Starting phenix.real_space_refine on Tue Mar 19 19:12:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxc_26857/03_2024/7uxc_26857_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxc_26857/03_2024/7uxc_26857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxc_26857/03_2024/7uxc_26857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxc_26857/03_2024/7uxc_26857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxc_26857/03_2024/7uxc_26857_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxc_26857/03_2024/7uxc_26857_trim_updated.pdb" } resolution = 3.2 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= 0.030 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 293 5.16 5 C 30191 2.51 5 N 8255 2.21 5 O 8825 1.98 5 H 47565 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1967": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2255": "OE1" <-> "OE2" Residue "A ASP 2517": "OD1" <-> "OD2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 530": "OE1" <-> "OE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1134": "OE1" <-> "OE2" Residue "C ASP 1160": "OD1" <-> "OD2" Residue "C TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 287": "OD1" <-> "OD2" Residue "L PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 95147 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 35404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2188, 35404 Classifications: {'peptide': 2188} Link IDs: {'PTRANS': 84, 'TRANS': 2103} Chain breaks: 14 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4797 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "C" Number of atoms: 18025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 18025 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 65, 'TRANS': 1067} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4882 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 4523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4523 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain breaks: 2 Chain: "F" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1738 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain breaks: 1 Chain: "G" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1888 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "H" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1892 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "I" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1294 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "J" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1311 Classifications: {'peptide': 89} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "K" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4889 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4446 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain breaks: 2 Chain: "M" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1791 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1888 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "O" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1892 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1294 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "Q" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1311 Classifications: {'peptide': 89} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "R" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1724 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 9, 'TRANS': 97} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.71, per 1000 atoms: 0.35 Number of scatterers: 95147 At special positions: 0 Unit cell: (186.9, 306.6, 166.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 293 16.00 P 16 15.00 Mg 2 11.99 O 8825 8.00 N 8255 7.00 C 30191 6.00 H 47565 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.70 Conformation dependent library (CDL) restraints added in 8.6 seconds 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 35 sheets defined 49.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.29 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.803A pdb=" N ASN A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.723A pdb=" N GLU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 156 removed outlier: 4.017A pdb=" N ALA A 142 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 143 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.506A pdb=" N GLN A 185 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 187 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN A 188 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Proline residue: A 189 - end of helix removed outlier: 4.327A pdb=" N ILE A 194 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 360 through 368 Processing helix chain 'A' and resid 370 through 382 removed outlier: 4.721A pdb=" N ASN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 402 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.723A pdb=" N VAL A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 481 through 493 removed outlier: 4.226A pdb=" N MET A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 511 removed outlier: 5.414A pdb=" N GLN A 499 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 506 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 529 through 547 removed outlier: 4.529A pdb=" N LYS A 533 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 534 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 535 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 616 through 631 removed outlier: 5.041A pdb=" N THR A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 690 through 701 removed outlier: 4.706A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 Processing helix chain 'A' and resid 723 through 742 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.626A pdb=" N VAL A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 removed outlier: 3.503A pdb=" N VAL A 817 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP A 818 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 819 " --> pdb=" O TRP A 816 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 829 " --> pdb=" O ASP A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 864 through 872 removed outlier: 4.074A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 943 through 959 Proline residue: A 948 - end of helix Processing helix chain 'A' and resid 962 through 982 removed outlier: 5.182A pdb=" N HIS A 966 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR A 969 " --> pdb=" O HIS A 966 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1003 Proline residue: A 991 - end of helix removed outlier: 4.775A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1009 through 1041 removed outlier: 6.738A pdb=" N SER A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS A1026 " --> pdb=" O PHE A1022 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG A1028 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 4.393A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1083 removed outlier: 7.590A pdb=" N GLY A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLU A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A1070 " --> pdb=" O GLU A1066 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1091 through 1102 removed outlier: 3.762A pdb=" N LEU A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1107 Processing helix chain 'A' and resid 1111 through 1123 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1129 through 1144 removed outlier: 4.035A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1165 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1170 through 1184 Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1192 through 1201 Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1266 through 1269 No H-bonds generated for 'chain 'A' and resid 1266 through 1269' Processing helix chain 'A' and resid 1277 through 1293 Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 3.780A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1318 through 1328 removed outlier: 4.298A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1346 Processing helix chain 'A' and resid 1351 through 1366 Processing helix chain 'A' and resid 1374 through 1376 No H-bonds generated for 'chain 'A' and resid 1374 through 1376' Processing helix chain 'A' and resid 1380 through 1389 Processing helix chain 'A' and resid 1393 through 1406 Processing helix chain 'A' and resid 1410 through 1422 Processing helix chain 'A' and resid 1426 through 1439 Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'A' and resid 1456 through 1467 Processing helix chain 'A' and resid 1474 through 1487 Processing helix chain 'A' and resid 1490 through 1499 Processing helix chain 'A' and resid 1506 through 1523 removed outlier: 4.331A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 4.594A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 Processing helix chain 'A' and resid 1557 through 1579 removed outlier: 4.312A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1605 removed outlier: 4.751A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1624 removed outlier: 4.022A pdb=" N ARG A1612 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU A1613 " --> pdb=" O GLU A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1642 removed outlier: 4.221A pdb=" N LEU A1642 " --> pdb=" O MET A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1662 Processing helix chain 'A' and resid 1666 through 1677 Processing helix chain 'A' and resid 1694 through 1706 Processing helix chain 'A' and resid 1710 through 1730 Processing helix chain 'A' and resid 1738 through 1762 Processing helix chain 'A' and resid 1766 through 1782 Proline residue: A1770 - end of helix Processing helix chain 'A' and resid 1787 through 1811 Processing helix chain 'A' and resid 1868 through 1877 Processing helix chain 'A' and resid 1881 through 1895 Processing helix chain 'A' and resid 1901 through 1913 Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1934 through 1945 removed outlier: 3.915A pdb=" N ILE A1939 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Proline residue: A1940 - end of helix removed outlier: 3.727A pdb=" N ILE A1943 " --> pdb=" O PRO A1940 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A1944 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1966 removed outlier: 4.071A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1971 No H-bonds generated for 'chain 'A' and resid 1969 through 1971' Processing helix chain 'A' and resid 1973 through 1981 removed outlier: 3.819A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2020 removed outlier: 4.260A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR A2004 " --> pdb=" O GLU A2000 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU A2005 " --> pdb=" O HIS A2001 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A2006 " --> pdb=" O SER A2002 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN A2007 " --> pdb=" O ASN A2003 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A2015 " --> pdb=" O MET A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2023 through 2041 Processing helix chain 'A' and resid 2045 through 2058 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2065 through 2091 removed outlier: 5.789A pdb=" N ARG A2076 " --> pdb=" O GLN A2072 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A2078 " --> pdb=" O TYR A2074 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2113 removed outlier: 4.203A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2128 through 2131 No H-bonds generated for 'chain 'A' and resid 2128 through 2131' Processing helix chain 'A' and resid 2193 through 2211 Processing helix chain 'A' and resid 2213 through 2218 Processing helix chain 'A' and resid 2246 through 2256 Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2275 through 2277 No H-bonds generated for 'chain 'A' and resid 2275 through 2277' Processing helix chain 'A' and resid 2280 through 2292 Processing helix chain 'A' and resid 2298 through 2306 Processing helix chain 'A' and resid 2310 through 2334 Processing helix chain 'A' and resid 2381 through 2385 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2422 Processing helix chain 'A' and resid 2493 through 2508 Processing helix chain 'A' and resid 2521 through 2532 Processing helix chain 'A' and resid 2535 through 2539 Processing helix chain 'C' and resid 33 through 36 No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 127 through 140 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 200 through 222 Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 262 through 268 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.777A pdb=" N GLU C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 297' Processing helix chain 'C' and resid 313 through 327 Processing helix chain 'C' and resid 330 through 336 Processing helix chain 'C' and resid 341 through 360 removed outlier: 3.557A pdb=" N LEU C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 391 Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 408 through 420 Processing helix chain 'C' and resid 431 through 438 Proline residue: C 434 - end of helix Processing helix chain 'C' and resid 446 through 459 removed outlier: 3.813A pdb=" N LEU C 459 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 473 through 481 removed outlier: 3.891A pdb=" N LEU C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 499 Proline residue: C 489 - end of helix removed outlier: 3.657A pdb=" N VAL C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP C 495 " --> pdb=" O VAL C 492 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 499 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 511 removed outlier: 3.640A pdb=" N GLN C 506 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 511 " --> pdb=" O ASP C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 531 through 542 Processing helix chain 'C' and resid 547 through 554 Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 571 through 584 Processing helix chain 'C' and resid 589 through 597 Processing helix chain 'C' and resid 600 through 604 Processing helix chain 'C' and resid 613 through 624 Processing helix chain 'C' and resid 637 through 651 removed outlier: 3.866A pdb=" N GLN C 650 " --> pdb=" O MET C 646 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU C 651 " --> pdb=" O MET C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 673 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 781 through 788 Processing helix chain 'C' and resid 807 through 819 Processing helix chain 'C' and resid 824 through 841 Processing helix chain 'C' and resid 959 through 968 removed outlier: 4.022A pdb=" N TYR C 966 " --> pdb=" O TRP C 962 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C 968 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1006 removed outlier: 3.813A pdb=" N ASN C 995 " --> pdb=" O ARG C 991 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 996 " --> pdb=" O PHE C 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 78 through 81 No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 99 through 116 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 134 through 150 removed outlier: 3.686A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.658A pdb=" N TRP D 173 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER D 174 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 177 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.991A pdb=" N LYS D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 300 removed outlier: 3.923A pdb=" N LYS D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 81 Processing helix chain 'E' and resid 151 through 167 Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 185 through 203 removed outlier: 3.834A pdb=" N ILE E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 235 removed outlier: 3.690A pdb=" N PHE E 229 " --> pdb=" O PHE E 226 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN E 234 " --> pdb=" O LYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 254 Processing helix chain 'E' and resid 279 through 299 Processing helix chain 'E' and resid 346 through 366 removed outlier: 5.758A pdb=" N GLY E 350 " --> pdb=" O GLU E 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 78 through 98 Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 126 through 144 Processing helix chain 'G' and resid 4 through 14 removed outlier: 3.628A pdb=" N ALA G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 63 removed outlier: 4.028A pdb=" N ASN G 59 " --> pdb=" O TYR G 56 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY G 60 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN G 62 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA G 63 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 123 removed outlier: 3.619A pdb=" N TYR G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Proline residue: G 118 - end of helix removed outlier: 3.833A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 removed outlier: 4.466A pdb=" N LYS H 12 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) Proline residue: H 14 - end of helix Processing helix chain 'H' and resid 47 through 62 removed outlier: 3.688A pdb=" N SER H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU H 55 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 4.273A pdb=" N GLU H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Proline residue: H 112 - end of helix removed outlier: 4.575A pdb=" N GLN H 119 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 50 Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'K' and resid 20 through 28 Processing helix chain 'K' and resid 33 through 38 removed outlier: 3.517A pdb=" N ARG K 37 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 73 Processing helix chain 'K' and resid 78 through 81 No H-bonds generated for 'chain 'K' and resid 78 through 81' Processing helix chain 'K' and resid 99 through 116 Processing helix chain 'K' and resid 129 through 131 No H-bonds generated for 'chain 'K' and resid 129 through 131' Processing helix chain 'K' and resid 134 through 149 removed outlier: 3.551A pdb=" N ASP K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU K 139 " --> pdb=" O ASP K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 179 removed outlier: 3.675A pdb=" N TYR K 170 " --> pdb=" O GLU K 167 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP K 173 " --> pdb=" O TYR K 170 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER K 174 " --> pdb=" O LYS K 171 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 177 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR K 178 " --> pdb=" O SER K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 197 Processing helix chain 'K' and resid 228 through 245 removed outlier: 3.585A pdb=" N ILE K 235 " --> pdb=" O ILE K 231 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS K 244 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 300 removed outlier: 4.036A pdb=" N LYS K 295 " --> pdb=" O ARG K 291 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS K 299 " --> pdb=" O LYS K 295 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU K 300 " --> pdb=" O HIS K 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 82 Processing helix chain 'L' and resid 151 through 167 Processing helix chain 'L' and resid 180 through 182 No H-bonds generated for 'chain 'L' and resid 180 through 182' Processing helix chain 'L' and resid 185 through 203 removed outlier: 3.755A pdb=" N ILE L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 236 removed outlier: 4.305A pdb=" N LYS L 235 " --> pdb=" O LYS L 231 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU L 236 " --> pdb=" O VAL L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 254 Processing helix chain 'L' and resid 279 through 298 Processing helix chain 'L' and resid 343 through 346 No H-bonds generated for 'chain 'L' and resid 343 through 346' Processing helix chain 'L' and resid 349 through 366 Processing helix chain 'M' and resid 49 through 64 Processing helix chain 'M' and resid 78 through 98 Processing helix chain 'M' and resid 116 through 119 No H-bonds generated for 'chain 'M' and resid 116 through 119' Processing helix chain 'M' and resid 126 through 144 Processing helix chain 'N' and resid 4 through 14 removed outlier: 3.610A pdb=" N ALA N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 63 Processing helix chain 'N' and resid 101 through 123 removed outlier: 4.855A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Proline residue: N 118 - end of helix removed outlier: 3.538A pdb=" N GLN N 121 " --> pdb=" O GLU N 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL N 122 " --> pdb=" O PRO N 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 12 removed outlier: 3.533A pdb=" N LYS O 11 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS O 12 " --> pdb=" O PHE O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 45 No H-bonds generated for 'chain 'O' and resid 43 through 45' Processing helix chain 'O' and resid 47 through 62 removed outlier: 4.381A pdb=" N THR O 52 " --> pdb=" O GLY O 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 120 Proline residue: O 112 - end of helix removed outlier: 5.042A pdb=" N GLN O 119 " --> pdb=" O GLU O 115 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL O 120 " --> pdb=" O GLU O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'Q' and resid 3 through 13 Processing helix chain 'Q' and resid 39 through 54 removed outlier: 5.798A pdb=" N GLY Q 43 " --> pdb=" O GLU Q 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE Q 45 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA Q 52 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA Q 53 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS Q 54 " --> pdb=" O GLN Q 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 40 Processing helix chain 'R' and resid 67 through 70 No H-bonds generated for 'chain 'R' and resid 67 through 70' Processing helix chain 'R' and resid 81 through 107 removed outlier: 8.421A pdb=" N ASN R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA R 106 " --> pdb=" O ASN R 102 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'A' and resid 2227 through 2229 Processing sheet with id= C, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id= D, first strand: chain 'B' and resid 36 through 39 removed outlier: 3.961A pdb=" N ARG B 36 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 19 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.603A pdb=" N ALA B 47 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 124 through 126 removed outlier: 4.186A pdb=" N THR B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= H, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.739A pdb=" N SER B 175 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 214 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN B 198 " --> pdb=" O PRO B 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 226 through 228 removed outlier: 3.541A pdb=" N ILE B 246 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR B 256 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG B 248 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 254 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.671A pdb=" N ALA B 277 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 118 through 123 removed outlier: 8.351A pdb=" N ARG C 145 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 60 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 147 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU C 62 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS C 149 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU C 64 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 151 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 191 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR C 150 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 193 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 241 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N TYR C 194 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU C 243 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 163 through 167 Processing sheet with id= M, first strand: chain 'C' and resid 1028 through 1031 Processing sheet with id= N, first strand: chain 'C' and resid 1070 through 1076 removed outlier: 6.980A pdb=" N ALA C1087 " --> pdb=" O THR C1071 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET C1073 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C1085 " --> pdb=" O MET C1073 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR C1075 " --> pdb=" O LEU C1083 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C1083 " --> pdb=" O TYR C1075 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA C1092 " --> pdb=" O THR C1088 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS C1097 " --> pdb=" O MET C1108 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N MET C1108 " --> pdb=" O LYS C1097 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1127 through 1131 removed outlier: 4.723A pdb=" N GLY C1142 " --> pdb=" O ILE C1146 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C1146 " --> pdb=" O GLY C1142 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP C1151 " --> pdb=" O LYS C1157 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LYS C1157 " --> pdb=" O ASP C1151 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1190 through 1193 Processing sheet with id= Q, first strand: chain 'C' and resid 1237 through 1239 Processing sheet with id= R, first strand: chain 'C' and resid 1258 through 1261 removed outlier: 3.739A pdb=" N ALA C1258 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C1288 " --> pdb=" O ILE C1279 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASN C1281 " --> pdb=" O LEU C1286 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU C1286 " --> pdb=" O ASN C1281 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1015 through 1021 removed outlier: 6.429A pdb=" N VAL C1327 " --> pdb=" O ILE C1017 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU C1019 " --> pdb=" O ILE C1325 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE C1325 " --> pdb=" O LEU C1019 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR C1324 " --> pdb=" O SER C1320 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 157 through 161 removed outlier: 6.780A pdb=" N ILE D 122 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE D 160 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS D 124 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 57 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY D 14 " --> pdb=" O CYS D 63 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 262 through 265 removed outlier: 3.730A pdb=" N SER D 215 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU D 207 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL D 213 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 111 through 114 removed outlier: 7.598A pdb=" N LEU E 65 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU E 140 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET E 67 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR E 142 " --> pdb=" O MET E 67 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN E 172 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TYR E 142 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU E 174 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE E 144 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE E 176 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 269 through 272 removed outlier: 6.793A pdb=" N LEU E 261 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR E 272 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA E 259 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 258 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 337 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU E 330 " --> pdb=" O LEU E 337 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N CYS E 339 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU E 328 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU E 341 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU E 326 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 71 through 75 Processing sheet with id= Y, first strand: chain 'H' and resid 70 through 74 removed outlier: 6.117A pdb=" N SER H 95 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU H 19 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 24 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 33 " --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 66 through 69 Processing sheet with id= AA, first strand: chain 'J' and resid 83 through 86 removed outlier: 3.657A pdb=" N GLY J 32 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 157 through 161 removed outlier: 6.853A pdb=" N ILE K 122 " --> pdb=" O ALA K 158 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE K 160 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS K 124 " --> pdb=" O PHE K 160 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL K 57 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL K 10 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN K 59 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU K 12 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP K 61 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLY K 14 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP K 62 " --> pdb=" O GLU K 46 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 270 through 274 removed outlier: 3.884A pdb=" N SER K 215 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU K 207 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL K 213 " --> pdb=" O GLU K 207 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 111 through 114 removed outlier: 3.727A pdb=" N GLN L 113 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU L 66 " --> pdb=" O GLN L 113 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU L 65 " --> pdb=" O GLY L 138 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU L 140 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET L 67 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR L 142 " --> pdb=" O MET L 67 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN L 172 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N TYR L 142 " --> pdb=" O ASN L 172 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU L 174 " --> pdb=" O TYR L 142 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE L 144 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE L 176 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER L 214 " --> pdb=" O VAL L 175 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE L 177 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR L 216 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 315 through 319 removed outlier: 3.663A pdb=" N ALA L 271 " --> pdb=" O LEU L 261 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP L 263 " --> pdb=" O TYR L 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR L 269 " --> pdb=" O ASP L 263 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 71 through 76 Processing sheet with id= AG, first strand: chain 'O' and resid 70 through 74 removed outlier: 3.621A pdb=" N VAL O 90 " --> pdb=" O PHE O 83 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER O 95 " --> pdb=" O LEU O 19 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU O 19 " --> pdb=" O SER O 95 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'P' and resid 66 through 69 Processing sheet with id= AI, first strand: chain 'Q' and resid 65 through 67 removed outlier: 3.586A pdb=" N ASN Q 73 " --> pdb=" O LYS Q 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN Q 77 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL Q 21 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY Q 32 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) 2234 hydrogen bonds defined for protein. 6126 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: 44.07 Time building geometry restraints manager: 68.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 47451 1.02 - 1.22: 117 1.22 - 1.42: 20086 1.42 - 1.62: 27962 1.62 - 1.82: 478 Bond restraints: 96094 Sorted by residual: bond pdb=" CG LEU K 212 " pdb=" CD2 LEU K 212 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.87e+00 bond pdb=" CB VAL N 81 " pdb=" CG1 VAL N 81 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.08e+00 bond pdb=" CA ASN A2003 " pdb=" CB ASN A2003 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.03e+00 bond pdb=" CB CYS L 358 " pdb=" SG CYS L 358 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.73e+00 bond pdb=" SD MET C1205 " pdb=" CE MET C1205 " ideal model delta sigma weight residual 1.791 1.751 0.040 2.50e-02 1.60e+03 2.52e+00 ... (remaining 96089 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.80: 627 103.80 - 112.03: 109291 112.03 - 120.25: 37077 120.25 - 128.47: 26212 128.47 - 136.69: 533 Bond angle restraints: 173740 Sorted by residual: angle pdb=" CA TYR A1967 " pdb=" CB TYR A1967 " pdb=" CG TYR A1967 " ideal model delta sigma weight residual 113.90 123.25 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C ARG A1966 " pdb=" CA ARG A1966 " pdb=" CB ARG A1966 " ideal model delta sigma weight residual 110.79 117.77 -6.98 1.66e+00 3.63e-01 1.77e+01 angle pdb=" CB MET A2329 " pdb=" CG MET A2329 " pdb=" SD MET A2329 " ideal model delta sigma weight residual 112.70 124.89 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CA TYR A2038 " pdb=" CB TYR A2038 " pdb=" CG TYR A2038 " ideal model delta sigma weight residual 113.90 121.20 -7.30 1.80e+00 3.09e-01 1.65e+01 angle pdb=" CA ARG D 227 " pdb=" CB ARG D 227 " pdb=" CG ARG D 227 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 ... (remaining 173735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 43847 35.76 - 71.52: 1090 71.52 - 107.28: 73 107.28 - 143.03: 5 143.03 - 178.79: 6 Dihedral angle restraints: 45021 sinusoidal: 24661 harmonic: 20360 Sorted by residual: dihedral pdb=" O3B GTP K 401 " pdb=" O3A GTP K 401 " pdb=" PB GTP K 401 " pdb=" PA GTP K 401 " ideal model delta sinusoidal sigma weight residual 291.08 112.29 178.79 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP D 401 " pdb=" O3A GTP D 401 " pdb=" PB GTP D 401 " pdb=" PA GTP D 401 " ideal model delta sinusoidal sigma weight residual -68.92 91.25 -160.17 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C8 GTP K 401 " pdb=" C1' GTP K 401 " pdb=" N9 GTP K 401 " pdb=" O4' GTP K 401 " ideal model delta sinusoidal sigma weight residual 104.59 -52.51 157.10 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 45018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 7472 1.011 - 2.022: 0 2.022 - 3.033: 0 3.033 - 4.045: 0 4.045 - 5.056: 3 Chirality restraints: 7475 Sorted by residual: chirality pdb=" C2 IHP A2601 " pdb=" C1 IHP A2601 " pdb=" C3 IHP A2601 " pdb=" O12 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.52 2.54 -5.06 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C4 IHP A2601 " pdb=" C3 IHP A2601 " pdb=" C5 IHP A2601 " pdb=" O14 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.48 -2.55 5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 -2.50 4.82 2.00e-01 2.50e+01 5.80e+02 ... (remaining 7472 not shown) Planarity restraints: 14075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 118 " 0.820 9.50e-02 1.11e+02 2.75e-01 8.93e+01 pdb=" NE ARG C 118 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG C 118 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG C 118 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 118 " -0.015 2.00e-02 2.50e+03 pdb="HH11 ARG C 118 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C 118 " 0.009 2.00e-02 2.50e+03 pdb="HH21 ARG C 118 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 118 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 65 " 0.658 9.50e-02 1.11e+02 2.20e-01 5.86e+01 pdb=" NE ARG I 65 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG I 65 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG I 65 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG I 65 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG I 65 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG I 65 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG I 65 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG I 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 65 " 0.653 9.50e-02 1.11e+02 2.19e-01 5.81e+01 pdb=" NE ARG P 65 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG P 65 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG P 65 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG P 65 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG P 65 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG P 65 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG P 65 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG P 65 " 0.012 2.00e-02 2.50e+03 ... (remaining 14072 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 4127 2.17 - 2.78: 188535 2.78 - 3.39: 270385 3.39 - 3.99: 346349 3.99 - 4.60: 541932 Nonbonded interactions: 1351328 Sorted by model distance: nonbonded pdb=" O THR C 307 " pdb=" H GLY C 310 " model vdw 1.563 1.850 nonbonded pdb=" OE1 GLU L 303 " pdb=" H GLU L 303 " model vdw 1.572 1.850 nonbonded pdb=" O ARG F 86 " pdb=" HG SER F 89 " model vdw 1.587 1.850 nonbonded pdb=" O GLN A 962 " pdb=" HG SER A 965 " model vdw 1.596 1.850 nonbonded pdb=" HG1 THR C1170 " pdb=" O VAL C1214 " model vdw 1.600 1.850 ... (remaining 1351323 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 'D' selection = (chain 'K' and (resid 5 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 43 through 302 or resid 4 \ 01 through 402)) } ncs_group { reference = (chain 'E' and (resid 59 through 83 or resid 106 through 116 or (resid 131 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or r \ esid 132 through 371 or resid 401)) selection = chain 'L' } ncs_group { reference = chain 'F' selection = (chain 'M' and (resid 47 through 72 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 78 through 161)) } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'Q' } 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=0.50 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: 8.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.080 Extract box with map and model: 41.400 Check model and map are aligned: 1.060 Set scattering table: 0.640 Process input model: 257.090 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.630 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: 0.030 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 315.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.005 0.065 48529 Z= 0.305 Angle : 0.888 12.186 65760 Z= 0.455 Chirality : 0.111 5.056 7475 Planarity : 0.010 0.357 8391 Dihedral : 15.046 178.792 18049 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 5873 helix: -0.52 (0.08), residues: 3008 sheet: -0.73 (0.18), residues: 757 loop : -1.45 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1049 HIS 0.012 0.001 HIS E 187 PHE 0.035 0.002 PHE A1122 TYR 0.044 0.002 TYR K 106 ARG 0.053 0.002 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 681 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 5.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 548 MET cc_start: 0.2535 (tmm) cc_final: 0.2181 (tmm) REVERT: A 1930 ILE cc_start: 0.7133 (tp) cc_final: 0.6921 (tt) REVERT: A 1960 LEU cc_start: 0.8867 (tp) cc_final: 0.8651 (tt) REVERT: A 2166 LYS cc_start: 0.8282 (pttt) cc_final: 0.7933 (ttpt) REVERT: C 31 MET cc_start: 0.8456 (mmt) cc_final: 0.8249 (mmt) REVERT: C 782 GLU cc_start: 0.7347 (tp30) cc_final: 0.6853 (tp30) REVERT: C 1080 ASP cc_start: 0.6801 (t70) cc_final: 0.6508 (t0) REVERT: C 1081 CYS cc_start: 0.7362 (m) cc_final: 0.6919 (m) REVERT: G 72 ILE cc_start: 0.7021 (mm) cc_final: 0.6706 (mm) REVERT: H 118 ARG cc_start: 0.7141 (mmm-85) cc_final: 0.6794 (tpt90) REVERT: I 45 GLU cc_start: 0.6108 (tm-30) cc_final: 0.5351 (mt-10) REVERT: J 29 LEU cc_start: 0.7832 (mt) cc_final: 0.7450 (mt) REVERT: L 115 TRP cc_start: 0.3239 (t60) cc_final: 0.2832 (t60) REVERT: L 135 ARG cc_start: 0.3301 (mmp80) cc_final: 0.2134 (tmm160) REVERT: M 67 ASP cc_start: 0.7428 (t70) cc_final: 0.7036 (t70) REVERT: M 82 MET cc_start: 0.8372 (mmm) cc_final: 0.8158 (tpp) REVERT: N 116 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7623 (tm-30) REVERT: O 11 LYS cc_start: 0.7605 (mttp) cc_final: 0.7391 (mtpt) REVERT: Q 29 LEU cc_start: 0.7725 (mm) cc_final: 0.7478 (mm) REVERT: Q 39 ASP cc_start: 0.6478 (t0) cc_final: 0.6197 (m-30) REVERT: Q 78 LYS cc_start: 0.6118 (tmmt) cc_final: 0.5815 (ptmm) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 1.3064 time to fit residues: 1436.0869 Evaluate side-chains 532 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 5.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 495 optimal weight: 0.8980 chunk 444 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 300 optimal weight: 0.8980 chunk 237 optimal weight: 8.9990 chunk 460 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 342 optimal weight: 0.8980 chunk 533 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2282 GLN C 183 GLN C 361 ASN C 513 ASN C1020 ASN D 258 ASN F 51 GLN J 15 ASN O 59 GLN R 27 GLN R 28 GLN R 41 GLN R 89 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48529 Z= 0.250 Angle : 0.602 8.111 65760 Z= 0.314 Chirality : 0.042 0.249 7475 Planarity : 0.005 0.110 8391 Dihedral : 8.210 179.580 6522 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 0.50 % Allowed : 5.13 % Favored : 94.38 % 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: -0.48 (0.11), residues: 5873 helix: 0.41 (0.09), residues: 3053 sheet: -0.68 (0.18), residues: 761 loop : -1.15 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 585 HIS 0.010 0.001 HIS L 187 PHE 0.022 0.001 PHE K 211 TYR 0.025 0.001 TYR A2038 ARG 0.009 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 580 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 554 time to evaluate : 5.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1930 ILE cc_start: 0.7220 (tp) cc_final: 0.6998 (tt) REVERT: B 56 MET cc_start: 0.2149 (pmm) cc_final: 0.1905 (pmm) REVERT: C 31 MET cc_start: 0.8517 (mmt) cc_final: 0.8316 (mmt) REVERT: C 280 MET cc_start: 0.8102 (mtt) cc_final: 0.7753 (mtt) REVERT: C 411 GLU cc_start: 0.4465 (tm-30) cc_final: 0.3302 (mm-30) REVERT: C 995 ASN cc_start: 0.7603 (m-40) cc_final: 0.7289 (m-40) REVERT: C 1080 ASP cc_start: 0.6960 (t70) cc_final: 0.6657 (t0) REVERT: C 1081 CYS cc_start: 0.7321 (m) cc_final: 0.6848 (m) REVERT: H 118 ARG cc_start: 0.7219 (mmm-85) cc_final: 0.6685 (tpt90) REVERT: I 45 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5499 (mt-10) REVERT: J 75 MET cc_start: 0.2659 (mmt) cc_final: -0.0290 (tpt) REVERT: L 115 TRP cc_start: 0.3532 (t60) cc_final: 0.3185 (t60) REVERT: L 135 ARG cc_start: 0.3523 (mmp80) cc_final: 0.2717 (ttp80) REVERT: M 67 ASP cc_start: 0.7495 (t70) cc_final: 0.7126 (t70) REVERT: N 116 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7534 (tm-30) REVERT: O 84 ASN cc_start: 0.7773 (t0) cc_final: 0.7302 (t0) REVERT: Q 48 LEU cc_start: 0.8305 (tp) cc_final: 0.7928 (mp) outliers start: 26 outliers final: 21 residues processed: 568 average time/residue: 1.2782 time to fit residues: 1164.2366 Evaluate side-chains 531 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 510 time to evaluate : 5.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 58 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 296 optimal weight: 0.0270 chunk 165 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 534 optimal weight: 5.9990 chunk 576 optimal weight: 2.9990 chunk 475 optimal weight: 1.9990 chunk 529 optimal weight: 0.0020 chunk 182 optimal weight: 4.9990 chunk 428 optimal weight: 2.9990 overall best weight: 1.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 HIS C 208 GLN C 547 HIS C 677 ASN H 99 ASN K 107 GLN N 121 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 48529 Z= 0.335 Angle : 0.590 7.915 65760 Z= 0.311 Chirality : 0.042 0.284 7475 Planarity : 0.005 0.074 8391 Dihedral : 7.567 175.363 6522 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 0.86 % Allowed : 6.68 % Favored : 92.46 % 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: -0.26 (0.11), residues: 5873 helix: 0.68 (0.09), residues: 3049 sheet: -0.69 (0.18), residues: 782 loop : -1.14 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 585 HIS 0.008 0.001 HIS C1315 PHE 0.035 0.002 PHE H 53 TYR 0.023 0.002 TYR R 100 ARG 0.010 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 564 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 519 time to evaluate : 5.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: 0.1123 (mpp) cc_final: 0.0821 (mpp) REVERT: A 1930 ILE cc_start: 0.7334 (tp) cc_final: 0.7119 (tt) REVERT: B 56 MET cc_start: 0.1956 (pmm) cc_final: 0.1707 (pmm) REVERT: C 31 MET cc_start: 0.8506 (mmt) cc_final: 0.8268 (mmt) REVERT: C 118 ARG cc_start: 0.6757 (ptp90) cc_final: 0.6554 (ptt-90) REVERT: C 280 MET cc_start: 0.8256 (mtt) cc_final: 0.7969 (mtt) REVERT: C 411 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.2584 (mm-30) REVERT: C 995 ASN cc_start: 0.7657 (m-40) cc_final: 0.7257 (m-40) REVERT: G 34 TYR cc_start: 0.6513 (t80) cc_final: 0.5755 (t80) REVERT: H 118 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6710 (tpt90) REVERT: I 45 GLU cc_start: 0.6303 (tm-30) cc_final: 0.5507 (mt-10) REVERT: J 75 MET cc_start: 0.2471 (mmt) cc_final: -0.0392 (tpt) REVERT: L 135 ARG cc_start: 0.3497 (mmp80) cc_final: 0.2754 (ttp80) REVERT: M 67 ASP cc_start: 0.7592 (t70) cc_final: 0.7186 (t70) REVERT: N 116 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7519 (tm-30) REVERT: O 84 ASN cc_start: 0.7664 (t0) cc_final: 0.7154 (t0) REVERT: Q 48 LEU cc_start: 0.8306 (tp) cc_final: 0.7881 (mp) REVERT: Q 75 MET cc_start: 0.5291 (ptt) cc_final: 0.4753 (ptp) REVERT: Q 77 GLN cc_start: 0.3733 (pt0) cc_final: 0.3448 (pt0) outliers start: 45 outliers final: 35 residues processed: 550 average time/residue: 1.2810 time to fit residues: 1141.1578 Evaluate side-chains 533 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 497 time to evaluate : 5.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1336 GLU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2096 ASP Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1108 MET Chi-restraints excluded: chain C residue 1239 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 357 HIS Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain P residue 23 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 527 optimal weight: 0.6980 chunk 401 optimal weight: 1.9990 chunk 277 optimal weight: 0.0770 chunk 59 optimal weight: 0.6980 chunk 254 optimal weight: 0.6980 chunk 358 optimal weight: 1.9990 chunk 535 optimal weight: 3.9990 chunk 567 optimal weight: 0.9980 chunk 280 optimal weight: 0.8980 chunk 507 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS L 196 HIS ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48529 Z= 0.197 Angle : 0.530 6.947 65760 Z= 0.276 Chirality : 0.040 0.174 7475 Planarity : 0.004 0.064 8391 Dihedral : 7.269 174.708 6522 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.84 % Allowed : 7.90 % Favored : 91.26 % 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: 0.02 (0.11), residues: 5873 helix: 0.94 (0.09), residues: 3046 sheet: -0.69 (0.18), residues: 772 loop : -1.02 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1313 HIS 0.006 0.001 HIS K 127 PHE 0.024 0.001 PHE A2421 TYR 0.019 0.001 TYR A2038 ARG 0.008 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 562 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 518 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 756 MET cc_start: 0.8720 (tpp) cc_final: 0.8450 (tpt) REVERT: A 1930 ILE cc_start: 0.7269 (tp) cc_final: 0.7061 (tt) REVERT: A 2132 MET cc_start: 0.7842 (ppp) cc_final: 0.7544 (pmm) REVERT: B 56 MET cc_start: 0.1998 (pmm) cc_final: 0.1729 (pmm) REVERT: C 31 MET cc_start: 0.8533 (mmt) cc_final: 0.8312 (mmt) REVERT: C 55 MET cc_start: 0.7828 (ttp) cc_final: 0.7503 (ttp) REVERT: C 118 ARG cc_start: 0.6765 (ptp90) cc_final: 0.6554 (ptt-90) REVERT: C 280 MET cc_start: 0.8225 (mtt) cc_final: 0.8022 (mtt) REVERT: C 339 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7973 (tm-30) REVERT: C 411 GLU cc_start: 0.4401 (tm-30) cc_final: 0.3226 (mm-30) REVERT: C 995 ASN cc_start: 0.7618 (m-40) cc_final: 0.7214 (m-40) REVERT: G 34 TYR cc_start: 0.6599 (t80) cc_final: 0.6028 (t80) REVERT: H 118 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6713 (tpt90) REVERT: I 45 GLU cc_start: 0.6222 (tm-30) cc_final: 0.5452 (mt-10) REVERT: J 75 MET cc_start: 0.2540 (mmt) cc_final: -0.0260 (tpt) REVERT: L 135 ARG cc_start: 0.3504 (mmp80) cc_final: 0.2612 (ttp80) REVERT: M 67 ASP cc_start: 0.7566 (t70) cc_final: 0.7237 (t70) REVERT: N 116 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7454 (tm-30) REVERT: O 84 ASN cc_start: 0.7637 (t0) cc_final: 0.7171 (t0) REVERT: P 21 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.3740 (mp) REVERT: Q 75 MET cc_start: 0.5187 (ptt) cc_final: 0.4726 (ptp) outliers start: 44 outliers final: 34 residues processed: 547 average time/residue: 1.3347 time to fit residues: 1175.5473 Evaluate side-chains 523 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 488 time to evaluate : 5.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 1336 GLU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 1239 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 357 HIS Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 65 ASN Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 23 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 472 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 422 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 484 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 0.0980 chunk 509 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS G 51 ASN H 59 GLN ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 GLN O 84 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 48529 Z= 0.278 Angle : 0.546 7.837 65760 Z= 0.285 Chirality : 0.041 0.176 7475 Planarity : 0.004 0.052 8391 Dihedral : 7.005 176.425 6522 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 1.09 % Allowed : 8.47 % Favored : 90.44 % 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: 0.08 (0.11), residues: 5873 helix: 1.04 (0.10), residues: 3038 sheet: -0.79 (0.18), residues: 784 loop : -1.01 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1313 HIS 0.008 0.001 HIS K 226 PHE 0.037 0.002 PHE H 53 TYR 0.017 0.001 TYR A2038 ARG 0.010 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 556 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 499 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1930 ILE cc_start: 0.7388 (tp) cc_final: 0.7179 (tt) REVERT: A 2132 MET cc_start: 0.7902 (ppp) cc_final: 0.7609 (pmm) REVERT: B 56 MET cc_start: 0.2005 (pmm) cc_final: 0.1752 (pmm) REVERT: C 31 MET cc_start: 0.8510 (mmt) cc_final: 0.8251 (mmt) REVERT: C 118 ARG cc_start: 0.6644 (ptp90) cc_final: 0.6425 (ptt-90) REVERT: C 411 GLU cc_start: 0.4103 (OUTLIER) cc_final: 0.2386 (mm-30) REVERT: G 34 TYR cc_start: 0.6719 (t80) cc_final: 0.6390 (t80) REVERT: H 118 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.6675 (tpt90) REVERT: I 45 GLU cc_start: 0.6325 (tm-30) cc_final: 0.5466 (mt-10) REVERT: J 75 MET cc_start: 0.2419 (mmt) cc_final: -0.0380 (tpt) REVERT: K 252 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7449 (tpt) REVERT: N 116 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7475 (tm-30) REVERT: P 21 LEU cc_start: 0.3919 (OUTLIER) cc_final: 0.3675 (mp) REVERT: Q 29 LEU cc_start: 0.7712 (mm) cc_final: 0.7386 (mm) REVERT: Q 75 MET cc_start: 0.5355 (ptt) cc_final: 0.4907 (ptp) REVERT: R 94 GLU cc_start: 0.7403 (tp30) cc_final: 0.7074 (tp30) outliers start: 57 outliers final: 41 residues processed: 535 average time/residue: 1.2682 time to fit residues: 1100.8563 Evaluate side-chains 520 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 476 time to evaluate : 5.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2096 ASP Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1108 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 252 MET Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 78 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 190 optimal weight: 0.0870 chunk 510 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 333 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 567 optimal weight: 0.6980 chunk 471 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN A2147 ASN ** C1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48529 Z= 0.224 Angle : 0.519 7.952 65760 Z= 0.270 Chirality : 0.040 0.190 7475 Planarity : 0.004 0.049 8391 Dihedral : 6.859 176.533 6522 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 0.86 % Allowed : 9.33 % Favored : 89.80 % 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: 0.22 (0.11), residues: 5873 helix: 1.17 (0.10), residues: 3030 sheet: -0.74 (0.18), residues: 781 loop : -0.95 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1313 HIS 0.006 0.001 HIS K 127 PHE 0.031 0.001 PHE K 141 TYR 0.015 0.001 TYR A2038 ARG 0.010 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 533 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 488 time to evaluate : 5.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1930 ILE cc_start: 0.7371 (tp) cc_final: 0.7152 (tt) REVERT: A 2132 MET cc_start: 0.7907 (ppp) cc_final: 0.7614 (pmm) REVERT: C 31 MET cc_start: 0.8514 (mmt) cc_final: 0.8261 (mmt) REVERT: C 118 ARG cc_start: 0.6625 (ptp90) cc_final: 0.6401 (ptt-90) REVERT: C 411 GLU cc_start: 0.4239 (OUTLIER) cc_final: 0.2912 (mm-30) REVERT: H 118 ARG cc_start: 0.7460 (mmm-85) cc_final: 0.6679 (tpt90) REVERT: I 45 GLU cc_start: 0.6318 (tm-30) cc_final: 0.5461 (mt-10) REVERT: J 75 MET cc_start: 0.2633 (mmt) cc_final: -0.0263 (tpt) REVERT: K 252 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7608 (tpt) REVERT: K 266 PHE cc_start: 0.8479 (t80) cc_final: 0.8181 (t80) REVERT: M 67 ASP cc_start: 0.7534 (t70) cc_final: 0.7222 (t70) REVERT: N 116 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7546 (tm-30) REVERT: O 84 ASN cc_start: 0.7684 (t0) cc_final: 0.7172 (t0) REVERT: P 21 LEU cc_start: 0.3942 (OUTLIER) cc_final: 0.3725 (mp) REVERT: Q 29 LEU cc_start: 0.7590 (mm) cc_final: 0.7278 (mm) REVERT: Q 75 MET cc_start: 0.5478 (ptt) cc_final: 0.5042 (ptp) outliers start: 45 outliers final: 34 residues processed: 517 average time/residue: 1.2902 time to fit residues: 1083.3740 Evaluate side-chains 509 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 472 time to evaluate : 5.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2421 PHE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1229 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 252 MET Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 78 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 547 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 414 optimal weight: 0.7980 chunk 321 optimal weight: 0.0870 chunk 478 optimal weight: 0.0030 chunk 317 optimal weight: 0.5980 chunk 565 optimal weight: 5.9990 chunk 354 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 48529 Z= 0.180 Angle : 0.507 8.181 65760 Z= 0.263 Chirality : 0.039 0.204 7475 Planarity : 0.004 0.050 8391 Dihedral : 6.695 177.476 6522 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 0.82 % Allowed : 9.83 % Favored : 89.35 % 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: 0.39 (0.11), residues: 5873 helix: 1.29 (0.10), residues: 3038 sheet: -0.67 (0.18), residues: 779 loop : -0.84 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1313 HIS 0.006 0.001 HIS K 127 PHE 0.023 0.001 PHE A2421 TYR 0.015 0.001 TYR A2038 ARG 0.008 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 529 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 486 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1930 ILE cc_start: 0.7382 (tp) cc_final: 0.7156 (tt) REVERT: A 2132 MET cc_start: 0.7848 (ppp) cc_final: 0.7565 (pmm) REVERT: C 31 MET cc_start: 0.8522 (mmt) cc_final: 0.8268 (mmt) REVERT: C 118 ARG cc_start: 0.6600 (ptp90) cc_final: 0.6376 (ptt-90) REVERT: C 411 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.3023 (mm-30) REVERT: G 74 MET cc_start: 0.6780 (mmp) cc_final: 0.6388 (mmp) REVERT: H 85 ARG cc_start: 0.7947 (mmt90) cc_final: 0.7649 (mmt90) REVERT: H 118 ARG cc_start: 0.7451 (mmm-85) cc_final: 0.6734 (tpt90) REVERT: I 45 GLU cc_start: 0.6275 (tm-30) cc_final: 0.5380 (mt-10) REVERT: J 75 MET cc_start: 0.2666 (mmt) cc_final: -0.0293 (tpt) REVERT: K 252 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7573 (tpt) REVERT: K 266 PHE cc_start: 0.8447 (t80) cc_final: 0.8122 (t80) REVERT: N 116 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7526 (tm-30) REVERT: O 84 ASN cc_start: 0.7568 (t0) cc_final: 0.7076 (t0) REVERT: P 21 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3740 (mp) REVERT: Q 29 LEU cc_start: 0.7588 (mm) cc_final: 0.7296 (mm) REVERT: Q 75 MET cc_start: 0.5457 (ptt) cc_final: 0.5022 (ptp) outliers start: 43 outliers final: 35 residues processed: 515 average time/residue: 1.2821 time to fit residues: 1078.2253 Evaluate side-chains 510 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 472 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2096 ASP Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2421 PHE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 1229 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain K residue 252 MET Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 78 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 350 optimal weight: 0.3980 chunk 225 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 359 optimal weight: 2.9990 chunk 385 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 444 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1937 GLN C 153 HIS ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 48529 Z= 0.297 Angle : 0.539 8.600 65760 Z= 0.282 Chirality : 0.041 0.199 7475 Planarity : 0.004 0.049 8391 Dihedral : 6.678 179.359 6522 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 1.03 % Allowed : 9.83 % Favored : 89.14 % 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: 0.24 (0.11), residues: 5873 helix: 1.22 (0.10), residues: 3035 sheet: -0.82 (0.18), residues: 794 loop : -0.95 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1313 HIS 0.006 0.001 HIS K 127 PHE 0.023 0.001 PHE A2421 TYR 0.029 0.001 TYR G 34 ARG 0.013 0.000 ARG C 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 532 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 478 time to evaluate : 5.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 756 MET cc_start: 0.8664 (tpp) cc_final: 0.8406 (tpp) REVERT: A 1930 ILE cc_start: 0.7431 (tp) cc_final: 0.7202 (tt) REVERT: A 2132 MET cc_start: 0.7780 (ppp) cc_final: 0.7525 (pmm) REVERT: C 31 MET cc_start: 0.8517 (mmt) cc_final: 0.8253 (mmt) REVERT: C 118 ARG cc_start: 0.6651 (ptp90) cc_final: 0.6430 (ptt-90) REVERT: C 411 GLU cc_start: 0.3986 (OUTLIER) cc_final: 0.2563 (mm-30) REVERT: H 85 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7685 (mmt90) REVERT: H 118 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.6752 (tpt90) REVERT: I 45 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5389 (mt-10) REVERT: J 75 MET cc_start: 0.2676 (mmt) cc_final: -0.0302 (tpt) REVERT: K 252 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7587 (tpt) REVERT: K 266 PHE cc_start: 0.8567 (t80) cc_final: 0.8318 (t80) REVERT: N 116 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7554 (tm-30) REVERT: O 84 ASN cc_start: 0.7637 (t0) cc_final: 0.7189 (t0) REVERT: P 21 LEU cc_start: 0.3939 (OUTLIER) cc_final: 0.3681 (mp) REVERT: Q 75 MET cc_start: 0.5676 (ptt) cc_final: 0.5283 (ptp) outliers start: 54 outliers final: 42 residues processed: 514 average time/residue: 1.3026 time to fit residues: 1086.7210 Evaluate side-chains 508 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 463 time to evaluate : 5.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1376 ASP Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 1719 HIS Chi-restraints excluded: chain A residue 2096 ASP Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2421 PHE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1229 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain K residue 252 MET Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 78 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 514 optimal weight: 1.9990 chunk 542 optimal weight: 1.9990 chunk 494 optimal weight: 0.6980 chunk 527 optimal weight: 0.9990 chunk 541 optimal weight: 1.9990 chunk 317 optimal weight: 0.4980 chunk 229 optimal weight: 5.9990 chunk 414 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 476 optimal weight: 0.7980 chunk 498 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 48529 Z= 0.220 Angle : 0.520 8.596 65760 Z= 0.270 Chirality : 0.040 0.253 7475 Planarity : 0.004 0.049 8391 Dihedral : 6.564 179.696 6522 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 0.88 % Allowed : 10.20 % Favored : 88.93 % 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: 0.36 (0.11), residues: 5873 helix: 1.30 (0.10), residues: 3036 sheet: -0.74 (0.18), residues: 772 loop : -0.89 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C1313 HIS 0.006 0.001 HIS K 127 PHE 0.023 0.001 PHE A2421 TYR 0.015 0.001 TYR R 100 ARG 0.012 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 478 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1930 ILE cc_start: 0.7386 (tp) cc_final: 0.7170 (tt) REVERT: A 2079 MET cc_start: 0.6288 (tpt) cc_final: 0.6087 (tpt) REVERT: A 2132 MET cc_start: 0.7810 (ppp) cc_final: 0.7601 (pmm) REVERT: C 31 MET cc_start: 0.8504 (mmt) cc_final: 0.8214 (mmt) REVERT: C 118 ARG cc_start: 0.6630 (ptp90) cc_final: 0.6406 (ptt-90) REVERT: C 411 GLU cc_start: 0.4151 (OUTLIER) cc_final: 0.2798 (mm-30) REVERT: G 74 MET cc_start: 0.6334 (mmp) cc_final: 0.6021 (mmp) REVERT: H 85 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7604 (mmt90) REVERT: H 118 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.6755 (tpt90) REVERT: I 45 GLU cc_start: 0.6334 (tm-30) cc_final: 0.5374 (mt-10) REVERT: J 75 MET cc_start: 0.2760 (mmt) cc_final: -0.0174 (tpt) REVERT: K 165 TRP cc_start: 0.8079 (m100) cc_final: 0.7516 (m100) REVERT: K 252 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7550 (tpt) REVERT: K 266 PHE cc_start: 0.8539 (t80) cc_final: 0.8206 (t80) REVERT: N 116 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7545 (tm-30) REVERT: O 84 ASN cc_start: 0.7614 (t0) cc_final: 0.7172 (t0) REVERT: P 21 LEU cc_start: 0.3984 (OUTLIER) cc_final: 0.3726 (mp) REVERT: Q 29 LEU cc_start: 0.7536 (mm) cc_final: 0.7109 (mm) REVERT: Q 75 MET cc_start: 0.5567 (ptt) cc_final: 0.5340 (ptp) outliers start: 46 outliers final: 39 residues processed: 507 average time/residue: 1.3122 time to fit residues: 1075.1441 Evaluate side-chains 514 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 472 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 2096 ASP Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2421 PHE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1229 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain K residue 252 MET Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 78 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 525 optimal weight: 1.9990 chunk 346 optimal weight: 0.9990 chunk 557 optimal weight: 0.7980 chunk 340 optimal weight: 0.1980 chunk 264 optimal weight: 0.9990 chunk 387 optimal weight: 0.0980 chunk 584 optimal weight: 0.0070 chunk 538 optimal weight: 4.9990 chunk 465 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 359 optimal weight: 0.7980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 48529 Z= 0.160 Angle : 0.500 8.445 65760 Z= 0.258 Chirality : 0.039 0.278 7475 Planarity : 0.004 0.077 8391 Dihedral : 6.363 176.676 6522 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 0.59 % Allowed : 10.65 % Favored : 88.75 % 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: 0.58 (0.11), residues: 5873 helix: 1.46 (0.10), residues: 3034 sheet: -0.66 (0.18), residues: 765 loop : -0.75 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1313 HIS 0.006 0.001 HIS K 127 PHE 0.023 0.001 PHE A2421 TYR 0.018 0.001 TYR G 34 ARG 0.011 0.000 ARG R 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1662 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Evaluate side-chains 518 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 487 time to evaluate : 5.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1930 ILE cc_start: 0.7358 (tp) cc_final: 0.7147 (tt) REVERT: A 2132 MET cc_start: 0.7794 (ppp) cc_final: 0.7585 (pmm) REVERT: C 31 MET cc_start: 0.8516 (mmt) cc_final: 0.8227 (mmt) REVERT: C 118 ARG cc_start: 0.6714 (ptp90) cc_final: 0.6489 (ptt-90) REVERT: C 411 GLU cc_start: 0.4348 (OUTLIER) cc_final: 0.3138 (mm-30) REVERT: H 85 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7578 (mmt90) REVERT: H 118 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.6706 (tpt90) REVERT: I 45 GLU cc_start: 0.6321 (tm-30) cc_final: 0.5375 (mt-10) REVERT: J 75 MET cc_start: 0.2743 (mmt) cc_final: -0.0109 (tpt) REVERT: K 165 TRP cc_start: 0.7930 (m100) cc_final: 0.7327 (m100) REVERT: K 252 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7471 (tpt) REVERT: K 266 PHE cc_start: 0.8472 (t80) cc_final: 0.8057 (t80) REVERT: N 116 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7532 (tm-30) REVERT: P 21 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3661 (mp) REVERT: Q 29 LEU cc_start: 0.7448 (mm) cc_final: 0.7103 (mm) REVERT: Q 75 MET cc_start: 0.5663 (ptt) cc_final: 0.5384 (ptp) outliers start: 31 outliers final: 27 residues processed: 506 average time/residue: 1.2929 time to fit residues: 1049.4263 Evaluate side-chains 506 residues out of total 5233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 476 time to evaluate : 6.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1714 PHE Chi-restraints excluded: chain A residue 2101 TRP Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2421 PHE Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 1229 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain K residue 252 MET Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 365 GLU Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 78 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 285 optimal weight: 0.0980 chunk 369 optimal weight: 0.8980 chunk 496 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 429 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 466 optimal weight: 0.0980 chunk 195 optimal weight: 0.6980 chunk 478 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 84 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.151140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104331 restraints weight = 289233.504| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.25 r_work: 0.3319 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48529 Z= 0.170 Angle : 0.500 8.358 65760 Z= 0.258 Chirality : 0.039 0.282 7475 Planarity : 0.004 0.083 8391 Dihedral : 6.242 173.149 6522 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 0.63 % Allowed : 10.67 % Favored : 88.70 % 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: 0.63 (0.11), residues: 5873 helix: 1.52 (0.10), residues: 3034 sheet: -0.70 (0.18), residues: 777 loop : -0.72 (0.15), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1313 HIS 0.019 0.001 HIS R 89 PHE 0.027 0.001 PHE L 356 TYR 0.039 0.001 TYR G 34 ARG 0.009 0.000 ARG L 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22534.36 seconds wall clock time: 391 minutes 10.22 seconds (23470.22 seconds total)