Starting phenix.real_space_refine on Fri Mar 15 20:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8h_9781/03_2024/6j8h_9781_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8h_9781/03_2024/6j8h_9781.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/6j8h_9781/03_2024/6j8h_9781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8h_9781/03_2024/6j8h_9781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8h_9781/03_2024/6j8h_9781_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8h_9781/03_2024/6j8h_9781_neut_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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 7724 2.51 5 N 1861 2.21 5 O 2081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A GLU 1477": "OE1" <-> "OE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A GLU 1672": "OE1" <-> "OE2" Residue "A GLU 1768": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11763 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 9192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9192 Classifications: {'peptide': 1140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1107} Chain breaks: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'9SL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.83, per 1000 atoms: 0.58 Number of scatterers: 11763 At special positions: 0 Unit cell: (133.102, 141.83, 112.373, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 2081 8.00 N 1861 7.00 C 7724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.57 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.45 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=1.90 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.68 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.00 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=1.95 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.12 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=1.88 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.00 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 Atom "HETATM11600 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2005 " - " ASN A1375 " " NAG A2006 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.2 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 8 sheets defined 62.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.666A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.570A pdb=" N TYR A 163 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 169 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 173 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.059A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 4.314A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 267 removed outlier: 3.750A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.849A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.540A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.700A pdb=" N ILE A 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 386 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 416 removed outlier: 3.533A pdb=" N GLU A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.663A pdb=" N ILE A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 761 removed outlier: 3.762A pdb=" N THR A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 798 removed outlier: 3.704A pdb=" N ALA A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 807 through 824 removed outlier: 3.782A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 823 " --> pdb=" O SER A 819 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 846 removed outlier: 3.575A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 845 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.621A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 4.404A pdb=" N ASN A 868 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 880 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 884 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 888 " --> pdb=" O MET A 885 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 889 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS A 890 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 892 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 895 " --> pdb=" O TYR A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 924 Processing helix chain 'A' and resid 928 through 939 removed outlier: 4.025A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 971 Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1192 through 1211 removed outlier: 3.984A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1220 through 1254 removed outlier: 3.894A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A1232 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1278 Processing helix chain 'A' and resid 1287 through 1303 removed outlier: 3.911A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA A1294 " --> pdb=" O ARG A1290 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU A1295 " --> pdb=" O THR A1291 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG A1296 " --> pdb=" O LEU A1292 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 4.688A pdb=" N ALA A1300 " --> pdb=" O ARG A1296 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A1301 " --> pdb=" O PRO A1297 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1303' Processing helix chain 'A' and resid 1305 through 1343 removed outlier: 3.611A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.503A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1376 removed outlier: 3.640A pdb=" N ALA A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1404 removed outlier: 3.515A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1417 Processing helix chain 'A' and resid 1432 through 1444 removed outlier: 4.032A pdb=" N GLY A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1466 Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 3.763A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1513 removed outlier: 3.660A pdb=" N ILE A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1533 removed outlier: 3.539A pdb=" N MET A1532 " --> pdb=" O ASN A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1575 removed outlier: 7.399A pdb=" N HIS A1571 " --> pdb=" O ILE A1567 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A1572 " --> pdb=" O SER A1568 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A1574 " --> pdb=" O ARG A1570 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1575 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1602 Processing helix chain 'A' and resid 1606 through 1626 removed outlier: 4.365A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1666 removed outlier: 3.505A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1696 removed outlier: 4.331A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1733 through 1767 Processing helix chain 'B' and resid 154 through 191 removed outlier: 3.501A pdb=" N TYR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 31 through 34 Processing sheet with id= B, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.686A pdb=" N LEU C 38 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 46 through 48 Processing sheet with id= D, first strand: chain 'A' and resid 273 through 277 Processing sheet with id= E, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id= F, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.522A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 36 through 41 Processing sheet with id= H, first strand: chain 'B' and resid 133 through 144 removed outlier: 3.503A pdb=" N VAL B 138 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1746 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: 3.63 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.34: 3525 1.34 - 1.50: 3627 1.50 - 1.67: 4730 1.67 - 1.84: 154 1.84 - 2.01: 2 Bond restraints: 12038 Sorted by residual: bond pdb=" C12 9SL A2007 " pdb=" N11 9SL A2007 " ideal model delta sigma weight residual 1.284 1.505 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 NAG A2005 " pdb=" C2 NAG A2005 " ideal model delta sigma weight residual 1.532 1.663 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 1.808 2.008 -0.200 3.30e-02 9.18e+02 3.68e+01 bond pdb=" C12 9SL A2007 " pdb=" N13 9SL A2007 " ideal model delta sigma weight residual 1.370 1.486 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C CYS A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.332 1.398 -0.067 1.26e-02 6.30e+03 2.81e+01 ... (remaining 12033 not shown) Histogram of bond angle deviations from ideal: 94.36 - 103.49: 157 103.49 - 112.61: 6114 112.61 - 121.74: 7595 121.74 - 130.86: 2375 130.86 - 139.99: 69 Bond angle restraints: 16310 Sorted by residual: angle pdb=" N TYR A 302 " pdb=" CA TYR A 302 " pdb=" C TYR A 302 " ideal model delta sigma weight residual 111.36 124.73 -13.37 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N CYS A 925 " pdb=" CA CYS A 925 " pdb=" C CYS A 925 " ideal model delta sigma weight residual 110.55 94.36 16.19 1.35e+00 5.49e-01 1.44e+02 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 110.97 123.84 -12.87 1.09e+00 8.42e-01 1.39e+02 angle pdb=" N GLN A1378 " pdb=" CA GLN A1378 " pdb=" C GLN A1378 " ideal model delta sigma weight residual 111.36 124.09 -12.73 1.09e+00 8.42e-01 1.36e+02 angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 111.07 122.02 -10.95 1.07e+00 8.73e-01 1.05e+02 ... (remaining 16305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5829 17.78 - 35.56: 838 35.56 - 53.35: 438 53.35 - 71.13: 146 71.13 - 88.91: 20 Dihedral angle restraints: 7271 sinusoidal: 3069 harmonic: 4202 Sorted by residual: dihedral pdb=" CB CYS B 40 " pdb=" SG CYS B 40 " pdb=" SG CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sinusoidal sigma weight residual -86.00 -23.93 -62.07 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 152.13 -59.13 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 33.93 59.07 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 7268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1670 0.152 - 0.303: 203 0.303 - 0.455: 19 0.455 - 0.607: 8 0.607 - 0.758: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.44e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.98e+01 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 1898 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " 0.359 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG B 301 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " -0.549 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 110 " 0.198 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" CG ASN B 110 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN B 110 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 110 " -0.430 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.294 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 135 " -0.091 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" CG ASN B 135 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN B 135 " -0.121 2.00e-02 2.50e+03 pdb=" ND2 ASN B 135 " 0.388 2.00e-02 2.50e+03 pdb=" C1 NAG B 304 " -0.239 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 146 2.49 - 3.09: 9523 3.09 - 3.69: 17184 3.69 - 4.30: 25648 4.30 - 4.90: 41718 Nonbonded interactions: 94219 Sorted by model distance: nonbonded pdb=" N GLN A1541 " pdb=" OE1 GLN A1541 " model vdw 1.886 2.520 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 1.980 2.440 nonbonded pdb=" OD1 ASN A1375 " pdb=" O5 NAG A2005 " model vdw 2.032 3.040 nonbonded pdb=" O SER A1430 " pdb=" N TYR A1432 " model vdw 2.036 2.520 nonbonded pdb=" NE2 GLN A 360 " pdb=" OG SER A 390 " model vdw 2.047 2.520 ... (remaining 94214 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 'E' } 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=0.41 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.650 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.830 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.010 0.221 12038 Z= 0.678 Angle : 1.540 17.086 16310 Z= 1.055 Chirality : 0.104 0.758 1901 Planarity : 0.010 0.308 1986 Dihedral : 21.716 88.910 4527 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 58.60 Ramachandran Plot: Outliers : 1.34 % Allowed : 2.04 % Favored : 96.62 % Rotamer: Outliers : 27.17 % Allowed : 18.94 % Favored : 53.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.21), residues: 1421 helix: 3.08 (0.16), residues: 810 sheet: 1.54 (0.44), residues: 132 loop : -0.14 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1700 HIS 0.009 0.001 HIS A 766 PHE 0.022 0.002 PHE B 54 TYR 0.025 0.002 TYR A1429 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 230 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5433 (mpp) REVERT: A 143 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: A 181 PHE cc_start: 0.2690 (OUTLIER) cc_final: 0.1815 (m-10) REVERT: A 206 ASN cc_start: 0.3090 (OUTLIER) cc_final: 0.2354 (t0) REVERT: A 209 ASN cc_start: 0.3988 (OUTLIER) cc_final: 0.3122 (t0) REVERT: A 298 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 371 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 379 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: A 387 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 410 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: A 761 MET cc_start: 0.7465 (mtm) cc_final: 0.7018 (mtm) REVERT: A 764 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 769 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7563 (p) REVERT: A 774 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6784 (t0) REVERT: A 780 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6930 (t0) REVERT: A 831 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4355 (tp) REVERT: A 848 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7796 (m) REVERT: A 893 LYS cc_start: 0.8318 (tptm) cc_final: 0.8004 (tttm) REVERT: A 1226 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 1251 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (ttpt) REVERT: A 1296 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8223 (mtt180) REVERT: A 1323 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7572 (m-40) REVERT: A 1358 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6064 (mtm-85) REVERT: A 1385 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 1399 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 1465 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7867 (tttm) REVERT: A 1474 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8820 (mtp) REVERT: A 1478 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: A 1497 ILE cc_start: 0.4665 (OUTLIER) cc_final: 0.4414 (mt) REVERT: A 1503 LYS cc_start: 0.3753 (OUTLIER) cc_final: 0.2863 (tptm) REVERT: A 1515 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6612 (pp30) REVERT: A 1533 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: A 1537 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: A 1566 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7648 (mp) REVERT: A 1570 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6400 (mtm180) REVERT: A 1582 ASP cc_start: 0.7685 (t0) cc_final: 0.7362 (t0) REVERT: A 1621 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 1634 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 1735 VAL cc_start: 0.9035 (p) cc_final: 0.8811 (p) REVERT: A 1755 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6200 (t80) REVERT: B 46 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7868 (mtp-110) REVERT: B 101 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 131 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.7200 (t0) REVERT: B 162 MET cc_start: 0.7124 (tpt) cc_final: 0.6450 (ttp) REVERT: B 178 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.5057 (ttt) outliers start: 350 outliers final: 134 residues processed: 497 average time/residue: 0.2656 time to fit residues: 180.1061 Evaluate side-chains 351 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 177 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 838 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 LYS Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1293 ARG Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1296 ARG Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1474 MET Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1486 LYS Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1528 ASN Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1570 ARG Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1673 ASP Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1707 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1725 SER Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN C 82 GLN C 89 ASN C 118 GLN A 125 HIS A 146 ASN A 270 ASN A 278 ASN A 360 GLN A 410 GLN A 766 HIS A 774 ASN A 909 HIS A 911 ASN A1276 ASN A1551 ASN A1571 HIS A1709 ASN A1721 HIS A1732 ASN A1762 ASN B 61 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12038 Z= 0.241 Angle : 0.808 14.662 16310 Z= 0.404 Chirality : 0.050 0.710 1901 Planarity : 0.005 0.057 1986 Dihedral : 16.110 98.822 2198 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.89 % Favored : 96.76 % Rotamer: Outliers : 12.81 % Allowed : 22.67 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.22), residues: 1421 helix: 1.91 (0.17), residues: 820 sheet: 0.92 (0.45), residues: 126 loop : -0.60 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 151 HIS 0.007 0.002 HIS A 766 PHE 0.027 0.002 PHE B 54 TYR 0.029 0.002 TYR A1755 ARG 0.006 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 239 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.4839 (mpp) REVERT: A 133 MET cc_start: 0.8199 (tmm) cc_final: 0.7923 (tmm) REVERT: A 181 PHE cc_start: 0.2393 (OUTLIER) cc_final: 0.0274 (t80) REVERT: A 190 TRP cc_start: 0.7725 (m-10) cc_final: 0.7366 (m-10) REVERT: A 206 ASN cc_start: 0.3069 (OUTLIER) cc_final: 0.2294 (t0) REVERT: A 209 ASN cc_start: 0.4006 (OUTLIER) cc_final: 0.3472 (t0) REVERT: A 298 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8407 (t0) REVERT: A 371 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 387 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: A 764 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: A 780 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7285 (t0) REVERT: A 857 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6662 (tttp) REVERT: A 893 LYS cc_start: 0.8319 (tptm) cc_final: 0.7903 (tttm) REVERT: A 918 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 971 PHE cc_start: 0.6832 (t80) cc_final: 0.6224 (t80) REVERT: A 1204 LEU cc_start: 0.8703 (mt) cc_final: 0.8470 (mp) REVERT: A 1251 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8244 (ttpt) REVERT: A 1269 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8299 (m) REVERT: A 1295 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8947 (mt) REVERT: A 1296 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7614 (mtt180) REVERT: A 1323 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7505 (m-40) REVERT: A 1386 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7991 (ttpt) REVERT: A 1399 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 1449 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 1461 ASN cc_start: 0.7838 (m-40) cc_final: 0.7608 (m-40) REVERT: A 1465 LYS cc_start: 0.8280 (tppt) cc_final: 0.7896 (tttm) REVERT: A 1474 MET cc_start: 0.8957 (mtt) cc_final: 0.8734 (mtp) REVERT: A 1479 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8146 (mtpt) REVERT: A 1503 LYS cc_start: 0.3955 (OUTLIER) cc_final: 0.3343 (tptm) REVERT: A 1515 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6148 (pp30) REVERT: A 1537 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: A 1570 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6965 (mtm180) REVERT: A 1602 TYR cc_start: 0.5093 (OUTLIER) cc_final: 0.3581 (t80) REVERT: A 1711 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7596 (pttt) REVERT: A 1749 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 1755 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.5954 (t80) REVERT: B 32 TYR cc_start: 0.8701 (t80) cc_final: 0.8280 (t80) REVERT: B 100 ASP cc_start: 0.8187 (p0) cc_final: 0.7880 (p0) REVERT: B 101 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7962 (mt) REVERT: B 131 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7404 (t0) REVERT: B 178 MET cc_start: 0.7466 (mmm) cc_final: 0.5480 (ttt) outliers start: 165 outliers final: 74 residues processed: 361 average time/residue: 0.2197 time to fit residues: 114.9619 Evaluate side-chains 295 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 192 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1251 LYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1296 ARG Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1386 LYS Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1570 ARG Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.0050 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 136 HIS A1528 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12038 Z= 0.292 Angle : 0.700 9.539 16310 Z= 0.355 Chirality : 0.046 0.519 1901 Planarity : 0.004 0.046 1986 Dihedral : 13.118 70.133 1989 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.31 % Favored : 96.41 % Rotamer: Outliers : 10.02 % Allowed : 24.15 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.96 (0.22), residues: 1421 helix: 1.51 (0.17), residues: 834 sheet: 0.66 (0.45), residues: 127 loop : -0.97 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1408 HIS 0.005 0.001 HIS A 765 PHE 0.020 0.002 PHE B 54 TYR 0.026 0.002 TYR A1755 ARG 0.006 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 198 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.4915 (mpp) REVERT: C 148 MET cc_start: 0.0709 (mmm) cc_final: 0.0290 (mmt) REVERT: A 181 PHE cc_start: 0.2424 (OUTLIER) cc_final: 0.0308 (t80) REVERT: A 184 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 268 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8517 (ptp) REVERT: A 298 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 371 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8779 (mp) REVERT: A 387 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: A 403 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6776 (mtm) REVERT: A 764 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 780 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7389 (t0) REVERT: A 794 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5982 (ttmm) REVERT: A 839 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8368 (pp) REVERT: A 893 LYS cc_start: 0.8354 (tptm) cc_final: 0.7834 (tttt) REVERT: A 918 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8889 (mt) REVERT: A 971 PHE cc_start: 0.6738 (t80) cc_final: 0.6155 (t80) REVERT: A 1251 LYS cc_start: 0.8583 (tmmt) cc_final: 0.8339 (ttmt) REVERT: A 1295 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8965 (mt) REVERT: A 1323 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7540 (m-40) REVERT: A 1399 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 1465 LYS cc_start: 0.8331 (tppt) cc_final: 0.7965 (tttm) REVERT: A 1485 MET cc_start: 0.7438 (mtm) cc_final: 0.7225 (ttm) REVERT: A 1503 LYS cc_start: 0.3737 (OUTLIER) cc_final: 0.3091 (tptm) REVERT: A 1515 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6326 (pp30) REVERT: A 1537 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: A 1602 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.3772 (t80) REVERT: A 1711 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7619 (pttt) REVERT: A 1756 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8724 (mm) REVERT: B 32 TYR cc_start: 0.8692 (t80) cc_final: 0.8286 (t80) REVERT: B 100 ASP cc_start: 0.8346 (p0) cc_final: 0.8098 (p0) REVERT: B 101 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7943 (mt) REVERT: B 131 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7552 (t0) REVERT: B 141 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8404 (mtmm) REVERT: B 178 MET cc_start: 0.7460 (mmm) cc_final: 0.5747 (ttt) outliers start: 129 outliers final: 73 residues processed: 298 average time/residue: 0.2196 time to fit residues: 95.5410 Evaluate side-chains 283 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 185 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1478 GLN B 115 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12038 Z= 0.252 Angle : 0.663 13.590 16310 Z= 0.331 Chirality : 0.044 0.443 1901 Planarity : 0.004 0.040 1986 Dihedral : 11.612 68.454 1929 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.85 % Rotamer: Outliers : 9.86 % Allowed : 25.00 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.69 (0.22), residues: 1421 helix: 1.37 (0.18), residues: 835 sheet: 0.26 (0.44), residues: 133 loop : -1.17 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1408 HIS 0.003 0.001 HIS A 765 PHE 0.020 0.001 PHE B 54 TYR 0.019 0.002 TYR B 180 ARG 0.005 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 195 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2240 (OUTLIER) cc_final: 0.0062 (t80) REVERT: A 204 PHE cc_start: 0.3790 (OUTLIER) cc_final: 0.3459 (t80) REVERT: A 206 ASN cc_start: 0.2734 (OUTLIER) cc_final: 0.2055 (t0) REVERT: A 214 ARG cc_start: 0.8124 (mmp80) cc_final: 0.7893 (mmp80) REVERT: A 371 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 387 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7433 (m-10) REVERT: A 403 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6747 (mtm) REVERT: A 764 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: A 780 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7462 (t0) REVERT: A 794 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5962 (ttmm) REVERT: A 839 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8384 (pp) REVERT: A 918 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8880 (mt) REVERT: A 971 PHE cc_start: 0.6698 (t80) cc_final: 0.6138 (t80) REVERT: A 1251 LYS cc_start: 0.8625 (tmmt) cc_final: 0.8305 (ttmt) REVERT: A 1299 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7830 (ptp-110) REVERT: A 1322 MET cc_start: 0.8042 (mmm) cc_final: 0.7656 (mmm) REVERT: A 1323 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7527 (m-40) REVERT: A 1399 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 1465 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7978 (tttm) REVERT: A 1503 LYS cc_start: 0.3571 (OUTLIER) cc_final: 0.2927 (tptm) REVERT: A 1515 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6292 (pp30) REVERT: A 1537 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 1541 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: A 1602 TYR cc_start: 0.5026 (OUTLIER) cc_final: 0.3549 (t80) REVERT: A 1637 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 1711 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7746 (pttm) REVERT: B 79 GLN cc_start: 0.7362 (mt0) cc_final: 0.7138 (mt0) REVERT: B 100 ASP cc_start: 0.8531 (p0) cc_final: 0.8249 (p0) REVERT: B 131 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7551 (t0) REVERT: B 141 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8462 (mtmm) REVERT: B 142 ILE cc_start: 0.8642 (mm) cc_final: 0.8442 (mt) REVERT: B 178 MET cc_start: 0.7205 (mmm) cc_final: 0.5753 (ttt) outliers start: 127 outliers final: 71 residues processed: 295 average time/residue: 0.2062 time to fit residues: 90.1036 Evaluate side-chains 281 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 186 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12038 Z= 0.213 Angle : 0.632 13.026 16310 Z= 0.313 Chirality : 0.042 0.403 1901 Planarity : 0.004 0.038 1986 Dihedral : 10.834 68.555 1907 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.01 % Favored : 95.78 % Rotamer: Outliers : 8.31 % Allowed : 25.47 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.65 (0.22), residues: 1421 helix: 1.37 (0.18), residues: 833 sheet: 0.17 (0.44), residues: 133 loop : -1.24 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1408 HIS 0.002 0.001 HIS B 115 PHE 0.019 0.001 PHE B 54 TYR 0.017 0.001 TYR B 180 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 201 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2368 (OUTLIER) cc_final: 0.0228 (t80) REVERT: A 182 THR cc_start: 0.4887 (OUTLIER) cc_final: 0.4541 (p) REVERT: A 206 ASN cc_start: 0.2685 (OUTLIER) cc_final: 0.1939 (t0) REVERT: A 371 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 387 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: A 403 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6819 (mtm) REVERT: A 764 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 780 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7392 (t0) REVERT: A 794 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5917 (ttmm) REVERT: A 839 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8351 (pp) REVERT: A 971 PHE cc_start: 0.6636 (t80) cc_final: 0.6114 (t80) REVERT: A 1251 LYS cc_start: 0.8642 (tmmt) cc_final: 0.8334 (ttmt) REVERT: A 1270 LEU cc_start: 0.8976 (tt) cc_final: 0.8702 (tp) REVERT: A 1299 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7797 (ptp-110) REVERT: A 1322 MET cc_start: 0.8015 (mmm) cc_final: 0.7626 (mmm) REVERT: A 1323 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7465 (m-40) REVERT: A 1399 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8601 (mp) REVERT: A 1464 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7982 (tttp) REVERT: A 1465 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7965 (tttm) REVERT: A 1503 LYS cc_start: 0.3575 (OUTLIER) cc_final: 0.2930 (tptm) REVERT: A 1515 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6288 (pp30) REVERT: A 1537 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: A 1541 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: A 1602 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.3393 (t80) REVERT: A 1637 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 1711 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7794 (pttm) REVERT: B 79 GLN cc_start: 0.7393 (mt0) cc_final: 0.7192 (mt0) REVERT: B 100 ASP cc_start: 0.8420 (p0) cc_final: 0.8133 (p0) REVERT: B 178 MET cc_start: 0.7046 (mmm) cc_final: 0.5879 (tmm) outliers start: 107 outliers final: 71 residues processed: 281 average time/residue: 0.2276 time to fit residues: 93.5120 Evaluate side-chains 289 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 196 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN A 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12038 Z= 0.229 Angle : 0.629 11.955 16310 Z= 0.312 Chirality : 0.042 0.395 1901 Planarity : 0.004 0.039 1986 Dihedral : 10.420 67.852 1895 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 8.46 % Allowed : 25.39 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.69 (0.22), residues: 1421 helix: 1.42 (0.18), residues: 820 sheet: 0.19 (0.44), residues: 133 loop : -1.18 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 57 HIS 0.003 0.001 HIS B 122 PHE 0.019 0.001 PHE B 54 TYR 0.027 0.001 TYR B 32 ARG 0.010 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 197 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2280 (OUTLIER) cc_final: 0.0224 (t80) REVERT: A 182 THR cc_start: 0.4977 (OUTLIER) cc_final: 0.4599 (p) REVERT: A 371 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 387 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: A 413 ILE cc_start: 0.7090 (tt) cc_final: 0.6887 (mt) REVERT: A 764 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 771 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6519 (pt0) REVERT: A 794 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6082 (ttmm) REVERT: A 839 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8436 (pp) REVERT: A 971 PHE cc_start: 0.6620 (t80) cc_final: 0.6129 (t80) REVERT: A 1251 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8338 (ttpt) REVERT: A 1270 LEU cc_start: 0.8980 (tt) cc_final: 0.8773 (tp) REVERT: A 1299 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7840 (ptp-110) REVERT: A 1322 MET cc_start: 0.7893 (mmm) cc_final: 0.7486 (mmm) REVERT: A 1323 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7436 (m-40) REVERT: A 1374 MET cc_start: 0.7343 (mtt) cc_final: 0.7112 (mtt) REVERT: A 1399 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 1464 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7997 (tttp) REVERT: A 1465 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7955 (tttm) REVERT: A 1503 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.2916 (tptm) REVERT: A 1515 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6242 (pp30) REVERT: A 1537 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 1541 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: A 1602 TYR cc_start: 0.5239 (OUTLIER) cc_final: 0.3435 (t80) REVERT: A 1637 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 100 ASP cc_start: 0.8414 (p0) cc_final: 0.8083 (p0) REVERT: B 178 MET cc_start: 0.7052 (mmm) cc_final: 0.5922 (tmm) outliers start: 109 outliers final: 76 residues processed: 277 average time/residue: 0.2132 time to fit residues: 87.1120 Evaluate side-chains 285 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 190 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 0.0030 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1551 ASN A1762 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12038 Z= 0.176 Angle : 0.600 12.446 16310 Z= 0.296 Chirality : 0.041 0.384 1901 Planarity : 0.003 0.038 1986 Dihedral : 10.163 68.042 1889 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 7.53 % Allowed : 26.24 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.72 (0.22), residues: 1421 helix: 1.48 (0.18), residues: 825 sheet: 0.27 (0.44), residues: 133 loop : -1.29 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 151 HIS 0.002 0.001 HIS B 134 PHE 0.017 0.001 PHE B 54 TYR 0.026 0.001 TYR B 32 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 201 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2517 (OUTLIER) cc_final: 0.1753 (m-80) REVERT: A 371 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8697 (mp) REVERT: A 387 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: A 771 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6402 (pt0) REVERT: A 778 ILE cc_start: 0.7963 (tt) cc_final: 0.7569 (pt) REVERT: A 794 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6183 (ttmm) REVERT: A 971 PHE cc_start: 0.6537 (t80) cc_final: 0.6079 (t80) REVERT: A 1251 LYS cc_start: 0.8628 (tmmt) cc_final: 0.8355 (ttpt) REVERT: A 1322 MET cc_start: 0.7817 (mmm) cc_final: 0.7415 (mmm) REVERT: A 1323 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7408 (m-40) REVERT: A 1367 ARG cc_start: 0.7594 (ttt90) cc_final: 0.7233 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 1465 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7948 (tttm) REVERT: A 1503 LYS cc_start: 0.3791 (OUTLIER) cc_final: 0.3059 (tptm) REVERT: A 1515 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6241 (pp30) REVERT: A 1537 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: A 1541 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: A 1602 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.3447 (t80) REVERT: A 1637 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8494 (tp) REVERT: B 84 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: B 100 ASP cc_start: 0.8414 (p0) cc_final: 0.8087 (p0) REVERT: B 178 MET cc_start: 0.6928 (mmm) cc_final: 0.5898 (tmm) outliers start: 97 outliers final: 60 residues processed: 273 average time/residue: 0.2291 time to fit residues: 90.8133 Evaluate side-chains 274 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 199 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 125 optimal weight: 8.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A1762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12038 Z= 0.172 Angle : 0.599 12.791 16310 Z= 0.295 Chirality : 0.041 0.373 1901 Planarity : 0.003 0.041 1986 Dihedral : 9.500 67.136 1875 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 6.91 % Allowed : 26.94 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.80 (0.22), residues: 1421 helix: 1.56 (0.18), residues: 827 sheet: 0.33 (0.44), residues: 133 loop : -1.30 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1408 HIS 0.002 0.001 HIS B 134 PHE 0.017 0.001 PHE B 54 TYR 0.027 0.001 TYR B 32 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 198 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2670 (OUTLIER) cc_final: 0.1951 (m-80) REVERT: A 371 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 387 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7330 (m-10) REVERT: A 771 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6362 (pt0) REVERT: A 778 ILE cc_start: 0.7963 (tt) cc_final: 0.7579 (pt) REVERT: A 794 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6145 (ttmm) REVERT: A 893 LYS cc_start: 0.8413 (tptm) cc_final: 0.7999 (tmtt) REVERT: A 1224 ILE cc_start: 0.8540 (tp) cc_final: 0.7956 (pt) REVERT: A 1251 LYS cc_start: 0.8625 (tmmt) cc_final: 0.8362 (ttpt) REVERT: A 1322 MET cc_start: 0.7815 (mmm) cc_final: 0.7406 (mmm) REVERT: A 1323 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7373 (m-40) REVERT: A 1367 ARG cc_start: 0.7593 (ttt90) cc_final: 0.7248 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 1465 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7942 (tttm) REVERT: A 1503 LYS cc_start: 0.3917 (OUTLIER) cc_final: 0.3201 (tptm) REVERT: A 1515 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6070 (pp30) REVERT: A 1537 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 1541 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: A 1602 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.3515 (t80) REVERT: B 84 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 100 ASP cc_start: 0.8417 (p0) cc_final: 0.8086 (p0) REVERT: B 178 MET cc_start: 0.6896 (mmm) cc_final: 0.5964 (tmm) outliers start: 89 outliers final: 68 residues processed: 261 average time/residue: 0.2082 time to fit residues: 81.1571 Evaluate side-chains 277 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 195 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1551 ASN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12038 Z= 0.203 Angle : 0.613 12.621 16310 Z= 0.300 Chirality : 0.041 0.372 1901 Planarity : 0.003 0.037 1986 Dihedral : 9.420 66.559 1875 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.01 % Favored : 95.78 % Rotamer: Outliers : 6.99 % Allowed : 26.86 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.73 (0.22), residues: 1421 helix: 1.49 (0.18), residues: 827 sheet: 0.34 (0.44), residues: 133 loop : -1.34 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 57 HIS 0.003 0.001 HIS B 134 PHE 0.017 0.001 PHE B 54 TYR 0.026 0.001 TYR B 32 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 199 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2552 (OUTLIER) cc_final: 0.1845 (m-80) REVERT: A 371 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 387 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: A 771 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6348 (pt0) REVERT: A 778 ILE cc_start: 0.7938 (tt) cc_final: 0.7571 (pt) REVERT: A 794 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6329 (ttmm) REVERT: A 893 LYS cc_start: 0.8426 (tptm) cc_final: 0.8019 (tmtt) REVERT: A 943 MET cc_start: 0.6752 (mmp) cc_final: 0.6495 (mmt) REVERT: A 952 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7556 (ttt) REVERT: A 971 PHE cc_start: 0.6823 (t80) cc_final: 0.6307 (t80) REVERT: A 1224 ILE cc_start: 0.8550 (tp) cc_final: 0.7962 (pt) REVERT: A 1251 LYS cc_start: 0.8595 (tmmt) cc_final: 0.8332 (ttmt) REVERT: A 1323 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7359 (m-40) REVERT: A 1367 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7274 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8712 (mp) REVERT: A 1464 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7984 (tttp) REVERT: A 1465 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7937 (tttm) REVERT: A 1503 LYS cc_start: 0.4175 (OUTLIER) cc_final: 0.3372 (tptm) REVERT: A 1515 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.6030 (pp30) REVERT: A 1537 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 1541 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: A 1602 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.3573 (t80) REVERT: B 84 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 100 ASP cc_start: 0.8399 (p0) cc_final: 0.8055 (p0) REVERT: B 178 MET cc_start: 0.6899 (mmm) cc_final: 0.5978 (tmm) outliers start: 90 outliers final: 66 residues processed: 263 average time/residue: 0.2120 time to fit residues: 81.9175 Evaluate side-chains 280 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 198 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12038 Z= 0.297 Angle : 0.665 12.004 16310 Z= 0.330 Chirality : 0.044 0.409 1901 Planarity : 0.004 0.036 1986 Dihedral : 9.623 67.011 1875 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.64 % Rotamer: Outliers : 7.07 % Allowed : 26.71 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.50 (0.22), residues: 1421 helix: 1.27 (0.18), residues: 836 sheet: 0.20 (0.44), residues: 133 loop : -1.39 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1408 HIS 0.004 0.001 HIS B 122 PHE 0.020 0.001 PHE A1343 TYR 0.029 0.002 TYR B 32 ARG 0.004 0.000 ARG A1622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 194 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2588 (OUTLIER) cc_final: 0.1843 (m-80) REVERT: A 371 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 387 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: A 771 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6371 (pt0) REVERT: A 778 ILE cc_start: 0.7953 (tt) cc_final: 0.7576 (pt) REVERT: A 794 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6176 (ttmm) REVERT: A 893 LYS cc_start: 0.8469 (tptm) cc_final: 0.8061 (tmtt) REVERT: A 952 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7580 (ttt) REVERT: A 971 PHE cc_start: 0.6908 (t80) cc_final: 0.6366 (t80) REVERT: A 1251 LYS cc_start: 0.8601 (tmmt) cc_final: 0.8344 (ttmt) REVERT: A 1323 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7407 (m-40) REVERT: A 1399 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8692 (mp) REVERT: A 1465 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7954 (tttm) REVERT: A 1503 LYS cc_start: 0.3790 (OUTLIER) cc_final: 0.2814 (tptm) REVERT: A 1515 GLN cc_start: 0.6237 (OUTLIER) cc_final: 0.5923 (pp30) REVERT: A 1537 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: A 1541 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: A 1602 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.3634 (t80) REVERT: B 100 ASP cc_start: 0.8451 (p0) cc_final: 0.8087 (p0) REVERT: B 178 MET cc_start: 0.6950 (mmm) cc_final: 0.5941 (tmm) outliers start: 91 outliers final: 68 residues processed: 261 average time/residue: 0.2054 time to fit residues: 79.5888 Evaluate side-chains 272 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 190 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 116 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.0170 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 ASN A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124530 restraints weight = 15341.215| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.88 r_work: 0.3202 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12038 Z= 0.151 Angle : 0.599 13.659 16310 Z= 0.292 Chirality : 0.040 0.362 1901 Planarity : 0.003 0.035 1986 Dihedral : 9.288 65.374 1875 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.64 % Rotamer: Outliers : 5.75 % Allowed : 28.11 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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: 0.70 (0.22), residues: 1421 helix: 1.46 (0.18), residues: 839 sheet: 0.26 (0.45), residues: 128 loop : -1.37 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 151 HIS 0.003 0.001 HIS C 139 PHE 0.016 0.001 PHE B 54 TYR 0.024 0.001 TYR B 32 ARG 0.003 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.69 seconds wall clock time: 55 minutes 6.05 seconds (3306.05 seconds total)