Starting phenix.real_space_refine on Mon May 19 00:44:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wea_37476/05_2025/8wea_37476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wea_37476/05_2025/8wea_37476.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/cci-nas-00/data/ceres_data/8wea_37476/05_2025/8wea_37476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wea_37476/05_2025/8wea_37476.map" model { file = "/net/cci-nas-00/data/ceres_data/8wea_37476/05_2025/8wea_37476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wea_37476/05_2025/8wea_37476.cif" } 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= 0.081 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Br 1 7.06 5 S 92 5.16 5 C 11099 2.51 5 N 2826 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9335 Classifications: {'peptide': 1206} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 39, 'TRANS': 1166} Chain breaks: 12 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 211 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 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 Chain: "C" 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: 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 Chain: "F" 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: "G" 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: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' CA': 1, '9Z9': 1, 'WB9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 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 Time building chain proxies: 9.35, per 1000 atoms: 0.54 Number of scatterers: 17188 At special positions: 0 Unit cell: (137.022, 141.478, 176.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 1 34.99 Ca 2 19.99 S 92 16.00 O 3168 8.00 N 2826 7.00 C 11099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.02 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.02 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.04 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG E 3 " - " NAG E 4 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG C 1 " - " ASN D 348 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 468 " " NAG F 1 " - " ASN D 613 " " NAG G 1 " - " ASN D 895 " Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.0 seconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 14 sheets defined 55.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.513A pdb=" N ILE A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.703A pdb=" N SER A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 181 removed outlier: 3.654A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.579A pdb=" N ASP A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.872A pdb=" N VAL A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.672A pdb=" N VAL A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 270 removed outlier: 3.690A pdb=" N HIS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 271 through 291 removed outlier: 3.687A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.581A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 4.250A pdb=" N TYR A 384 " --> pdb=" O TRP A 380 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 419 removed outlier: 3.638A pdb=" N LEU A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 445 removed outlier: 4.033A pdb=" N TRP A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 523 Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.759A pdb=" N TYR A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 578 removed outlier: 3.962A pdb=" N VAL A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 586 through 607 Processing helix chain 'A' and resid 613 through 623 Processing helix chain 'A' and resid 623 through 630 removed outlier: 4.465A pdb=" N ILE A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 630 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 removed outlier: 4.374A pdb=" N ASN A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 673 Processing helix chain 'A' and resid 691 through 705 Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 729 through 755 removed outlier: 3.814A pdb=" N PHE A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 737 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 741 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 761 Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 898 through 902 removed outlier: 6.054A pdb=" N ILE A 901 " --> pdb=" O ASN A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 912 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.118A pdb=" N LEU A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 970 removed outlier: 3.866A pdb=" N LEU A 953 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 954 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN A 955 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 956 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1005 Processing helix chain 'A' and resid 1006 through 1008 No H-bonds generated for 'chain 'A' and resid 1006 through 1008' Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1018 through 1021 Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 4.078A pdb=" N LEU A1026 " --> pdb=" O VAL A1022 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A1028 " --> pdb=" O ARG A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1072 removed outlier: 3.509A pdb=" N THR A1056 " --> pdb=" O ILE A1052 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A1069 " --> pdb=" O CYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1120 through 1133 removed outlier: 3.637A pdb=" N SER A1132 " --> pdb=" O LEU A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1186 removed outlier: 3.781A pdb=" N TYR A1169 " --> pdb=" O PHE A1165 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE A1170 " --> pdb=" O PHE A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1192 Processing helix chain 'A' and resid 1206 through 1214 Processing helix chain 'A' and resid 1226 through 1238 removed outlier: 3.556A pdb=" N VAL A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1254 removed outlier: 3.530A pdb=" N GLU A1242 " --> pdb=" O SER A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1291 Processing helix chain 'A' and resid 1294 through 1300 Processing helix chain 'A' and resid 1301 through 1323 Processing helix chain 'A' and resid 1374 through 1383 removed outlier: 3.798A pdb=" N PHE A1379 " --> pdb=" O PHE A1375 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A1382 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1388 Processing helix chain 'A' and resid 1391 through 1403 removed outlier: 3.526A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1430 Processing helix chain 'A' and resid 1449 through 1462 Processing helix chain 'A' and resid 1465 through 1472 removed outlier: 3.739A pdb=" N ILE A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1526 Processing helix chain 'A' and resid 1542 through 1550 removed outlier: 4.296A pdb=" N LYS A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1566 removed outlier: 3.629A pdb=" N VAL A1566 " --> pdb=" O LEU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1594 removed outlier: 4.010A pdb=" N LYS A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1618 removed outlier: 4.115A pdb=" N THR A1609 " --> pdb=" O MET A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1634 removed outlier: 3.644A pdb=" N GLN A1628 " --> pdb=" O GLY A1624 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 52 removed outlier: 3.579A pdb=" N ILE D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.686A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.722A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 111 removed outlier: 3.507A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.693A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.680A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.690A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.531A pdb=" N VAL D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.529A pdb=" N LYS D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.551A pdb=" N LEU D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.589A pdb=" N ASN D 377 " --> pdb=" O PHE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.696A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.526A pdb=" N THR D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.561A pdb=" N LEU D 430 " --> pdb=" O TYR D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 4.134A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.711A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.679A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 647 through 651 Proline residue: D 650 - end of helix No H-bonds generated for 'chain 'D' and resid 647 through 651' Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 675 through 685 Processing helix chain 'D' and resid 699 through 719 removed outlier: 3.987A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.757A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.601A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN D 770 " --> pdb=" O ARG D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.591A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 827 " --> pdb=" O GLU D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 871 removed outlier: 3.728A pdb=" N ILE D 871 " --> pdb=" O THR D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 879 removed outlier: 3.707A pdb=" N ILE D 878 " --> pdb=" O PHE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 889 Processing helix chain 'D' and resid 1021 through 1024 Processing helix chain 'D' and resid 1042 through 1047 removed outlier: 3.540A pdb=" N VAL D1047 " --> pdb=" O PRO D1043 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298 removed outlier: 3.761A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 333 " --> pdb=" O THR A 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1077 through 1078 Processing sheet with id=AA3, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.027A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 464 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.027A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 464 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA8, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.182A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.618A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 515 " --> pdb=" O SER D 618 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 618 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 658 through 659 Processing sheet with id=AB2, first strand: chain 'D' and resid 729 through 736 removed outlier: 4.364A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB4, first strand: chain 'D' and resid 859 through 861 removed outlier: 4.601A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 852 " --> pdb=" O MET D 861 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D1017 " --> pdb=" O HIS D1004 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.606A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 976 " --> pdb=" O ASP D 899 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2424 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: 6.54 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 4326 1.33 - 1.48: 5584 1.48 - 1.63: 7502 1.63 - 1.78: 2 1.78 - 1.92: 138 Bond restraints: 17552 Sorted by residual: bond pdb=" CA ASP A 311 " pdb=" C ASP A 311 " ideal model delta sigma weight residual 1.524 1.467 0.057 7.00e-03 2.04e+04 6.68e+01 bond pdb=" CA PRO A 146 " pdb=" CB PRO A 146 " ideal model delta sigma weight residual 1.535 1.447 0.088 1.12e-02 7.97e+03 6.13e+01 bond pdb=" CA CYS A 316 " pdb=" C CYS A 316 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.24e-02 6.50e+03 4.81e+01 bond pdb=" CA ILE A 145 " pdb=" C ILE A 145 " ideal model delta sigma weight residual 1.524 1.452 0.072 1.05e-02 9.07e+03 4.75e+01 bond pdb=" CA PHE A 147 " pdb=" C PHE A 147 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.26e-02 6.30e+03 4.22e+01 ... (remaining 17547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.93: 23796 8.93 - 17.86: 18 17.86 - 26.78: 3 26.78 - 35.71: 2 35.71 - 44.64: 3 Bond angle restraints: 23822 Sorted by residual: angle pdb=" C02 WB9 A2303 " pdb=" C03 WB9 A2303 " pdb=" C04 WB9 A2303 " ideal model delta sigma weight residual 110.97 66.33 44.64 3.00e+00 1.11e-01 2.21e+02 angle pdb=" C02 WB9 A2303 " pdb=" C07 WB9 A2303 " pdb=" C06 WB9 A2303 " ideal model delta sigma weight residual 110.79 67.13 43.66 3.00e+00 1.11e-01 2.12e+02 angle pdb=" C07 WB9 A2303 " pdb=" C02 WB9 A2303 " pdb=" C32 WB9 A2303 " ideal model delta sigma weight residual 119.67 79.82 39.85 3.00e+00 1.11e-01 1.76e+02 angle pdb=" N ALA A1032 " pdb=" CA ALA A1032 " pdb=" C ALA A1032 " ideal model delta sigma weight residual 113.21 99.40 13.81 1.15e+00 7.56e-01 1.44e+02 angle pdb=" C01 WB9 A2303 " pdb=" C02 WB9 A2303 " pdb=" C03 WB9 A2303 " ideal model delta sigma weight residual 112.11 78.74 33.37 3.00e+00 1.11e-01 1.24e+02 ... (remaining 23817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 9907 27.72 - 55.43: 688 55.43 - 83.15: 104 83.15 - 110.87: 43 110.87 - 138.59: 5 Dihedral angle restraints: 10747 sinusoidal: 4454 harmonic: 6293 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 174.29 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 -148.84 62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -140.31 54.31 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 10744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 2736 0.234 - 0.469: 20 0.469 - 0.703: 3 0.703 - 0.938: 0 0.938 - 1.172: 2 Chirality restraints: 2761 Sorted by residual: chirality pdb=" C1 NAG E 3 " pdb=" O4 NAG E 2 " pdb=" C2 NAG E 3 " pdb=" O5 NAG E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.38e+02 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 -2.19 -0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG E 4 " pdb=" O4 NAG E 3 " pdb=" C2 NAG E 4 " pdb=" O5 NAG E 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.16e+01 ... (remaining 2758 not shown) Planarity restraints: 3005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 4 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 4 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 4 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 4 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG E 4 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 3 " -0.321 2.00e-02 2.50e+03 2.71e-01 9.15e+02 pdb=" C7 NAG E 3 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 3 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG E 3 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 3 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.103 2.00e-02 2.50e+03 8.30e-02 8.62e+01 pdb=" C7 NAG E 2 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.129 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.025 2.00e-02 2.50e+03 ... (remaining 3002 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 188 2.52 - 3.12: 14833 3.12 - 3.71: 26911 3.71 - 4.31: 38097 4.31 - 4.90: 60195 Nonbonded interactions: 140224 Sorted by model distance: nonbonded pdb=" NH2 ARG A 511 " pdb=" CE2 PHE A 512 " model vdw 1.927 3.420 nonbonded pdb=" CZ ARG A 511 " pdb=" CE2 PHE A 512 " model vdw 1.966 3.570 nonbonded pdb=" OH TYR D 788 " pdb=" O THR D 868 " model vdw 2.197 3.040 nonbonded pdb=" O4 NAG C 2 " pdb=" O7 NAG C 2 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR D 599 " pdb=" OD2 ASP D 854 " model vdw 2.203 3.040 ... (remaining 140219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } 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: 1.830 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.870 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.008 0.089 17577 Z= 0.588 Angle : 1.311 44.639 23887 Z= 0.777 Chirality : 0.068 1.172 2761 Planarity : 0.009 0.291 2998 Dihedral : 19.629 138.585 6643 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.40 % Favored : 88.89 % Rotamer: Outliers : 5.51 % Allowed : 23.80 % Favored : 70.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % 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: -2.74 (0.17), residues: 2116 helix: -1.30 (0.15), residues: 1042 sheet: -0.95 (0.38), residues: 190 loop : -2.59 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 336 HIS 0.004 0.001 HIS A1540 PHE 0.024 0.001 PHE D 686 TYR 0.025 0.001 TYR A 144 ARG 0.013 0.001 ARG D 114 Details of bonding type rmsd link_NAG-ASN : bond 0.01394 ( 7) link_NAG-ASN : angle 5.58628 ( 21) link_BETA1-4 : bond 0.00786 ( 8) link_BETA1-4 : angle 2.40316 ( 24) hydrogen bonds : bond 0.23228 ( 830) hydrogen bonds : angle 8.85376 ( 2424) SS BOND : bond 0.00479 ( 10) SS BOND : angle 0.97792 ( 20) covalent geometry : bond 0.00837 (17552) covalent geometry : angle 1.29996 (23822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 474 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5355 (mt) REVERT: A 175 PHE cc_start: 0.7273 (t80) cc_final: 0.6950 (t80) REVERT: A 214 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6261 (tt0) REVERT: A 234 LYS cc_start: 0.5331 (OUTLIER) cc_final: 0.5025 (ttmm) REVERT: A 263 LYS cc_start: 0.7276 (tptt) cc_final: 0.6481 (mptt) REVERT: A 267 PRO cc_start: 0.8161 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: A 322 HIS cc_start: 0.3873 (OUTLIER) cc_final: 0.2724 (t70) REVERT: A 337 ASP cc_start: 0.4996 (OUTLIER) cc_final: 0.4043 (t0) REVERT: A 531 ILE cc_start: 0.7509 (mp) cc_final: 0.7276 (mm) REVERT: A 625 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7342 (tp) REVERT: A 713 TYR cc_start: 0.5840 (m-10) cc_final: 0.5518 (m-80) REVERT: A 1070 LEU cc_start: 0.8569 (mt) cc_final: 0.8365 (mt) REVERT: A 1102 ASP cc_start: 0.7065 (p0) cc_final: 0.6803 (p0) REVERT: A 1126 MET cc_start: 0.8149 (ptp) cc_final: 0.7776 (ptt) REVERT: A 1159 ARG cc_start: 0.5400 (ttp-110) cc_final: 0.4884 (ttt180) REVERT: A 1161 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: A 1218 PRO cc_start: 0.6318 (Cg_endo) cc_final: 0.5884 (Cg_exo) REVERT: A 1316 ILE cc_start: 0.7708 (pt) cc_final: 0.7439 (pt) REVERT: A 1509 MET cc_start: 0.8055 (mmt) cc_final: 0.7593 (mmt) REVERT: A 1594 MET cc_start: -0.0176 (pmm) cc_final: -0.0399 (mpp) REVERT: D 578 MET cc_start: 0.8747 (mtp) cc_final: 0.8299 (mtp) REVERT: D 595 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7527 (tp40) REVERT: D 678 GLU cc_start: 0.8627 (pt0) cc_final: 0.7971 (mm-30) REVERT: D 680 LEU cc_start: 0.8379 (tp) cc_final: 0.8108 (tt) REVERT: D 719 TYR cc_start: 0.7785 (t80) cc_final: 0.7468 (t80) REVERT: D 848 MET cc_start: 0.4981 (mmm) cc_final: 0.4079 (mmt) REVERT: D 869 ASN cc_start: 0.8866 (t0) cc_final: 0.8471 (t0) REVERT: D 875 PHE cc_start: 0.7172 (t80) cc_final: 0.6778 (t80) REVERT: D 1010 ASN cc_start: 0.7582 (m110) cc_final: 0.7292 (t0) REVERT: D 1017 MET cc_start: 0.6958 (ttm) cc_final: 0.6353 (tpt) outliers start: 99 outliers final: 29 residues processed: 542 average time/residue: 0.2911 time to fit residues: 233.6801 Evaluate side-chains 337 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1260 HIS Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 852 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 0.0670 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 259 ASN A 341 HIS A 510 ASN A 556 GLN A 560 ASN A1103 HIS A1113 ASN A1157 ASN A1205 ASN A1252 ASN A1259 GLN A1260 HIS ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 GLN D 77 GLN D 324 ASN D 406 ASN D 422 ASN D 526 ASN D 713 ASN D1004 HIS D1010 ASN D1033 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.229911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.181703 restraints weight = 23970.723| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.60 r_work: 0.3763 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17577 Z= 0.179 Angle : 0.908 34.599 23887 Z= 0.424 Chirality : 0.047 0.301 2761 Planarity : 0.005 0.084 2998 Dihedral : 15.247 147.082 2840 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.33 % Favored : 93.38 % Rotamer: Outliers : 4.67 % Allowed : 25.53 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.18), residues: 2116 helix: -0.13 (0.16), residues: 1054 sheet: -1.08 (0.36), residues: 212 loop : -2.09 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.007 0.001 HIS A 931 PHE 0.048 0.002 PHE A 909 TYR 0.038 0.002 TYR A1169 ARG 0.006 0.001 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.01071 ( 7) link_NAG-ASN : angle 4.91491 ( 21) link_BETA1-4 : bond 0.00748 ( 8) link_BETA1-4 : angle 3.02314 ( 24) hydrogen bonds : bond 0.05837 ( 830) hydrogen bonds : angle 5.67576 ( 2424) SS BOND : bond 0.00530 ( 10) SS BOND : angle 2.78564 ( 20) covalent geometry : bond 0.00390 (17552) covalent geometry : angle 0.88837 (23822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 327 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ASN cc_start: 0.7791 (m110) cc_final: 0.7570 (m110) REVERT: A 263 LYS cc_start: 0.7265 (tptt) cc_final: 0.6518 (mmtp) REVERT: A 532 PHE cc_start: 0.7590 (t80) cc_final: 0.6458 (t80) REVERT: A 551 TRP cc_start: 0.6927 (t-100) cc_final: 0.6693 (t60) REVERT: A 620 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7806 (mtp85) REVERT: A 683 GLN cc_start: 0.5353 (tp40) cc_final: 0.5131 (mp10) REVERT: A 706 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6688 (tt0) REVERT: A 713 TYR cc_start: 0.6807 (m-10) cc_final: 0.6416 (m-80) REVERT: A 1117 ASP cc_start: 0.7402 (p0) cc_final: 0.7168 (p0) REVERT: A 1126 MET cc_start: 0.7919 (ptp) cc_final: 0.7715 (ptt) REVERT: A 1230 TYR cc_start: 0.7669 (t80) cc_final: 0.7341 (t80) REVERT: A 1242 GLU cc_start: 0.7688 (mp0) cc_final: 0.7462 (mp0) REVERT: A 1509 MET cc_start: 0.7823 (mmt) cc_final: 0.7407 (mmt) REVERT: A 1594 MET cc_start: 0.0120 (pmm) cc_final: -0.0132 (mpp) REVERT: A 1619 ARG cc_start: 0.5343 (OUTLIER) cc_final: 0.4363 (ptt90) REVERT: A 1646 MET cc_start: 0.4442 (pmm) cc_final: 0.3747 (pmm) REVERT: D 41 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: D 578 MET cc_start: 0.8618 (mtp) cc_final: 0.8350 (mtp) REVERT: D 678 GLU cc_start: 0.8608 (pt0) cc_final: 0.7882 (mm-30) REVERT: D 848 MET cc_start: 0.5454 (mmm) cc_final: 0.5235 (mmp) REVERT: D 869 ASN cc_start: 0.8913 (t0) cc_final: 0.8444 (t0) REVERT: D 875 PHE cc_start: 0.7914 (t80) cc_final: 0.7557 (t80) REVERT: D 886 LEU cc_start: 0.8931 (mt) cc_final: 0.8706 (mt) REVERT: D 1017 MET cc_start: 0.7281 (ttm) cc_final: 0.6580 (tpt) outliers start: 84 outliers final: 34 residues processed: 385 average time/residue: 0.2743 time to fit residues: 164.1855 Evaluate side-chains 308 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1260 HIS Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 655 GLU Chi-restraints excluded: chain D residue 711 PHE Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1058 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 chunk 24 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 177 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN A1252 ASN D 77 GLN D 406 ASN D 526 ASN D 684 ASN D 713 ASN D 885 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.212636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170586 restraints weight = 22619.617| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.46 r_work: 0.3445 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17577 Z= 0.185 Angle : 0.777 12.417 23887 Z= 0.376 Chirality : 0.046 0.338 2761 Planarity : 0.005 0.081 2998 Dihedral : 12.786 161.159 2792 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.28 % Rotamer: Outliers : 5.51 % Allowed : 23.80 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2116 helix: 0.28 (0.16), residues: 1059 sheet: -0.96 (0.35), residues: 202 loop : -1.88 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 336 HIS 0.007 0.001 HIS A1260 PHE 0.041 0.002 PHE A 909 TYR 0.018 0.002 TYR A1169 ARG 0.016 0.001 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 7) link_NAG-ASN : angle 4.81375 ( 21) link_BETA1-4 : bond 0.00718 ( 8) link_BETA1-4 : angle 3.32550 ( 24) hydrogen bonds : bond 0.04630 ( 830) hydrogen bonds : angle 5.04299 ( 2424) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.60596 ( 20) covalent geometry : bond 0.00420 (17552) covalent geometry : angle 0.75592 (23822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 287 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.4515 (tp) REVERT: A 151 ASP cc_start: 0.7978 (p0) cc_final: 0.7650 (p0) REVERT: A 179 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7556 (tp) REVERT: A 263 LYS cc_start: 0.7268 (tptt) cc_final: 0.6476 (mmtp) REVERT: A 273 LEU cc_start: 0.8472 (tp) cc_final: 0.8186 (tp) REVERT: A 344 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8018 (p) REVERT: A 526 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5910 (p90) REVERT: A 532 PHE cc_start: 0.7796 (t80) cc_final: 0.6650 (t80) REVERT: A 533 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7835 (tp) REVERT: A 546 TYR cc_start: 0.7073 (t80) cc_final: 0.6712 (t80) REVERT: A 655 LEU cc_start: 0.8170 (mt) cc_final: 0.7788 (mp) REVERT: A 706 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6832 (tt0) REVERT: A 921 ASP cc_start: 0.7044 (t0) cc_final: 0.6653 (t0) REVERT: A 1117 ASP cc_start: 0.7579 (p0) cc_final: 0.7306 (p0) REVERT: A 1125 MET cc_start: 0.8519 (mtt) cc_final: 0.8252 (mtp) REVERT: A 1126 MET cc_start: 0.7901 (ptp) cc_final: 0.7654 (ptt) REVERT: A 1230 TYR cc_start: 0.7567 (t80) cc_final: 0.7283 (t80) REVERT: A 1401 PHE cc_start: 0.7360 (m-80) cc_final: 0.7044 (m-80) REVERT: A 1470 MET cc_start: 0.7219 (tmm) cc_final: 0.6811 (ptm) REVERT: A 1509 MET cc_start: 0.7909 (mmt) cc_final: 0.7544 (mmt) REVERT: A 1541 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.4842 (t-170) REVERT: A 1594 MET cc_start: -0.0116 (pmm) cc_final: -0.0323 (mpp) REVERT: D 41 GLN cc_start: 0.7471 (tt0) cc_final: 0.6945 (tm-30) REVERT: D 424 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8383 (pt0) REVERT: D 578 MET cc_start: 0.8509 (mtp) cc_final: 0.8220 (mtp) REVERT: D 678 GLU cc_start: 0.8417 (pt0) cc_final: 0.7716 (mm-30) REVERT: D 861 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.6117 (ptt) REVERT: D 869 ASN cc_start: 0.8936 (t0) cc_final: 0.8563 (t0) REVERT: D 875 PHE cc_start: 0.8002 (t80) cc_final: 0.7662 (t80) REVERT: D 1017 MET cc_start: 0.7411 (ttm) cc_final: 0.6730 (tpt) outliers start: 99 outliers final: 43 residues processed: 362 average time/residue: 0.2624 time to fit residues: 148.8036 Evaluate side-chains 295 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 167 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 31 optimal weight: 0.0070 chunk 100 optimal weight: 0.0000 chunk 181 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 overall best weight: 0.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN A 537 ASN A 556 GLN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 ASN D 374 ASN D 526 ASN D 751 ASN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.213268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.165435 restraints weight = 22730.799| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.62 r_work: 0.3462 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17577 Z= 0.134 Angle : 0.696 9.340 23887 Z= 0.337 Chirality : 0.044 0.363 2761 Planarity : 0.005 0.085 2998 Dihedral : 11.922 163.489 2789 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 4.06 % Allowed : 25.36 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2116 helix: 0.61 (0.16), residues: 1056 sheet: -0.90 (0.36), residues: 193 loop : -1.73 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1399 HIS 0.004 0.001 HIS A1260 PHE 0.033 0.002 PHE A1405 TYR 0.027 0.001 TYR A1169 ARG 0.012 0.000 ARG A 378 Details of bonding type rmsd link_NAG-ASN : bond 0.00978 ( 7) link_NAG-ASN : angle 4.38294 ( 21) link_BETA1-4 : bond 0.01087 ( 8) link_BETA1-4 : angle 3.25842 ( 24) hydrogen bonds : bond 0.04005 ( 830) hydrogen bonds : angle 4.70843 ( 2424) SS BOND : bond 0.00160 ( 10) SS BOND : angle 1.33863 ( 20) covalent geometry : bond 0.00293 (17552) covalent geometry : angle 0.67525 (23822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 268 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.4648 (tp) REVERT: A 263 LYS cc_start: 0.7126 (tptt) cc_final: 0.6448 (mptt) REVERT: A 273 LEU cc_start: 0.8432 (tp) cc_final: 0.8174 (tp) REVERT: A 344 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 526 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.6031 (p90) REVERT: A 532 PHE cc_start: 0.7857 (t80) cc_final: 0.6847 (t80) REVERT: A 655 LEU cc_start: 0.8287 (mt) cc_final: 0.7887 (mp) REVERT: A 706 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6938 (tt0) REVERT: A 713 TYR cc_start: 0.7237 (m-10) cc_final: 0.6558 (m-80) REVERT: A 1117 ASP cc_start: 0.7867 (p0) cc_final: 0.7550 (p0) REVERT: A 1125 MET cc_start: 0.8460 (mtt) cc_final: 0.8221 (mtp) REVERT: A 1126 MET cc_start: 0.7930 (ptp) cc_final: 0.7671 (ptt) REVERT: A 1230 TYR cc_start: 0.7374 (t80) cc_final: 0.7154 (t80) REVERT: A 1233 TRP cc_start: 0.8363 (t60) cc_final: 0.7990 (t60) REVERT: A 1258 MET cc_start: 0.6982 (tpp) cc_final: 0.6758 (ptm) REVERT: A 1470 MET cc_start: 0.7332 (tmm) cc_final: 0.6852 (ptm) REVERT: A 1509 MET cc_start: 0.7929 (mmt) cc_final: 0.7600 (mmt) REVERT: A 1541 HIS cc_start: 0.6362 (OUTLIER) cc_final: 0.5164 (t-170) REVERT: A 1619 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4070 (ptt90) REVERT: A 1646 MET cc_start: 0.3436 (pmm) cc_final: 0.3174 (pmm) REVERT: D 41 GLN cc_start: 0.7567 (tt0) cc_final: 0.7142 (tm-30) REVERT: D 424 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: D 678 GLU cc_start: 0.8262 (pt0) cc_final: 0.7637 (mm-30) REVERT: D 848 MET cc_start: 0.5547 (mmp) cc_final: 0.2075 (ptt) REVERT: D 861 MET cc_start: 0.6716 (ptt) cc_final: 0.6431 (ptt) REVERT: D 869 ASN cc_start: 0.8929 (t0) cc_final: 0.8569 (t0) REVERT: D 875 PHE cc_start: 0.7984 (t80) cc_final: 0.7652 (t80) REVERT: D 1017 MET cc_start: 0.7396 (ttm) cc_final: 0.6932 (tpt) outliers start: 73 outliers final: 38 residues processed: 319 average time/residue: 0.2490 time to fit residues: 124.6010 Evaluate side-chains 280 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 891 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1065 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 113 optimal weight: 0.0470 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 178 optimal weight: 0.0570 chunk 160 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 526 ASN D 641 GLN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.210264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168400 restraints weight = 22841.397| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.39 r_work: 0.3387 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17577 Z= 0.162 Angle : 0.698 13.471 23887 Z= 0.338 Chirality : 0.044 0.339 2761 Planarity : 0.005 0.088 2998 Dihedral : 11.350 164.383 2789 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 4.23 % Allowed : 25.92 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2116 helix: 0.73 (0.16), residues: 1059 sheet: -0.78 (0.37), residues: 191 loop : -1.70 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.006 0.001 HIS D 885 PHE 0.034 0.002 PHE A1405 TYR 0.016 0.001 TYR D 719 ARG 0.011 0.000 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 7) link_NAG-ASN : angle 4.75437 ( 21) link_BETA1-4 : bond 0.00775 ( 8) link_BETA1-4 : angle 3.38681 ( 24) hydrogen bonds : bond 0.03965 ( 830) hydrogen bonds : angle 4.55858 ( 2424) SS BOND : bond 0.00821 ( 10) SS BOND : angle 1.18573 ( 20) covalent geometry : bond 0.00376 (17552) covalent geometry : angle 0.67546 (23822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5658 (OUTLIER) cc_final: 0.4380 (tp) REVERT: A 179 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 263 LYS cc_start: 0.7196 (tptt) cc_final: 0.6725 (tppt) REVERT: A 273 LEU cc_start: 0.8727 (tp) cc_final: 0.8468 (tp) REVERT: A 281 ILE cc_start: 0.8535 (mt) cc_final: 0.8324 (tt) REVERT: A 418 ARG cc_start: 0.7095 (mmp80) cc_final: 0.6681 (mmm-85) REVERT: A 526 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5906 (p90) REVERT: A 532 PHE cc_start: 0.7825 (t80) cc_final: 0.6855 (t80) REVERT: A 655 LEU cc_start: 0.8187 (mt) cc_final: 0.7774 (mp) REVERT: A 672 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 706 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6954 (tt0) REVERT: A 921 ASP cc_start: 0.7474 (t0) cc_final: 0.7268 (t0) REVERT: A 1117 ASP cc_start: 0.7874 (p0) cc_final: 0.7604 (p0) REVERT: A 1125 MET cc_start: 0.8659 (mtt) cc_final: 0.8451 (mtp) REVERT: A 1126 MET cc_start: 0.7997 (ptp) cc_final: 0.7716 (ptt) REVERT: A 1230 TYR cc_start: 0.7512 (t80) cc_final: 0.7294 (t80) REVERT: A 1233 TRP cc_start: 0.8478 (t60) cc_final: 0.8121 (t60) REVERT: A 1276 MET cc_start: 0.7888 (mmm) cc_final: 0.7602 (mmm) REVERT: A 1420 PHE cc_start: 0.7335 (t80) cc_final: 0.7078 (t80) REVERT: A 1470 MET cc_start: 0.7404 (tmm) cc_final: 0.7001 (ptm) REVERT: A 1509 MET cc_start: 0.8038 (mmt) cc_final: 0.7748 (mmt) REVERT: A 1541 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.4943 (t-170) REVERT: A 1646 MET cc_start: 0.3965 (pmm) cc_final: 0.3428 (pmm) REVERT: D 41 GLN cc_start: 0.7638 (tt0) cc_final: 0.7284 (tm-30) REVERT: D 171 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: D 366 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: D 424 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: D 678 GLU cc_start: 0.8359 (pt0) cc_final: 0.7698 (mm-30) REVERT: D 793 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7619 (ttm) REVERT: D 848 MET cc_start: 0.5465 (mmp) cc_final: 0.2118 (ptt) REVERT: D 854 ASP cc_start: 0.8304 (p0) cc_final: 0.7751 (p0) REVERT: D 861 MET cc_start: 0.7188 (ptt) cc_final: 0.6638 (ptt) REVERT: D 869 ASN cc_start: 0.8922 (t0) cc_final: 0.8565 (t0) REVERT: D 891 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.8017 (p) REVERT: D 1013 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7884 (mm) REVERT: D 1017 MET cc_start: 0.7300 (ttm) cc_final: 0.6891 (tpt) outliers start: 76 outliers final: 48 residues processed: 326 average time/residue: 0.2516 time to fit residues: 127.8577 Evaluate side-chains 297 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 891 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1013 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 207 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 chunk 138 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 526 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.206818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152079 restraints weight = 22681.617| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.63 r_work: 0.3371 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17577 Z= 0.158 Angle : 0.682 12.398 23887 Z= 0.330 Chirality : 0.044 0.328 2761 Planarity : 0.005 0.084 2998 Dihedral : 10.859 167.667 2786 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.34 % Allowed : 25.31 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2116 helix: 0.82 (0.16), residues: 1058 sheet: -0.72 (0.37), residues: 191 loop : -1.67 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.003 0.001 HIS A 341 PHE 0.023 0.002 PHE A 208 TYR 0.018 0.001 TYR A1169 ARG 0.009 0.001 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.00858 ( 7) link_NAG-ASN : angle 4.23703 ( 21) link_BETA1-4 : bond 0.00801 ( 8) link_BETA1-4 : angle 3.29294 ( 24) hydrogen bonds : bond 0.03762 ( 830) hydrogen bonds : angle 4.44276 ( 2424) SS BOND : bond 0.00506 ( 10) SS BOND : angle 0.90945 ( 20) covalent geometry : bond 0.00367 (17552) covalent geometry : angle 0.66211 (23822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 267 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5442 (OUTLIER) cc_final: 0.4022 (tp) REVERT: A 179 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7598 (tp) REVERT: A 263 LYS cc_start: 0.7335 (tptt) cc_final: 0.6908 (tppt) REVERT: A 273 LEU cc_start: 0.8869 (tp) cc_final: 0.8644 (tp) REVERT: A 418 ARG cc_start: 0.7107 (mmp80) cc_final: 0.6777 (mmm-85) REVERT: A 526 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5985 (p90) REVERT: A 532 PHE cc_start: 0.7678 (t80) cc_final: 0.6783 (t80) REVERT: A 539 LEU cc_start: 0.7873 (mt) cc_final: 0.7147 (mt) REVERT: A 672 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 706 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6832 (tt0) REVERT: A 905 LEU cc_start: 0.8361 (mp) cc_final: 0.7933 (tp) REVERT: A 921 ASP cc_start: 0.7569 (t0) cc_final: 0.7354 (t0) REVERT: A 924 GLN cc_start: 0.3252 (tm-30) cc_final: 0.2796 (tm-30) REVERT: A 1117 ASP cc_start: 0.7973 (p0) cc_final: 0.7720 (p0) REVERT: A 1126 MET cc_start: 0.7935 (ptp) cc_final: 0.7684 (ptt) REVERT: A 1230 TYR cc_start: 0.7525 (t80) cc_final: 0.7303 (t80) REVERT: A 1233 TRP cc_start: 0.8475 (t60) cc_final: 0.8196 (t60) REVERT: A 1420 PHE cc_start: 0.7528 (t80) cc_final: 0.7324 (t80) REVERT: A 1470 MET cc_start: 0.7442 (tmm) cc_final: 0.7143 (ptm) REVERT: A 1509 MET cc_start: 0.8142 (mmt) cc_final: 0.7886 (mmt) REVERT: A 1546 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6699 (tttm) REVERT: A 1619 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.3819 (ptt90) REVERT: A 1642 LYS cc_start: 0.3447 (OUTLIER) cc_final: 0.2043 (tmmt) REVERT: A 1646 MET cc_start: 0.3780 (pmm) cc_final: 0.3516 (pmm) REVERT: D 171 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: D 366 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: D 424 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: D 665 ASP cc_start: 0.8381 (t0) cc_final: 0.8176 (t0) REVERT: D 678 GLU cc_start: 0.8406 (pt0) cc_final: 0.7842 (mm-30) REVERT: D 781 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6534 (t0) REVERT: D 793 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7611 (ttm) REVERT: D 848 MET cc_start: 0.5641 (mmp) cc_final: 0.2341 (ptt) REVERT: D 861 MET cc_start: 0.7267 (ptt) cc_final: 0.6661 (ptt) REVERT: D 875 PHE cc_start: 0.7824 (t80) cc_final: 0.7483 (t80) REVERT: D 1013 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7904 (mm) REVERT: D 1017 MET cc_start: 0.7267 (ttm) cc_final: 0.7010 (tpt) outliers start: 78 outliers final: 46 residues processed: 326 average time/residue: 0.2645 time to fit residues: 132.9698 Evaluate side-chains 302 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1498 SER Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 891 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1013 LEU Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 164 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 0.0170 chunk 144 optimal weight: 0.1980 chunk 146 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN D 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.210455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159406 restraints weight = 22690.758| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.58 r_work: 0.3385 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17577 Z= 0.119 Angle : 0.661 11.694 23887 Z= 0.320 Chirality : 0.042 0.330 2761 Planarity : 0.004 0.080 2998 Dihedral : 10.457 172.361 2784 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.73 % Allowed : 26.36 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2116 helix: 0.97 (0.16), residues: 1065 sheet: -0.81 (0.36), residues: 206 loop : -1.65 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 185 HIS 0.002 0.001 HIS A 545 PHE 0.058 0.002 PHE A1405 TYR 0.022 0.001 TYR A1261 ARG 0.008 0.000 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.00866 ( 7) link_NAG-ASN : angle 3.89745 ( 21) link_BETA1-4 : bond 0.00826 ( 8) link_BETA1-4 : angle 3.26131 ( 24) hydrogen bonds : bond 0.03391 ( 830) hydrogen bonds : angle 4.29061 ( 2424) SS BOND : bond 0.00720 ( 10) SS BOND : angle 0.94749 ( 20) covalent geometry : bond 0.00259 (17552) covalent geometry : angle 0.64321 (23822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.4141 (tp) REVERT: A 263 LYS cc_start: 0.7434 (tptt) cc_final: 0.6950 (tppt) REVERT: A 418 ARG cc_start: 0.7075 (mmp80) cc_final: 0.6821 (mmm-85) REVERT: A 526 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.6041 (p90) REVERT: A 532 PHE cc_start: 0.7672 (t80) cc_final: 0.6751 (t80) REVERT: A 655 LEU cc_start: 0.8225 (mt) cc_final: 0.7840 (mp) REVERT: A 921 ASP cc_start: 0.7564 (t0) cc_final: 0.7308 (t0) REVERT: A 924 GLN cc_start: 0.3297 (tm-30) cc_final: 0.2785 (tm-30) REVERT: A 1117 ASP cc_start: 0.8104 (p0) cc_final: 0.7814 (p0) REVERT: A 1230 TYR cc_start: 0.7593 (t80) cc_final: 0.7311 (t80) REVERT: A 1233 TRP cc_start: 0.8503 (t60) cc_final: 0.8213 (t60) REVERT: A 1420 PHE cc_start: 0.7610 (t80) cc_final: 0.7346 (t80) REVERT: A 1470 MET cc_start: 0.7395 (tmm) cc_final: 0.7151 (ptm) REVERT: A 1546 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6695 (tttm) REVERT: A 1619 ARG cc_start: 0.5065 (OUTLIER) cc_final: 0.3875 (ptt90) REVERT: A 1642 LYS cc_start: 0.3307 (OUTLIER) cc_final: 0.1758 (tmmt) REVERT: D 41 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7068 (tm-30) REVERT: D 366 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: D 424 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: D 665 ASP cc_start: 0.8441 (t0) cc_final: 0.8216 (t0) REVERT: D 678 GLU cc_start: 0.8452 (pt0) cc_final: 0.7876 (mm-30) REVERT: D 781 ASN cc_start: 0.6712 (OUTLIER) cc_final: 0.6498 (t0) REVERT: D 848 MET cc_start: 0.5754 (mmp) cc_final: 0.2289 (ptt) REVERT: D 861 MET cc_start: 0.7324 (ptt) cc_final: 0.6781 (ptt) REVERT: D 875 PHE cc_start: 0.7781 (t80) cc_final: 0.7413 (t80) REVERT: D 1013 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7754 (mm) REVERT: D 1017 MET cc_start: 0.7180 (ttm) cc_final: 0.6910 (tpt) outliers start: 67 outliers final: 42 residues processed: 308 average time/residue: 0.2774 time to fit residues: 131.5132 Evaluate side-chains 295 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1013 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN D 682 ASN ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.205653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167732 restraints weight = 22369.100| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.22 r_work: 0.3335 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17577 Z= 0.167 Angle : 0.707 15.080 23887 Z= 0.344 Chirality : 0.044 0.320 2761 Planarity : 0.005 0.078 2998 Dihedral : 10.299 173.497 2784 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.73 % Allowed : 26.42 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2116 helix: 1.00 (0.16), residues: 1069 sheet: -0.70 (0.39), residues: 178 loop : -1.63 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1303 HIS 0.003 0.001 HIS D 306 PHE 0.057 0.002 PHE A1405 TYR 0.024 0.002 TYR D 719 ARG 0.010 0.001 ARG A1570 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 7) link_NAG-ASN : angle 3.98420 ( 21) link_BETA1-4 : bond 0.00813 ( 8) link_BETA1-4 : angle 3.38651 ( 24) hydrogen bonds : bond 0.03671 ( 830) hydrogen bonds : angle 4.35831 ( 2424) SS BOND : bond 0.00245 ( 10) SS BOND : angle 1.03343 ( 20) covalent geometry : bond 0.00392 (17552) covalent geometry : angle 0.68954 (23822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5498 (OUTLIER) cc_final: 0.3966 (tp) REVERT: A 179 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7707 (tp) REVERT: A 263 LYS cc_start: 0.7679 (tptt) cc_final: 0.7215 (tppt) REVERT: A 339 PRO cc_start: 0.8124 (Cg_endo) cc_final: 0.7773 (Cg_exo) REVERT: A 418 ARG cc_start: 0.7107 (mmp80) cc_final: 0.6660 (mmm-85) REVERT: A 526 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.6036 (p90) REVERT: A 532 PHE cc_start: 0.7755 (t80) cc_final: 0.6837 (t80) REVERT: A 655 LEU cc_start: 0.8359 (mt) cc_final: 0.7991 (mp) REVERT: A 670 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7937 (ptp) REVERT: A 672 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8069 (tp) REVERT: A 917 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6658 (pt) REVERT: A 921 ASP cc_start: 0.7528 (t0) cc_final: 0.7284 (t0) REVERT: A 972 MET cc_start: 0.5981 (mmm) cc_final: 0.5491 (mmm) REVERT: A 1117 ASP cc_start: 0.8123 (p0) cc_final: 0.7862 (p0) REVERT: A 1122 LEU cc_start: 0.8761 (tp) cc_final: 0.8496 (mp) REVERT: A 1230 TYR cc_start: 0.7627 (t80) cc_final: 0.7340 (t80) REVERT: A 1474 MET cc_start: 0.6562 (mmm) cc_final: 0.6353 (mmt) REVERT: A 1546 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6941 (tttm) REVERT: A 1619 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.3845 (ptt90) REVERT: A 1642 LYS cc_start: 0.3402 (OUTLIER) cc_final: 0.1676 (tmmt) REVERT: D 41 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 366 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: D 424 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: D 439 ASP cc_start: 0.7715 (m-30) cc_final: 0.7488 (t0) REVERT: D 665 ASP cc_start: 0.8422 (t0) cc_final: 0.8213 (t0) REVERT: D 678 GLU cc_start: 0.8366 (pt0) cc_final: 0.7916 (mm-30) REVERT: D 781 ASN cc_start: 0.6486 (OUTLIER) cc_final: 0.6232 (t0) REVERT: D 793 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7626 (ttm) REVERT: D 848 MET cc_start: 0.6086 (mmp) cc_final: 0.2940 (ptt) REVERT: D 861 MET cc_start: 0.7446 (ptt) cc_final: 0.6901 (ptt) REVERT: D 875 PHE cc_start: 0.7862 (t80) cc_final: 0.7507 (t80) REVERT: D 1013 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8011 (mm) outliers start: 67 outliers final: 44 residues processed: 303 average time/residue: 0.2738 time to fit residues: 130.7298 Evaluate side-chains 296 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1498 SER Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1013 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 50.0000 chunk 187 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN D 684 ASN ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.203306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149036 restraints weight = 22450.529| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.60 r_work: 0.3283 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17577 Z= 0.192 Angle : 0.740 22.340 23887 Z= 0.360 Chirality : 0.045 0.332 2761 Planarity : 0.005 0.080 2998 Dihedral : 10.184 171.218 2783 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.12 % Allowed : 26.70 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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: -0.38 (0.18), residues: 2116 helix: 0.94 (0.16), residues: 1067 sheet: -0.76 (0.38), residues: 182 loop : -1.66 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 720 HIS 0.007 0.001 HIS D 524 PHE 0.065 0.002 PHE A1405 TYR 0.024 0.002 TYR D 719 ARG 0.007 0.001 ARG D 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 7) link_NAG-ASN : angle 4.00688 ( 21) link_BETA1-4 : bond 0.00700 ( 8) link_BETA1-4 : angle 3.40417 ( 24) hydrogen bonds : bond 0.03765 ( 830) hydrogen bonds : angle 4.42905 ( 2424) SS BOND : bond 0.00595 ( 10) SS BOND : angle 1.08307 ( 20) covalent geometry : bond 0.00456 (17552) covalent geometry : angle 0.72301 (23822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5819 (OUTLIER) cc_final: 0.4212 (tp) REVERT: A 179 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7542 (tp) REVERT: A 263 LYS cc_start: 0.7822 (tptt) cc_final: 0.7306 (tppt) REVERT: A 418 ARG cc_start: 0.7020 (mmp80) cc_final: 0.6677 (mmm-85) REVERT: A 526 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6199 (p90) REVERT: A 532 PHE cc_start: 0.7759 (t80) cc_final: 0.6813 (t80) REVERT: A 539 LEU cc_start: 0.7318 (mt) cc_final: 0.7082 (tt) REVERT: A 672 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 917 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6941 (pt) REVERT: A 921 ASP cc_start: 0.7812 (t0) cc_final: 0.7518 (t0) REVERT: A 930 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7396 (p0) REVERT: A 1117 ASP cc_start: 0.8125 (p0) cc_final: 0.7742 (p0) REVERT: A 1122 LEU cc_start: 0.8779 (tp) cc_final: 0.8511 (mp) REVERT: A 1230 TYR cc_start: 0.7795 (t80) cc_final: 0.7460 (t80) REVERT: A 1286 MET cc_start: 0.7878 (ttp) cc_final: 0.7498 (ttt) REVERT: A 1474 MET cc_start: 0.6727 (mmm) cc_final: 0.6446 (mmt) REVERT: A 1483 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7486 (p) REVERT: A 1546 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.7012 (tttm) REVERT: A 1619 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.4462 (ptt90) REVERT: A 1642 LYS cc_start: 0.3544 (OUTLIER) cc_final: 0.1808 (tmmt) REVERT: D 41 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 366 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: D 424 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8107 (pt0) REVERT: D 665 ASP cc_start: 0.8452 (t0) cc_final: 0.8218 (t0) REVERT: D 678 GLU cc_start: 0.8538 (pt0) cc_final: 0.8044 (mm-30) REVERT: D 781 ASN cc_start: 0.6525 (OUTLIER) cc_final: 0.6305 (t0) REVERT: D 793 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7684 (ttm) REVERT: D 848 MET cc_start: 0.6259 (mmp) cc_final: 0.3102 (ptt) REVERT: D 854 ASP cc_start: 0.8294 (p0) cc_final: 0.7749 (p0) REVERT: D 875 PHE cc_start: 0.7840 (t80) cc_final: 0.7464 (t80) REVERT: D 1013 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7843 (mm) outliers start: 74 outliers final: 46 residues processed: 292 average time/residue: 0.2688 time to fit residues: 122.1083 Evaluate side-chains 295 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 527 TYR Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1498 SER Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1013 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 118 optimal weight: 0.0970 chunk 32 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 157 optimal weight: 0.0970 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.207071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152666 restraints weight = 22361.860| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.72 r_work: 0.3322 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17577 Z= 0.130 Angle : 0.719 14.603 23887 Z= 0.343 Chirality : 0.043 0.334 2761 Planarity : 0.004 0.077 2998 Dihedral : 9.474 172.910 2783 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.23 % Allowed : 27.42 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2116 helix: 1.06 (0.16), residues: 1073 sheet: -0.66 (0.37), residues: 194 loop : -1.61 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 185 HIS 0.002 0.001 HIS D 392 PHE 0.056 0.001 PHE A1405 TYR 0.024 0.001 TYR D 719 ARG 0.015 0.000 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.01645 ( 7) link_NAG-ASN : angle 5.62269 ( 21) link_BETA1-4 : bond 0.00778 ( 8) link_BETA1-4 : angle 3.27748 ( 24) hydrogen bonds : bond 0.03373 ( 830) hydrogen bonds : angle 4.30211 ( 2424) SS BOND : bond 0.00390 ( 10) SS BOND : angle 0.94548 ( 20) covalent geometry : bond 0.00288 (17552) covalent geometry : angle 0.69239 (23822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5152 (mt) REVERT: A 179 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7691 (tp) REVERT: A 213 GLU cc_start: 0.4819 (mm-30) cc_final: 0.4516 (mm-30) REVERT: A 263 LYS cc_start: 0.7831 (tptt) cc_final: 0.7329 (tppt) REVERT: A 418 ARG cc_start: 0.7065 (mmp80) cc_final: 0.6777 (mmm-85) REVERT: A 526 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6160 (p90) REVERT: A 532 PHE cc_start: 0.7747 (t80) cc_final: 0.6816 (t80) REVERT: A 539 LEU cc_start: 0.7345 (mt) cc_final: 0.7115 (tt) REVERT: A 917 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7019 (pt) REVERT: A 972 MET cc_start: 0.6138 (mmm) cc_final: 0.5678 (mmm) REVERT: A 1117 ASP cc_start: 0.8103 (p0) cc_final: 0.7727 (p0) REVERT: A 1122 LEU cc_start: 0.8735 (tp) cc_final: 0.8462 (mp) REVERT: A 1230 TYR cc_start: 0.7790 (t80) cc_final: 0.7450 (t80) REVERT: A 1286 MET cc_start: 0.7863 (ttp) cc_final: 0.7425 (ttt) REVERT: A 1474 MET cc_start: 0.6864 (mmm) cc_final: 0.6558 (mmt) REVERT: A 1483 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7346 (p) REVERT: A 1546 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.7021 (tttm) REVERT: A 1619 ARG cc_start: 0.5231 (OUTLIER) cc_final: 0.4263 (ptt90) REVERT: A 1642 LYS cc_start: 0.3381 (OUTLIER) cc_final: 0.1766 (tmmt) REVERT: D 41 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7280 (tm-30) REVERT: D 366 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: D 424 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: D 439 ASP cc_start: 0.7892 (m-30) cc_final: 0.7650 (t0) REVERT: D 665 ASP cc_start: 0.8446 (t0) cc_final: 0.8199 (t0) REVERT: D 678 GLU cc_start: 0.8460 (pt0) cc_final: 0.8014 (mm-30) REVERT: D 781 ASN cc_start: 0.6530 (OUTLIER) cc_final: 0.6302 (t0) REVERT: D 817 ASP cc_start: 0.6359 (p0) cc_final: 0.6067 (p0) REVERT: D 848 MET cc_start: 0.6225 (mmp) cc_final: 0.3141 (ptt) REVERT: D 861 MET cc_start: 0.7392 (ptt) cc_final: 0.6886 (ptt) REVERT: D 875 PHE cc_start: 0.7840 (t80) cc_final: 0.7447 (t80) REVERT: D 1013 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7881 (mm) outliers start: 58 outliers final: 42 residues processed: 288 average time/residue: 0.2775 time to fit residues: 124.0313 Evaluate side-chains 290 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 404 CYS Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1013 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 7.9990 chunk 155 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 190 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.206116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152347 restraints weight = 22279.139| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.45 r_work: 0.3358 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17577 Z= 0.126 Angle : 0.705 15.457 23887 Z= 0.338 Chirality : 0.043 0.328 2761 Planarity : 0.005 0.076 2998 Dihedral : 9.117 175.705 2783 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.06 % Allowed : 27.64 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2116 helix: 1.13 (0.16), residues: 1081 sheet: -0.54 (0.39), residues: 178 loop : -1.61 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 185 HIS 0.002 0.000 HIS A1562 PHE 0.066 0.001 PHE A1405 TYR 0.026 0.001 TYR D 719 ARG 0.014 0.000 ARG A1547 Details of bonding type rmsd link_NAG-ASN : bond 0.01480 ( 7) link_NAG-ASN : angle 5.80298 ( 21) link_BETA1-4 : bond 0.00818 ( 8) link_BETA1-4 : angle 3.18011 ( 24) hydrogen bonds : bond 0.03263 ( 830) hydrogen bonds : angle 4.26531 ( 2424) SS BOND : bond 0.00353 ( 10) SS BOND : angle 1.71040 ( 20) covalent geometry : bond 0.00281 (17552) covalent geometry : angle 0.67544 (23822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9829.43 seconds wall clock time: 170 minutes 11.50 seconds (10211.50 seconds total)