT: C 821 LEU cc_start: 0.7753 (tp) cc_final: 0.7452 (tt) REVERT: C 902 MET cc_start: 0.7861 (mmm) cc_final: 0.7354 (tpt) REVERT: C 934 ILE cc_start: 0.8121 (tt) cc_final: 0.7898 (tt) REVERT: C 979 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6229 (m-30) REVERT: C 990 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: C 994 ASP cc_start: 0.7128 (t0) cc_final: 0.6716 (t0) REVERT: C 1014 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7296 (mtm-85) REVERT: C 1019 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6785 (ttp80) REVERT: C 1031 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 1084 ASP cc_start: 0.7674 (m-30) cc_final: 0.7426 (t70) REVERT: C 1097 SER cc_start: 0.8618 (t) cc_final: 0.8131 (p) REVERT: C 1129 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8086 (p) REVERT: D 49 MET cc_start: 0.2662 (ppp) cc_final: 0.1665 (ppp) REVERT: E 238 MET cc_start: -0.2738 (mtm) cc_final: -0.3188 (mtm) REVERT: F 148 CYS cc_start: 0.3846 (OUTLIER) cc_final: 0.3261 (p) REVERT: G 67 LYS cc_start: 0.4900 (OUTLIER) cc_final: 0.4398 (tmmm) outliers start: 138 outliers final: 113 residues processed: 638 average time/residue: 0.4327 time to fit residues: 436.3531 Evaluate side-chains 650 residues out of total 3478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 526 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 3.9990 chunk 337 optimal weight: 50.0000 chunk 96 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 317 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 949 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.213558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153213 restraints weight = 50620.397| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.38 r_work: 0.3335 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 32130 Z= 0.444 Angle : 0.811 59.144 43725 Z= 0.445 Chirality : 0.050 0.571 4965 Planarity : 0.005 0.198 5648 Dihedral : 7.454 80.923 4951 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 4.00 % Allowed : 20.51 % Favored : 75.49 % Cbeta Deviations : 0.05 % 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: -2.49 (0.13), residues: 3963 helix: 0.81 (0.21), residues: 668 sheet: -1.49 (0.18), residues: 772 loop : -2.56 (0.11), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.332 0.005 HIS A 66 PHE 0.034 0.002 PHE A 541 TYR 0.030 0.002 TYR B1067 ARG 0.005 0.000 ARG C 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8834.42 seconds wall clock time: 159 minutes 27.60 seconds (9567.60 seconds total)