Starting phenix.real_space_refine on Fri Mar 15 20:37:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/03_2024/6j8g_9781_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/03_2024/6j8g_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/6j8g_9781/03_2024/6j8g_9781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/03_2024/6j8g_9781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/03_2024/6j8g_9781_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/03_2024/6j8g_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: 6.32, per 1000 atoms: 0.54 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: 5.05 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: 2.64 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: 3.80 Time building geometry restraints manager: 5.49 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: 6118 112.61 - 121.74: 7589 121.74 - 130.86: 2377 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: 5830 17.78 - 35.56: 836 35.56 - 53.35: 438 53.35 - 71.13: 147 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: 1669 0.152 - 0.303: 204 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: 147 2.49 - 3.09: 9531 3.09 - 3.69: 17184 3.69 - 4.30: 25645 4.30 - 4.90: 41717 Nonbonded interactions: 94224 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 94219 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.640 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.260 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- 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= 0.677 Angle : 1.538 17.086 16310 Z= 1.053 Chirality : 0.105 0.758 1901 Planarity : 0.010 0.308 1986 Dihedral : 21.728 88.910 4527 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 58.56 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: 2.85 (0.21), residues: 1421 helix: 3.07 (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 579 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 229 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5433 (mpp) REVERT: A 143 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: A 181 PHE cc_start: 0.2692 (OUTLIER) cc_final: 0.1816 (m-10) REVERT: A 206 ASN cc_start: 0.3091 (OUTLIER) cc_final: 0.2353 (t0) REVERT: A 209 ASN cc_start: 0.3985 (OUTLIER) cc_final: 0.3122 (t0) REVERT: A 298 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 371 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 379 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: A 387 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: A 410 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: A 761 MET cc_start: 0.7463 (mtm) cc_final: 0.7018 (mtm) REVERT: A 764 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: A 769 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 774 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6783 (t0) REVERT: A 780 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6931 (t0) REVERT: A 831 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4356 (tp) REVERT: A 848 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 893 LYS cc_start: 0.8319 (tptm) cc_final: 0.8003 (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: 0.8269 (ttpt) REVERT: A 1296 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8223 (mtt180) REVERT: A 1323 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7573 (m-40) REVERT: A 1358 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6064 (mtm-85) REVERT: A 1399 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 1465 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7859 (tttm) REVERT: A 1474 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8826 (mtp) REVERT: A 1478 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: A 1497 ILE cc_start: 0.4667 (OUTLIER) cc_final: 0.4415 (mt) REVERT: A 1503 LYS cc_start: 0.3754 (OUTLIER) cc_final: 0.2862 (tptm) REVERT: A 1515 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6613 (pp30) REVERT: A 1533 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8372 (mtt) REVERT: A 1537 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: A 1566 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7649 (mp) REVERT: A 1570 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6401 (mtm180) REVERT: A 1582 ASP cc_start: 0.7686 (t0) cc_final: 0.7362 (t0) REVERT: A 1621 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 1634 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A 1735 VAL cc_start: 0.9035 (p) cc_final: 0.8811 (p) REVERT: A 1754 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7709 (tmm) REVERT: B 46 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7866 (mtp-110) REVERT: B 101 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 162 MET cc_start: 0.7124 (tpt) cc_final: 0.6451 (ttp) REVERT: B 178 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.5058 (ttt) outliers start: 350 outliers final: 133 residues processed: 497 average time/residue: 0.2664 time to fit residues: 181.1373 Evaluate side-chains 348 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 177 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 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 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: 0.7590 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12038 Z= 0.238 Angle : 0.809 13.965 16310 Z= 0.405 Chirality : 0.051 0.749 1901 Planarity : 0.005 0.057 1986 Dihedral : 16.190 98.125 2192 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.10 % Favored : 96.55 % Rotamer: Outliers : 12.97 % Allowed : 22.52 % 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: 1.53 (0.22), residues: 1421 helix: 1.95 (0.17), residues: 819 sheet: 0.96 (0.45), residues: 126 loop : -0.63 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 151 HIS 0.008 0.002 HIS A 766 PHE 0.025 0.002 PHE B 54 TYR 0.029 0.002 TYR B 180 ARG 0.006 0.001 ARG C 94 *********************** 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 401 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 234 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4692 (mpp) REVERT: A 133 MET cc_start: 0.8163 (tmm) cc_final: 0.7940 (tmm) REVERT: A 181 PHE cc_start: 0.2383 (OUTLIER) cc_final: 0.0272 (t80) REVERT: A 190 TRP cc_start: 0.7755 (m-10) cc_final: 0.7375 (m-10) REVERT: A 206 ASN cc_start: 0.3049 (OUTLIER) cc_final: 0.2284 (t0) REVERT: A 209 ASN cc_start: 0.4014 (OUTLIER) cc_final: 0.3491 (t0) REVERT: A 298 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8414 (t0) REVERT: A 300 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8130 (mtt180) REVERT: A 371 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 387 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: A 755 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8076 (t) REVERT: A 764 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: A 780 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7178 (t0) REVERT: A 857 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6625 (tttp) REVERT: A 893 LYS cc_start: 0.8315 (tptm) cc_final: 0.7900 (tttm) REVERT: A 918 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8696 (mt) REVERT: A 971 PHE cc_start: 0.6851 (t80) cc_final: 0.6242 (t80) REVERT: A 1204 LEU cc_start: 0.8677 (mt) cc_final: 0.8433 (mp) REVERT: A 1251 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (ttpt) REVERT: A 1269 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8317 (m) REVERT: A 1277 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8206 (t) REVERT: A 1295 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8966 (mt) REVERT: A 1296 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7572 (mtt180) REVERT: A 1323 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7474 (m-40) REVERT: A 1399 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 1449 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 1461 ASN cc_start: 0.7765 (m-40) cc_final: 0.7525 (m-40) REVERT: A 1465 LYS cc_start: 0.8286 (tppt) cc_final: 0.7922 (tttm) REVERT: A 1479 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8168 (mtpt) REVERT: A 1503 LYS cc_start: 0.3826 (OUTLIER) cc_final: 0.3147 (tptm) REVERT: A 1515 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6172 (pp30) REVERT: A 1537 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 1570 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6966 (mtm180) REVERT: A 1602 TYR cc_start: 0.5084 (OUTLIER) cc_final: 0.3505 (t80) REVERT: A 1711 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7609 (pttt) REVERT: A 1754 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7797 (tmm) REVERT: B 100 ASP cc_start: 0.8168 (p0) cc_final: 0.7865 (p0) REVERT: B 101 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7959 (mt) REVERT: B 178 MET cc_start: 0.7421 (mmm) cc_final: 0.5435 (ttt) outliers start: 167 outliers final: 76 residues processed: 359 average time/residue: 0.2243 time to fit residues: 116.7607 Evaluate side-chains 297 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 192 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 137 LEU 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 300 ARG 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 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 750 ILE 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 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 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 1251 LYS Chi-restraints excluded: chain A residue 1269 SER 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 1296 ARG Chi-restraints excluded: chain A residue 1299 ARG 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 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 1754 MET Chi-restraints excluded: chain A residue 1756 ILE 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 123 VAL Chi-restraints excluded: chain B residue 130 GLU 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: 0.9990 chunk 108 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 82 GLN C 136 HIS A1478 GLN A1528 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12038 Z= 0.215 Angle : 0.667 9.404 16310 Z= 0.335 Chirality : 0.044 0.450 1901 Planarity : 0.004 0.042 1986 Dihedral : 13.019 68.906 1992 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.45 % Favored : 96.27 % Rotamer: Outliers : 9.94 % Allowed : 24.07 % Favored : 65.99 % 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: 1.06 (0.22), residues: 1421 helix: 1.59 (0.17), residues: 843 sheet: 0.77 (0.45), residues: 128 loop : -0.99 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1408 HIS 0.004 0.001 HIS C 136 PHE 0.018 0.001 PHE B 54 TYR 0.029 0.002 TYR A1755 ARG 0.007 0.001 ARG A1622 *********************** 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 342 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 214 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.4856 (mpp) REVERT: C 148 MET cc_start: 0.0628 (mmm) cc_final: 0.0243 (mmt) REVERT: A 181 PHE cc_start: 0.2390 (OUTLIER) cc_final: 0.0274 (t80) REVERT: A 184 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 298 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8390 (t0) REVERT: A 300 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8278 (mtt180) REVERT: A 371 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8771 (mp) REVERT: A 387 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7418 (m-10) REVERT: A 403 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6764 (mtm) REVERT: A 764 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: A 839 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8395 (pp) REVERT: A 893 LYS cc_start: 0.8332 (tptm) cc_final: 0.7784 (tttm) REVERT: A 918 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8868 (mt) REVERT: A 971 PHE cc_start: 0.6877 (t80) cc_final: 0.6277 (t80) REVERT: A 1251 LYS cc_start: 0.8526 (tmmt) cc_final: 0.8295 (ttmt) REVERT: A 1299 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7744 (ptp-110) REVERT: A 1323 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7525 (m-40) REVERT: A 1399 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 1449 LEU cc_start: 0.9045 (tm) cc_final: 0.8836 (tp) REVERT: A 1465 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7960 (tttm) REVERT: A 1479 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8082 (mtpt) REVERT: A 1503 LYS cc_start: 0.3730 (OUTLIER) cc_final: 0.3085 (tptm) REVERT: A 1515 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6202 (pp30) REVERT: A 1537 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: A 1602 TYR cc_start: 0.5054 (OUTLIER) cc_final: 0.3619 (t80) REVERT: A 1711 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7432 (pttt) REVERT: A 1754 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7743 (tmm) REVERT: B 32 TYR cc_start: 0.8672 (t80) cc_final: 0.8349 (t80) REVERT: B 100 ASP cc_start: 0.8364 (p0) cc_final: 0.8127 (p0) REVERT: B 178 MET cc_start: 0.7300 (mmm) cc_final: 0.5697 (ttt) outliers start: 128 outliers final: 67 residues processed: 313 average time/residue: 0.2190 time to fit residues: 100.1466 Evaluate side-chains 282 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 193 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU 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 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 241 SER 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 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 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 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 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 1264 LEU Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN 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 1479 LYS 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 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 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 109 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 MET 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: 0.9990 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1732 ASN B 115 HIS B 143 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12038 Z= 0.250 Angle : 0.659 14.456 16310 Z= 0.327 Chirality : 0.044 0.433 1901 Planarity : 0.004 0.039 1986 Dihedral : 11.770 68.239 1929 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.27 % Rotamer: Outliers : 9.55 % Allowed : 24.22 % 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: 0.81 (0.22), residues: 1421 helix: 1.44 (0.18), residues: 834 sheet: 0.51 (0.45), residues: 128 loop : -1.12 (0.28), residues: 459 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 0.026 0.002 TYR A1755 ARG 0.005 0.000 ARG A 174 *********************** 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 321 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 198 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2119 (OUTLIER) cc_final: -0.0112 (t80) REVERT: A 206 ASN cc_start: 0.2760 (OUTLIER) cc_final: 0.2003 (t0) REVERT: A 214 ARG cc_start: 0.8099 (mmp80) cc_final: 0.7850 (mmp80) REVERT: A 298 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8508 (t0) REVERT: A 300 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (mtt180) REVERT: A 371 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 387 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: A 403 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6749 (mtm) REVERT: A 764 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: A 839 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 893 LYS cc_start: 0.8443 (tptm) cc_final: 0.7942 (tttt) REVERT: A 971 PHE cc_start: 0.6769 (t80) cc_final: 0.6196 (t80) REVERT: A 1201 MET cc_start: 0.8458 (mmp) cc_final: 0.8240 (mmp) REVERT: A 1251 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8380 (ttmt) REVERT: A 1299 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7819 (ptp-110) REVERT: A 1322 MET cc_start: 0.8020 (mmm) cc_final: 0.7625 (mmm) REVERT: A 1323 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7530 (m-40) REVERT: A 1399 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 1464 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7919 (tttp) REVERT: A 1465 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7971 (tttm) REVERT: A 1479 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8089 (mtpt) REVERT: A 1503 LYS cc_start: 0.3511 (OUTLIER) cc_final: 0.2892 (tptm) REVERT: A 1515 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6207 (pp30) REVERT: A 1537 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: A 1541 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: A 1602 TYR cc_start: 0.4993 (OUTLIER) cc_final: 0.3483 (t80) REVERT: A 1711 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7877 (pttt) REVERT: A 1754 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7618 (tmm) REVERT: B 79 GLN cc_start: 0.7348 (mt0) cc_final: 0.7129 (mt0) REVERT: B 100 ASP cc_start: 0.8518 (p0) cc_final: 0.8226 (p0) REVERT: B 178 MET cc_start: 0.7111 (mmm) cc_final: 0.5698 (ttt) outliers start: 123 outliers final: 69 residues processed: 292 average time/residue: 0.2104 time to fit residues: 91.6481 Evaluate side-chains 280 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 189 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER 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 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 197 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 THR 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 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 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 758 THR 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 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 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 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 1264 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1277 THR 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 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 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 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 1614 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 395 ASN A1732 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12038 Z= 0.178 Angle : 0.608 11.798 16310 Z= 0.301 Chirality : 0.041 0.370 1901 Planarity : 0.003 0.035 1986 Dihedral : 10.928 68.551 1915 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.87 % Favored : 95.92 % Rotamer: Outliers : 6.99 % Allowed : 26.16 % Favored : 66.85 % 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: 0.86 (0.22), residues: 1421 helix: 1.54 (0.18), residues: 829 sheet: 0.41 (0.44), residues: 134 loop : -1.16 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1408 HIS 0.002 0.001 HIS B 115 PHE 0.018 0.001 PHE B 54 TYR 0.033 0.001 TYR A1755 ARG 0.004 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 300 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 210 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2386 (OUTLIER) cc_final: 0.0225 (t80) REVERT: A 204 PHE cc_start: 0.3502 (OUTLIER) cc_final: 0.3257 (t80) REVERT: A 371 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 387 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7360 (m-10) REVERT: A 764 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: A 780 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7482 (t0) REVERT: A 839 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8361 (pp) REVERT: A 971 PHE cc_start: 0.6632 (t80) cc_final: 0.6103 (t80) REVERT: A 1201 MET cc_start: 0.8439 (mmp) cc_final: 0.8219 (mmp) REVERT: A 1251 LYS cc_start: 0.8571 (tmmt) cc_final: 0.8300 (ttmt) REVERT: A 1270 LEU cc_start: 0.8983 (tt) cc_final: 0.8690 (tp) REVERT: A 1322 MET cc_start: 0.7910 (mmm) cc_final: 0.7503 (mmm) REVERT: A 1323 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: A 1367 ARG cc_start: 0.7562 (ttt90) cc_final: 0.7212 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8568 (mp) REVERT: A 1464 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7896 (tttp) REVERT: A 1465 LYS cc_start: 0.8301 (tppt) cc_final: 0.7959 (tttm) REVERT: A 1503 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.3192 (tptm) REVERT: A 1515 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.6106 (pp30) REVERT: A 1537 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: A 1541 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: A 1602 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.3339 (t80) REVERT: A 1711 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7931 (pttt) REVERT: A 1754 MET cc_start: 0.7988 (mmm) cc_final: 0.7648 (tmm) REVERT: B 100 ASP cc_start: 0.8474 (p0) cc_final: 0.8193 (p0) REVERT: B 178 MET cc_start: 0.6999 (mmm) cc_final: 0.5890 (tmm) outliers start: 90 outliers final: 55 residues processed: 277 average time/residue: 0.2155 time to fit residues: 87.1421 Evaluate side-chains 272 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 201 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 131 LEU 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 204 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 293 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 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 764 GLU Chi-restraints excluded: chain A residue 765 HIS 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 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 896 VAL 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 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1464 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 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 1640 SER Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS 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: 0.0050 chunk 124 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.0000 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN A1732 ASN A1762 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12038 Z= 0.145 Angle : 0.577 12.835 16310 Z= 0.285 Chirality : 0.040 0.374 1901 Planarity : 0.003 0.033 1986 Dihedral : 9.814 67.790 1886 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 6.44 % Allowed : 26.63 % Favored : 66.93 % 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: 1.62 (0.18), residues: 833 sheet: 0.56 (0.44), residues: 134 loop : -1.19 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1408 HIS 0.002 0.001 HIS C 139 PHE 0.017 0.001 PHE B 54 TYR 0.037 0.001 TYR A1755 ARG 0.006 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 286 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 203 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2369 (OUTLIER) cc_final: 0.0293 (t80) REVERT: A 204 PHE cc_start: 0.3760 (OUTLIER) cc_final: 0.3484 (t80) REVERT: A 371 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 387 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: A 772 PHE cc_start: 0.8236 (t80) cc_final: 0.8004 (t80) REVERT: A 839 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 971 PHE cc_start: 0.6546 (t80) cc_final: 0.6063 (t80) REVERT: A 1201 MET cc_start: 0.8408 (mmp) cc_final: 0.8196 (mmp) REVERT: A 1224 ILE cc_start: 0.8530 (tp) cc_final: 0.7973 (pt) REVERT: A 1251 LYS cc_start: 0.8567 (tmmt) cc_final: 0.8306 (ttmt) REVERT: A 1270 LEU cc_start: 0.8977 (tt) cc_final: 0.8742 (tp) REVERT: A 1323 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7407 (m-40) REVERT: A 1367 ARG cc_start: 0.7551 (ttt90) cc_final: 0.7212 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 1465 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (tttm) REVERT: A 1503 LYS cc_start: 0.3947 (OUTLIER) cc_final: 0.3343 (tptm) REVERT: A 1515 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.6022 (pp30) REVERT: A 1537 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 1602 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.3324 (t80) REVERT: A 1754 MET cc_start: 0.7994 (mmm) cc_final: 0.7702 (tmm) REVERT: B 100 ASP cc_start: 0.8398 (p0) cc_final: 0.8032 (p0) REVERT: B 178 MET cc_start: 0.6962 (mmm) cc_final: 0.5938 (tmm) outliers start: 83 outliers final: 49 residues processed: 264 average time/residue: 0.2080 time to fit residues: 81.1770 Evaluate side-chains 254 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 193 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER 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 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 215 THR 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 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 780 ASN Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 808 TRP 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 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 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 1537 GLU 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 1595 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 8.9990 chunk 15 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 0.0020 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12038 Z= 0.239 Angle : 0.617 12.074 16310 Z= 0.306 Chirality : 0.042 0.386 1901 Planarity : 0.004 0.038 1986 Dihedral : 9.485 67.026 1872 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 7.07 % Allowed : 25.93 % Favored : 67.00 % 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: 0.88 (0.22), residues: 1421 helix: 1.57 (0.18), residues: 824 sheet: 0.46 (0.44), residues: 134 loop : -1.17 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 57 HIS 0.002 0.001 HIS B 134 PHE 0.018 0.001 PHE B 54 TYR 0.032 0.002 TYR A1755 ARG 0.003 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 287 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 196 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2404 (OUTLIER) cc_final: 0.0246 (t80) REVERT: A 204 PHE cc_start: 0.3445 (OUTLIER) cc_final: 0.3089 (t80) REVERT: A 300 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8304 (mtt180) REVERT: A 371 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 387 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: A 771 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6543 (pt0) REVERT: A 839 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 952 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7516 (ttt) REVERT: A 971 PHE cc_start: 0.6588 (t80) cc_final: 0.6106 (t80) REVERT: A 1251 LYS cc_start: 0.8572 (tmmt) cc_final: 0.8298 (ttmt) REVERT: A 1322 MET cc_start: 0.7884 (mmm) cc_final: 0.7473 (mmm) REVERT: A 1323 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7460 (m-40) REVERT: A 1399 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 1464 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7923 (tttp) REVERT: A 1465 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8021 (tttm) REVERT: A 1478 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: A 1503 LYS cc_start: 0.3916 (OUTLIER) cc_final: 0.3186 (tptm) REVERT: A 1515 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6140 (pp30) REVERT: A 1537 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 1541 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: A 1602 TYR cc_start: 0.5298 (OUTLIER) cc_final: 0.3482 (t80) REVERT: A 1637 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8438 (tp) REVERT: A 1754 MET cc_start: 0.7978 (mmm) cc_final: 0.7613 (tmm) REVERT: B 100 ASP cc_start: 0.8454 (p0) cc_final: 0.8115 (p0) REVERT: B 178 MET cc_start: 0.6955 (mmm) cc_final: 0.5917 (tmm) outliers start: 91 outliers final: 60 residues processed: 260 average time/residue: 0.1994 time to fit residues: 78.1514 Evaluate side-chains 274 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 195 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 204 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 311 ASP 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 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 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 919 ILE 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 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 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 1478 GLN 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 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 1595 LEU 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 1694 ILE Chi-restraints excluded: chain A residue 1720 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 A1551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12038 Z= 0.191 Angle : 0.595 12.789 16310 Z= 0.293 Chirality : 0.041 0.368 1901 Planarity : 0.003 0.037 1986 Dihedral : 9.351 67.327 1872 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.01 % Favored : 95.78 % Rotamer: Outliers : 6.99 % Allowed : 26.24 % Favored : 66.77 % 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: 0.88 (0.22), residues: 1421 helix: 1.59 (0.18), residues: 826 sheet: 0.40 (0.44), residues: 134 loop : -1.22 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.002 0.001 HIS C 139 PHE 0.017 0.001 PHE B 54 TYR 0.031 0.001 TYR A1755 ARG 0.006 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 292 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 202 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2615 (OUTLIER) cc_final: 0.0560 (t80) REVERT: A 204 PHE cc_start: 0.3511 (OUTLIER) cc_final: 0.3155 (t80) REVERT: A 300 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8297 (mtt180) REVERT: A 371 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 387 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: A 771 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6421 (pt0) REVERT: A 839 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8445 (pp) REVERT: A 893 LYS cc_start: 0.8435 (tptm) cc_final: 0.8031 (tmtt) REVERT: A 952 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7532 (ttt) REVERT: A 1224 ILE cc_start: 0.8562 (tp) cc_final: 0.7991 (pt) REVERT: A 1251 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8316 (ttmt) REVERT: A 1322 MET cc_start: 0.7745 (mmm) cc_final: 0.7300 (mmm) REVERT: A 1323 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7394 (m-40) REVERT: A 1367 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7282 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 1464 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7914 (tttp) REVERT: A 1465 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8063 (tttm) REVERT: A 1478 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: A 1503 LYS cc_start: 0.3866 (OUTLIER) cc_final: 0.3169 (tptm) REVERT: A 1515 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6175 (pp30) REVERT: A 1537 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: A 1541 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: A 1602 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.3513 (t80) REVERT: A 1637 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 1754 MET cc_start: 0.7979 (mmm) cc_final: 0.7612 (tmm) REVERT: B 84 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: B 100 ASP cc_start: 0.8395 (p0) cc_final: 0.8039 (p0) REVERT: B 178 MET cc_start: 0.6896 (mmm) cc_final: 0.5908 (tmm) outliers start: 90 outliers final: 58 residues processed: 268 average time/residue: 0.2048 time to fit residues: 82.3456 Evaluate side-chains 277 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 199 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 PHE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 311 ASP 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 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 919 ILE 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 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 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 1478 GLN 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 1541 GLN 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 1720 VAL 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: 0.0770 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 55 optimal weight: 0.0970 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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 B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4983 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= 0.136 Angle : 0.572 13.316 16310 Z= 0.281 Chirality : 0.040 0.363 1901 Planarity : 0.003 0.032 1986 Dihedral : 9.018 63.950 1872 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 4.89 % Allowed : 28.34 % Favored : 66.77 % 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: 1.00 (0.22), residues: 1421 helix: 1.70 (0.18), residues: 834 sheet: 0.53 (0.44), residues: 128 loop : -1.26 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1408 HIS 0.002 0.001 HIS C 139 PHE 0.015 0.001 PHE B 54 TYR 0.031 0.001 TYR A1755 ARG 0.004 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 279 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 216 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2783 (OUTLIER) cc_final: 0.0742 (t80) REVERT: A 204 PHE cc_start: 0.3911 (OUTLIER) cc_final: 0.3480 (t80) REVERT: A 364 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: A 371 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8718 (mp) REVERT: A 387 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: A 771 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6123 (pm20) REVERT: A 778 ILE cc_start: 0.7879 (tt) cc_final: 0.7540 (pt) REVERT: A 893 LYS cc_start: 0.8415 (tptm) cc_final: 0.8013 (tmtt) REVERT: A 968 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7037 (tt) REVERT: A 971 PHE cc_start: 0.6748 (t80) cc_final: 0.6276 (t80) REVERT: A 1224 ILE cc_start: 0.8497 (tp) cc_final: 0.7988 (pt) REVERT: A 1251 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8395 (ttpt) REVERT: A 1323 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7332 (m-40) REVERT: A 1367 ARG cc_start: 0.7598 (ttt90) cc_final: 0.7276 (ttt-90) REVERT: A 1465 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8159 (tttm) REVERT: A 1478 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: A 1503 LYS cc_start: 0.4069 (OUTLIER) cc_final: 0.3413 (tptm) REVERT: A 1515 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5832 (pp30) REVERT: A 1537 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: A 1602 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.3532 (t80) REVERT: A 1754 MET cc_start: 0.8015 (mmm) cc_final: 0.7637 (tmm) REVERT: B 100 ASP cc_start: 0.8346 (p0) cc_final: 0.7964 (p0) REVERT: B 178 MET cc_start: 0.6819 (mmm) cc_final: 0.5971 (tmm) outliers start: 63 outliers final: 44 residues processed: 263 average time/residue: 0.2099 time to fit residues: 82.4093 Evaluate side-chains 266 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 SER 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 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 733 PHE 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 808 TRP 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 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 1419 VAL Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1478 GLN 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 1537 GLU 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 1694 ILE Chi-restraints excluded: chain A residue 1720 VAL 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 112 THR Chi-restraints excluded: chain B residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN A 270 ASN A1551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12038 Z= 0.410 Angle : 0.700 11.802 16310 Z= 0.354 Chirality : 0.046 0.460 1901 Planarity : 0.004 0.038 1986 Dihedral : 9.392 68.190 1867 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.78 % Rotamer: Outliers : 5.67 % Allowed : 27.56 % Favored : 66.77 % 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: 0.46 (0.22), residues: 1421 helix: 1.21 (0.18), residues: 836 sheet: 0.39 (0.46), residues: 130 loop : -1.42 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1408 HIS 0.004 0.001 HIS B 122 PHE 0.024 0.002 PHE A1343 TYR 0.029 0.002 TYR A 405 ARG 0.006 0.001 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 272 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 199 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.2701 (OUTLIER) cc_final: 0.0653 (t80) REVERT: A 371 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 387 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: A 771 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6523 (pt0) REVERT: A 778 ILE cc_start: 0.7922 (tt) cc_final: 0.7569 (pt) REVERT: A 799 ASP cc_start: 0.7083 (m-30) cc_final: 0.6856 (m-30) REVERT: A 893 LYS cc_start: 0.8478 (tptm) cc_final: 0.8104 (tmtt) REVERT: A 952 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7552 (ttt) REVERT: A 971 PHE cc_start: 0.6819 (t80) cc_final: 0.6271 (t80) REVERT: A 1251 LYS cc_start: 0.8544 (tmmt) cc_final: 0.8317 (ttmt) REVERT: A 1323 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7393 (m-40) REVERT: A 1464 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7990 (tttp) REVERT: A 1465 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8060 (tttm) REVERT: A 1478 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: A 1503 LYS cc_start: 0.3712 (OUTLIER) cc_final: 0.2706 (tptm) REVERT: A 1515 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.5984 (pp30) REVERT: A 1537 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 1602 TYR cc_start: 0.5338 (OUTLIER) cc_final: 0.3641 (t80) REVERT: A 1754 MET cc_start: 0.8023 (mmm) cc_final: 0.7644 (tmm) REVERT: B 84 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 100 ASP cc_start: 0.8515 (p0) cc_final: 0.8143 (p0) REVERT: B 178 MET cc_start: 0.6961 (mmm) cc_final: 0.5955 (tmm) outliers start: 73 outliers final: 48 residues processed: 252 average time/residue: 0.2045 time to fit residues: 77.4110 Evaluate side-chains 257 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 195 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 241 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP 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 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 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 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 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 1478 GLN 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 1537 GLU 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 1720 VAL 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 138 VAL Chi-restraints excluded: chain B residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123026 restraints weight = 15302.164| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.86 r_work: 0.3189 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 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 = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12038 Z= 0.175 Angle : 0.605 13.420 16310 Z= 0.300 Chirality : 0.041 0.358 1901 Planarity : 0.004 0.036 1986 Dihedral : 9.152 67.598 1867 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.66 % Favored : 96.06 % Rotamer: Outliers : 4.97 % Allowed : 28.42 % Favored : 66.61 % 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: 0.67 (0.22), residues: 1421 helix: 1.37 (0.18), residues: 843 sheet: 0.34 (0.46), residues: 128 loop : -1.30 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 57 HIS 0.003 0.001 HIS C 139 PHE 0.017 0.001 PHE B 54 TYR 0.028 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: 2985.41 seconds wall clock time: 54 minutes 9.45 seconds (3249.45 seconds total)