Starting phenix.real_space_refine on Wed Feb 14 23:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj8_25919/02_2024/7tj8_25919_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj8_25919/02_2024/7tj8_25919.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/7tj8_25919/02_2024/7tj8_25919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj8_25919/02_2024/7tj8_25919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj8_25919/02_2024/7tj8_25919_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj8_25919/02_2024/7tj8_25919_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= -0.008 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 C 7087 2.51 5 N 1598 2.21 5 O 1774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 655": "OE1" <-> "OE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A ARG 1020": "NH1" <-> "NH2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "A ARG 1033": "NH1" <-> "NH2" Residue "A GLU 1042": "OE1" <-> "OE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A GLU 1100": "OE1" <-> "OE2" Residue "A GLU 1114": "OE1" <-> "OE2" Residue "A ARG 1352": "NH1" <-> "NH2" Residue "A PHE 1397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1418": "OE1" <-> "OE2" Residue "A TYR 1475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1497": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10551 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8805 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 1045} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "A" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 382 Unusual residues: {'CLR': 1, 'NAG': 2, 'PEV': 3, 'PLM': 6, 'POV': 3} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 1, 'PLM:plan-1': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.41, per 1000 atoms: 0.61 Number of scatterers: 10551 At special positions: 0 Unit cell: (129.897, 110.37, 115.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 4 15.00 O 1774 8.00 N 1598 7.00 C 7087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2412 " - " ASN A 309 " " NAG A2414 " - " ASN A1103 " " NAG B 301 " - " ASN B 121 " Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 5 sheets defined 63.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 118 through 134 removed outlier: 3.835A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.919A pdb=" N GLU A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.833A pdb=" N ASP A 184 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 185 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 195 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.993A pdb=" N THR A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 221 through 259 removed outlier: 4.169A pdb=" N LYS A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 237 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.575A pdb=" N ILE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.906A pdb=" N GLU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 4.749A pdb=" N ASN A 518 " --> pdb=" O CYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 557 removed outlier: 4.583A pdb=" N LEU A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 570 through 582 removed outlier: 4.866A pdb=" N MET A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.773A pdb=" N PHE A 598 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 655 removed outlier: 3.631A pdb=" N SER A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 689 through 700 removed outlier: 4.328A pdb=" N ASP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 732 Proline residue: A 707 - end of helix Processing helix chain 'A' and resid 923 through 930 Processing helix chain 'A' and resid 934 through 953 removed outlier: 4.921A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 953 " --> pdb=" O GLY A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 959 removed outlier: 4.412A pdb=" N ASP A 959 " --> pdb=" O ILE A 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 962 through 989 removed outlier: 4.196A pdb=" N ILE A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 997 removed outlier: 3.931A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1019 removed outlier: 3.528A pdb=" N LEU A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1040 Proline residue: A1025 - end of helix removed outlier: 3.605A pdb=" N LYS A1030 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1042 through 1080 removed outlier: 3.580A pdb=" N VAL A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Proline residue: A1057 - end of helix removed outlier: 5.145A pdb=" N ASN A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1064 " --> pdb=" O ASN A1060 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A1079 " --> pdb=" O MET A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1108 Processing helix chain 'A' and resid 1128 through 1139 removed outlier: 3.610A pdb=" N LEU A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1153 Processing helix chain 'A' and resid 1167 through 1179 removed outlier: 3.510A pdb=" N PHE A1179 " --> pdb=" O PHE A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1203 removed outlier: 3.548A pdb=" N SER A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A1191 " --> pdb=" O MET A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1221 Processing helix chain 'A' and resid 1243 through 1248 removed outlier: 3.972A pdb=" N VAL A1248 " --> pdb=" O PHE A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1269 removed outlier: 3.513A pdb=" N ILE A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1303 removed outlier: 3.607A pdb=" N ALA A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A1286 " --> pdb=" O ALA A1282 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1329 removed outlier: 3.521A pdb=" N PHE A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1357 removed outlier: 4.225A pdb=" N ARG A1352 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A1354 " --> pdb=" O LEU A1350 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N HIS A1355 " --> pdb=" O SER A1351 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N MET A1356 " --> pdb=" O ARG A1352 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU A1357 " --> pdb=" O ILE A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1361 No H-bonds generated for 'chain 'A' and resid 1359 through 1361' Processing helix chain 'A' and resid 1364 through 1401 Proline residue: A1372 - end of helix Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1420 through 1431 Processing helix chain 'A' and resid 1437 through 1448 removed outlier: 3.753A pdb=" N ALA A1442 " --> pdb=" O GLY A1438 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS A1447 " --> pdb=" O ILE A1443 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP A1448 " --> pdb=" O PHE A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1503 removed outlier: 3.693A pdb=" N PHE A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A1494 " --> pdb=" O MET A1490 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1497 " --> pdb=" O VAL A1493 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A1503 " --> pdb=" O LEU A1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 185 removed outlier: 5.295A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 265 through 269 Processing sheet with id= B, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id= C, first strand: chain 'B' and resid 34 through 36 removed outlier: 7.787A pdb=" N ALA B 35 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 144 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= E, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.696A pdb=" N VAL B 122 " --> pdb=" O THR B 137 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1368 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: 2.81 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1618 1.32 - 1.45: 2939 1.45 - 1.57: 5925 1.57 - 1.69: 172 1.69 - 1.82: 151 Bond restraints: 10805 Sorted by residual: bond pdb=" C29 POV A2403 " pdb="C210 POV A2403 " ideal model delta sigma weight residual 1.333 1.642 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" O14 POV A2408 " pdb=" P POV A2408 " ideal model delta sigma weight residual 1.496 1.752 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C31 POV A2402 " pdb=" O31 POV A2402 " ideal model delta sigma weight residual 1.327 1.507 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C31 POV A2408 " pdb=" O31 POV A2408 " ideal model delta sigma weight residual 1.327 1.506 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C21 POV A2402 " pdb=" O21 POV A2402 " ideal model delta sigma weight residual 1.330 1.505 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 10800 not shown) Histogram of bond angle deviations from ideal: 96.54 - 104.06: 158 104.06 - 111.58: 4746 111.58 - 119.10: 4034 119.10 - 126.62: 5454 126.62 - 134.14: 160 Bond angle restraints: 14552 Sorted by residual: angle pdb=" N PHE B 72 " pdb=" CA PHE B 72 " pdb=" C PHE B 72 " ideal model delta sigma weight residual 111.37 130.06 -18.69 1.64e+00 3.72e-01 1.30e+02 angle pdb=" C PRO B 66 " pdb=" CA PRO B 66 " pdb=" CB PRO B 66 " ideal model delta sigma weight residual 111.56 96.54 15.02 1.65e+00 3.67e-01 8.28e+01 angle pdb=" N TYR B 64 " pdb=" CA TYR B 64 " pdb=" C TYR B 64 " ideal model delta sigma weight residual 111.33 121.18 -9.85 1.21e+00 6.83e-01 6.63e+01 angle pdb=" C PHE B 63 " pdb=" N TYR B 64 " pdb=" CA TYR B 64 " ideal model delta sigma weight residual 120.38 129.17 -8.79 1.37e+00 5.33e-01 4.12e+01 angle pdb=" O VAL B 84 " pdb=" C VAL B 84 " pdb=" N GLU B 85 " ideal model delta sigma weight residual 122.06 115.75 6.31 1.14e+00 7.69e-01 3.07e+01 ... (remaining 14547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6248 34.29 - 68.58: 231 68.58 - 102.87: 28 102.87 - 137.16: 4 137.16 - 171.45: 2 Dihedral angle restraints: 6513 sinusoidal: 2878 harmonic: 3635 Sorted by residual: dihedral pdb=" C PRO B 66 " pdb=" N PRO B 66 " pdb=" CA PRO B 66 " pdb=" CB PRO B 66 " ideal model delta harmonic sigma weight residual -120.70 -101.90 -18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" CA LEU A 581 " pdb=" C LEU A 581 " pdb=" N ILE A 582 " pdb=" CA ILE A 582 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA MET B 177 " pdb=" C MET B 177 " pdb=" N ILE B 178 " pdb=" CA ILE B 178 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1595 0.119 - 0.239: 36 0.239 - 0.358: 4 0.358 - 0.478: 2 0.478 - 0.597: 4 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG A2414 " pdb=" ND2 ASN A1103 " pdb=" C2 NAG A2414 " pdb=" O5 NAG A2414 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.91e+00 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 121 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C2 POV A2402 " pdb=" C1 POV A2402 " pdb=" C3 POV A2402 " pdb=" O21 POV A2402 " both_signs ideal model delta sigma weight residual False 2.43 2.94 -0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 1638 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A2403 " 0.235 2.00e-02 2.50e+03 2.35e-01 5.51e+02 pdb=" C29 POV A2403 " -0.236 2.00e-02 2.50e+03 pdb="C210 POV A2403 " -0.233 2.00e-02 2.50e+03 pdb="C211 POV A2403 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1331 " -0.109 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO A1332 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO A1332 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1332 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 84 " -0.032 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C VAL B 84 " 0.104 2.00e-02 2.50e+03 pdb=" O VAL B 84 " -0.037 2.00e-02 2.50e+03 pdb=" N GLU B 85 " -0.034 2.00e-02 2.50e+03 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 69 2.61 - 3.19: 9536 3.19 - 3.76: 14165 3.76 - 4.33: 20418 4.33 - 4.90: 33642 Nonbonded interactions: 77830 Sorted by model distance: nonbonded pdb=" O ASN B 95 " pdb=" OD1 ASN B 95 " model vdw 2.042 3.040 nonbonded pdb=" ND2 ASN B 95 " pdb=" C1 NAG B 302 " model vdw 2.086 3.550 nonbonded pdb=" ND2 ASN B 109 " pdb=" C1 NAG B 303 " model vdw 2.173 3.550 nonbonded pdb=" O ILE A1016 " pdb=" OG1 THR A1019 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR B 138 " pdb=" O7 NAG B 301 " model vdw 2.292 2.440 ... (remaining 77825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.520 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.015 0.309 10805 Z= 0.980 Angle : 1.032 18.692 14552 Z= 0.522 Chirality : 0.057 0.597 1641 Planarity : 0.010 0.235 1736 Dihedral : 17.586 171.453 4155 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.95 % Favored : 93.39 % Rotamer: Outliers : 0.80 % Allowed : 7.83 % Favored : 91.37 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.21), residues: 1226 helix: -1.82 (0.15), residues: 746 sheet: -2.10 (0.56), residues: 69 loop : -1.58 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 610 HIS 0.012 0.002 HIS B 131 PHE 0.026 0.002 PHE B 63 TYR 0.028 0.003 TYR A 354 ARG 0.037 0.003 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 229 time to evaluate : 1.189 Fit side-chains REVERT: A 538 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.8033 (m-40) REVERT: A 661 ASP cc_start: 0.8171 (t70) cc_final: 0.7836 (t0) REVERT: A 1256 ILE cc_start: 0.8828 (mm) cc_final: 0.8529 (mt) REVERT: A 1361 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7814 (mmpt) REVERT: A 1496 MET cc_start: 0.8201 (mmm) cc_final: 0.7902 (mmm) REVERT: A 1497 GLU cc_start: 0.8114 (tp30) cc_final: 0.7894 (tp30) outliers start: 9 outliers final: 4 residues processed: 233 average time/residue: 0.2092 time to fit residues: 71.0185 Evaluate side-chains 192 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.0000 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 960 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10805 Z= 0.172 Angle : 0.642 11.347 14552 Z= 0.327 Chirality : 0.044 0.339 1641 Planarity : 0.007 0.151 1736 Dihedral : 15.246 178.897 1784 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.22 % Allowed : 10.68 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1226 helix: 0.11 (0.19), residues: 753 sheet: -1.62 (0.61), residues: 69 loop : -1.21 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1448 HIS 0.010 0.001 HIS A1199 PHE 0.022 0.001 PHE A 246 TYR 0.014 0.001 TYR A1475 ARG 0.003 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 510 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6424 (t80) REVERT: A 538 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: A 581 LEU cc_start: 0.8385 (mt) cc_final: 0.8149 (mt) REVERT: A 619 SER cc_start: 0.9372 (t) cc_final: 0.8804 (p) REVERT: A 1218 TYR cc_start: 0.8120 (t80) cc_final: 0.7899 (t80) REVERT: A 1324 PHE cc_start: 0.8504 (m-80) cc_final: 0.8255 (m-80) REVERT: A 1361 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7779 (mmtt) outliers start: 25 outliers final: 7 residues processed: 218 average time/residue: 0.2005 time to fit residues: 64.4717 Evaluate side-chains 196 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1263 PHE Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 GLN A1264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10805 Z= 0.159 Angle : 0.577 10.454 14552 Z= 0.289 Chirality : 0.041 0.288 1641 Planarity : 0.006 0.131 1736 Dihedral : 13.888 177.147 1776 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 11.48 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.10 (0.25), residues: 1226 helix: 0.73 (0.19), residues: 756 sheet: -1.48 (0.63), residues: 69 loop : -1.22 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 94 HIS 0.005 0.001 HIS B 131 PHE 0.022 0.001 PHE A 246 TYR 0.013 0.001 TYR A1475 ARG 0.006 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.235 Fit side-chains REVERT: A 510 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6355 (t80) REVERT: A 560 HIS cc_start: 0.5912 (OUTLIER) cc_final: 0.5682 (m90) REVERT: A 619 SER cc_start: 0.9367 (t) cc_final: 0.8806 (p) REVERT: A 1110 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 1218 TYR cc_start: 0.8124 (t80) cc_final: 0.7911 (t80) REVERT: A 1361 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7690 (mmtt) outliers start: 26 outliers final: 11 residues processed: 215 average time/residue: 0.1986 time to fit residues: 64.0304 Evaluate side-chains 207 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 658 CYS Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1263 PHE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 146 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.0060 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10805 Z= 0.177 Angle : 0.565 11.191 14552 Z= 0.282 Chirality : 0.042 0.282 1641 Planarity : 0.004 0.093 1736 Dihedral : 13.159 179.143 1774 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.02 % Allowed : 12.99 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.18 (0.25), residues: 1226 helix: 1.01 (0.20), residues: 752 sheet: -1.34 (0.63), residues: 69 loop : -1.24 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 PHE 0.021 0.001 PHE A 246 TYR 0.014 0.001 TYR A1475 ARG 0.004 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 1.197 Fit side-chains REVERT: A 510 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 619 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 1110 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7888 (pp) REVERT: A 1361 LYS cc_start: 0.7866 (mmtp) cc_final: 0.7598 (mmtt) outliers start: 34 outliers final: 16 residues processed: 216 average time/residue: 0.1996 time to fit residues: 64.7491 Evaluate side-chains 218 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1263 PHE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A1195 ASN B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10805 Z= 0.278 Angle : 0.624 10.577 14552 Z= 0.317 Chirality : 0.044 0.296 1641 Planarity : 0.005 0.092 1736 Dihedral : 13.036 175.620 1774 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 3.38 % Allowed : 14.41 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.07 (0.25), residues: 1226 helix: 0.97 (0.20), residues: 749 sheet: -1.76 (0.59), residues: 69 loop : -1.28 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.007 0.001 HIS B 131 PHE 0.021 0.002 PHE A 246 TYR 0.018 0.001 TYR A1475 ARG 0.005 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 1.043 Fit side-chains REVERT: A 510 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 1296 MET cc_start: 0.6624 (tpp) cc_final: 0.6371 (tpp) REVERT: A 1361 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7594 (mmtt) REVERT: B 50 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8255 (mtmt) outliers start: 38 outliers final: 22 residues processed: 219 average time/residue: 0.1956 time to fit residues: 63.6430 Evaluate side-chains 214 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 659 HIS A 960 GLN B 93 GLN B 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10805 Z= 0.203 Angle : 0.569 10.643 14552 Z= 0.289 Chirality : 0.042 0.336 1641 Planarity : 0.004 0.091 1736 Dihedral : 12.503 170.270 1774 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 2.31 % Allowed : 16.37 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1226 helix: 1.14 (0.20), residues: 750 sheet: -1.65 (0.58), residues: 69 loop : -1.31 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.005 0.001 HIS B 131 PHE 0.021 0.001 PHE A 246 TYR 0.017 0.001 TYR A1475 ARG 0.005 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.198 Fit side-chains REVERT: A 510 PHE cc_start: 0.7445 (t80) cc_final: 0.6812 (t80) REVERT: A 1296 MET cc_start: 0.6619 (tpp) cc_final: 0.6373 (tpp) REVERT: A 1361 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7457 (mmtt) outliers start: 26 outliers final: 17 residues processed: 215 average time/residue: 0.1882 time to fit residues: 60.1193 Evaluate side-chains 211 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS B 93 GLN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10805 Z= 0.209 Angle : 0.572 10.242 14552 Z= 0.290 Chirality : 0.042 0.278 1641 Planarity : 0.004 0.089 1736 Dihedral : 12.272 165.132 1774 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 2.58 % Allowed : 16.73 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.30 (0.25), residues: 1226 helix: 1.20 (0.20), residues: 753 sheet: -1.66 (0.58), residues: 69 loop : -1.35 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 PHE 0.022 0.001 PHE A 246 TYR 0.016 0.001 TYR A1475 ARG 0.002 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.194 Fit side-chains REVERT: A 510 PHE cc_start: 0.7468 (t80) cc_final: 0.6855 (t80) REVERT: A 1361 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7451 (mmtt) REVERT: B 78 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6816 (mtt90) outliers start: 29 outliers final: 22 residues processed: 217 average time/residue: 0.2049 time to fit residues: 64.9099 Evaluate side-chains 217 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10805 Z= 0.155 Angle : 0.541 10.475 14552 Z= 0.273 Chirality : 0.041 0.239 1641 Planarity : 0.004 0.090 1736 Dihedral : 11.775 158.542 1774 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 2.05 % Allowed : 17.44 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.51 (0.25), residues: 1226 helix: 1.38 (0.20), residues: 752 sheet: -1.47 (0.60), residues: 69 loop : -1.31 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.003 0.001 HIS A 560 PHE 0.021 0.001 PHE A 246 TYR 0.015 0.001 TYR A1475 ARG 0.002 0.000 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.302 Fit side-chains REVERT: A 510 PHE cc_start: 0.7234 (t80) cc_final: 0.6631 (t80) REVERT: B 51 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8185 (mtp85) outliers start: 23 outliers final: 20 residues processed: 215 average time/residue: 0.2040 time to fit residues: 64.3729 Evaluate side-chains 214 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.1980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 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 659 HIS A1254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10805 Z= 0.176 Angle : 0.558 10.195 14552 Z= 0.281 Chirality : 0.041 0.240 1641 Planarity : 0.004 0.088 1736 Dihedral : 11.632 151.755 1774 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 2.05 % Allowed : 17.62 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.56 (0.25), residues: 1226 helix: 1.44 (0.20), residues: 752 sheet: -1.54 (0.59), residues: 69 loop : -1.30 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 94 HIS 0.003 0.001 HIS B 131 PHE 0.025 0.001 PHE B 63 TYR 0.015 0.001 TYR A1475 ARG 0.004 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 1.237 Fit side-chains REVERT: A 510 PHE cc_start: 0.7298 (t80) cc_final: 0.6708 (t80) outliers start: 23 outliers final: 22 residues processed: 215 average time/residue: 0.2068 time to fit residues: 64.3999 Evaluate side-chains 214 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10805 Z= 0.132 Angle : 0.535 10.489 14552 Z= 0.267 Chirality : 0.040 0.245 1641 Planarity : 0.004 0.090 1736 Dihedral : 11.187 139.808 1774 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 1.60 % Allowed : 18.68 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.74 (0.25), residues: 1226 helix: 1.62 (0.20), residues: 749 sheet: -1.65 (0.57), residues: 76 loop : -1.22 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 94 HIS 0.003 0.001 HIS A 560 PHE 0.025 0.001 PHE B 63 TYR 0.013 0.001 TYR A1475 ARG 0.007 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 510 PHE cc_start: 0.7061 (t80) cc_final: 0.6666 (t80) REVERT: A 680 ASN cc_start: 0.8913 (t0) cc_final: 0.8685 (t0) REVERT: A 1490 MET cc_start: 0.9302 (ttp) cc_final: 0.8968 (ttt) outliers start: 18 outliers final: 16 residues processed: 205 average time/residue: 0.1980 time to fit residues: 59.2592 Evaluate side-chains 204 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.1604 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117119 restraints weight = 16074.287| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.37 r_work: 0.3214 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10805 Z= 0.168 Angle : 0.558 10.196 14552 Z= 0.279 Chirality : 0.041 0.241 1641 Planarity : 0.004 0.086 1736 Dihedral : 11.110 129.288 1774 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 1.60 % Allowed : 18.51 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.78 (0.25), residues: 1226 helix: 1.64 (0.20), residues: 752 sheet: -1.64 (0.57), residues: 76 loop : -1.22 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 94 HIS 0.003 0.001 HIS A1199 PHE 0.023 0.001 PHE B 63 TYR 0.014 0.001 TYR A1475 ARG 0.006 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.56 seconds wall clock time: 44 minutes 32.34 seconds (2672.34 seconds total)