Starting phenix.real_space_refine on Sat Dec 9 23:50:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/12_2023/6j8g_9781_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/12_2023/6j8g_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_9781/12_2023/6j8g_9781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/12_2023/6j8g_9781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/12_2023/6j8g_9781_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8g_9781/12_2023/6j8g_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-1.21rc1-5172/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: 6.96, per 1000 atoms: 0.59 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: 5.31 Conformation dependent library (CDL) restraints added in 3.0 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 8 sheets defined 62.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 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: 4.14 Time building geometry restraints manager: 5.75 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.660 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.160 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- 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 : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 350 outliers final: 133 residues processed: 497 average time/residue: 0.2715 time to fit residues: 185.2174 Evaluate side-chains 313 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 180 time to evaluate : 1.224 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 2 residues processed: 133 average time/residue: 0.1651 time to fit residues: 37.2116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 68 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 270 ASN A 278 ASN A 360 GLN A 909 HIS A 911 ASN A1276 ASN A1528 ASN A1551 ASN A1571 HIS ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1721 HIS A1762 ASN B 61 GLN B 102 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12038 Z= 0.237 Angle : 0.812 14.251 16310 Z= 0.407 Chirality : 0.049 0.658 1901 Planarity : 0.005 0.056 1986 Dihedral : 8.648 75.639 1807 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.96 % Favored : 96.69 % Rotamer: Outliers : 4.27 % Allowed : 24.77 % Favored : 70.96 % 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: 1.48 (0.22), residues: 1421 helix: 1.90 (0.17), residues: 825 sheet: 1.06 (0.46), residues: 127 loop : -0.70 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 151 HIS 0.007 0.001 HIS A 766 PHE 0.025 0.002 PHE B 54 TYR 0.027 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 309 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 23 residues processed: 287 average time/residue: 0.2217 time to fit residues: 94.2766 Evaluate side-chains 219 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 1.325 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.1116 time to fit residues: 6.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 136 HIS A 412 ASN A1541 GLN ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12038 Z= 0.204 Angle : 0.671 9.736 16310 Z= 0.336 Chirality : 0.044 0.448 1901 Planarity : 0.004 0.042 1986 Dihedral : 8.121 69.212 1807 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.66 % Favored : 96.06 % Rotamer: Outliers : 4.27 % Allowed : 23.84 % Favored : 71.89 % 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: 1.20 (0.22), residues: 1421 helix: 1.67 (0.17), residues: 838 sheet: 1.02 (0.47), residues: 128 loop : -0.90 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1408 HIS 0.003 0.001 HIS A 766 PHE 0.017 0.001 PHE B 54 TYR 0.024 0.001 TYR A1755 ARG 0.006 0.001 ARG A 214 *********************** 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 271 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 216 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 257 average time/residue: 0.2047 time to fit residues: 79.4454 Evaluate side-chains 219 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.490 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.1191 time to fit residues: 7.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 115 HIS B 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12038 Z= 0.252 Angle : 0.673 14.871 16310 Z= 0.335 Chirality : 0.044 0.426 1901 Planarity : 0.004 0.038 1986 Dihedral : 7.897 72.942 1807 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.59 % Favored : 96.13 % Rotamer: Outliers : 3.03 % Allowed : 26.16 % Favored : 70.81 % 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: 0.91 (0.22), residues: 1421 helix: 1.43 (0.18), residues: 835 sheet: 0.77 (0.46), residues: 128 loop : -0.96 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1408 HIS 0.004 0.001 HIS A 765 PHE 0.018 0.001 PHE B 54 TYR 0.029 0.002 TYR A1755 ARG 0.007 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 228 average time/residue: 0.2087 time to fit residues: 72.8178 Evaluate side-chains 206 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.397 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.1135 time to fit residues: 6.1522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4454 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= 0.215 Angle : 0.635 11.193 16310 Z= 0.317 Chirality : 0.042 0.384 1901 Planarity : 0.004 0.038 1986 Dihedral : 7.587 76.763 1807 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 2.64 % Allowed : 26.01 % Favored : 71.35 % 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: 0.83 (0.22), residues: 1421 helix: 1.42 (0.18), residues: 832 sheet: 0.62 (0.45), residues: 134 loop : -1.07 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 808 HIS 0.003 0.001 HIS B 115 PHE 0.018 0.001 PHE A1763 TYR 0.032 0.002 TYR A1755 ARG 0.007 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 231 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 218 average time/residue: 0.2141 time to fit residues: 71.0263 Evaluate side-chains 196 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.431 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1133 time to fit residues: 5.1856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN A 189 ASN A 265 GLN A 412 ASN A1528 ASN ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12038 Z= 0.308 Angle : 0.669 9.969 16310 Z= 0.335 Chirality : 0.044 0.426 1901 Planarity : 0.004 0.037 1986 Dihedral : 7.550 77.456 1807 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.20 % Rotamer: Outliers : 2.48 % Allowed : 26.63 % Favored : 70.89 % 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: 0.64 (0.22), residues: 1421 helix: 1.29 (0.18), residues: 828 sheet: 0.44 (0.45), residues: 134 loop : -1.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 57 HIS 0.003 0.001 HIS B 122 PHE 0.020 0.001 PHE A1343 TYR 0.030 0.002 TYR A1755 ARG 0.009 0.001 ARG A 217 *********************** 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 218 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 210 average time/residue: 0.2137 time to fit residues: 68.2841 Evaluate side-chains 199 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1100 time to fit residues: 6.0847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1551 ASN ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12038 Z= 0.173 Angle : 0.616 9.689 16310 Z= 0.304 Chirality : 0.041 0.384 1901 Planarity : 0.004 0.041 1986 Dihedral : 7.517 79.195 1807 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 1.40 % Allowed : 27.87 % Favored : 70.73 % 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: 0.71 (0.22), residues: 1421 helix: 1.39 (0.18), residues: 831 sheet: 0.42 (0.45), residues: 134 loop : -1.22 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 92 HIS 0.002 0.001 HIS B 134 PHE 0.016 0.001 PHE B 54 TYR 0.028 0.001 TYR B 32 ARG 0.007 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 209 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 204 average time/residue: 0.2148 time to fit residues: 65.7011 Evaluate side-chains 192 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1118 time to fit residues: 2.9028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.0370 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12038 Z= 0.169 Angle : 0.611 9.801 16310 Z= 0.299 Chirality : 0.041 0.371 1901 Planarity : 0.004 0.035 1986 Dihedral : 7.164 77.298 1807 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 1.48 % Allowed : 28.34 % Favored : 70.19 % 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 (0.23), residues: 1421 helix: 1.45 (0.18), residues: 835 sheet: 0.50 (0.45), residues: 134 loop : -1.16 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1408 HIS 0.003 0.001 HIS B 134 PHE 0.015 0.001 PHE B 54 TYR 0.026 0.001 TYR B 32 ARG 0.008 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 220 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 212 average time/residue: 0.2139 time to fit residues: 68.8018 Evaluate side-chains 200 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1750 time to fit residues: 4.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 116 optimal weight: 0.0370 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12038 Z= 0.151 Angle : 0.617 16.562 16310 Z= 0.297 Chirality : 0.040 0.364 1901 Planarity : 0.003 0.034 1986 Dihedral : 7.190 75.821 1807 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 0.54 % Allowed : 28.96 % Favored : 70.50 % 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: 0.91 (0.23), residues: 1421 helix: 1.54 (0.18), residues: 832 sheet: 0.64 (0.46), residues: 128 loop : -1.12 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1700 HIS 0.002 0.000 HIS B 134 PHE 0.015 0.001 PHE B 54 TYR 0.025 0.001 TYR B 32 ARG 0.007 0.000 ARG A 217 *********************** 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 215 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 214 average time/residue: 0.2184 time to fit residues: 71.0539 Evaluate side-chains 199 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1124 time to fit residues: 2.5324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12038 Z= 0.308 Angle : 0.688 14.049 16310 Z= 0.339 Chirality : 0.044 0.401 1901 Planarity : 0.004 0.039 1986 Dihedral : 7.354 77.531 1807 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 0.47 % Allowed : 29.19 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1421 helix: 1.27 (0.18), residues: 839 sheet: 0.51 (0.46), residues: 131 loop : -1.15 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 808 HIS 0.003 0.001 HIS B 122 PHE 0.021 0.002 PHE A1343 TYR 0.025 0.002 TYR B 32 ARG 0.009 0.001 ARG A 217 ********************** 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 206 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 203 average time/residue: 0.2101 time to fit residues: 65.0894 Evaluate side-chains 196 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1926 time to fit residues: 2.3967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124974 restraints weight = 15333.481| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.00 r_work: 0.3191 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12038 Z= 0.190 Angle : 0.641 15.475 16310 Z= 0.313 Chirality : 0.041 0.360 1901 Planarity : 0.004 0.035 1986 Dihedral : 7.282 77.539 1807 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.15 % Favored : 95.57 % Rotamer: Outliers : 0.23 % Allowed : 29.89 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1421 helix: 1.33 (0.18), residues: 838 sheet: 0.50 (0.47), residues: 125 loop : -1.16 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1700 HIS 0.003 0.001 HIS B 134 PHE 0.016 0.001 PHE B 54 TYR 0.025 0.001 TYR B 32 ARG 0.006 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.20 seconds wall clock time: 52 minutes 0.51 seconds (3120.51 seconds total)