Starting phenix.real_space_refine on Sat Oct 11 20:51:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wea_37476/10_2025/8wea_37476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wea_37476/10_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_37476/10_2025/8wea_37476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wea_37476/10_2025/8wea_37476.map" model { file = "/net/cci-nas-00/data/ceres_data/8wea_37476/10_2025/8wea_37476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wea_37476/10_2025/8wea_37476.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'PHE:plan': 9, 'GLN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 5, 'TYR:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 5} 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: 4.10, per 1000 atoms: 0.24 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: 1.72 Conformation dependent library (CDL) restraints added in 753.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.70 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: 3.46 Time building geometry restraints manager: 2.21 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- 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 : 29.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG D 114 TYR 0.025 0.001 TYR A 144 PHE 0.024 0.001 PHE D 686 TRP 0.016 0.001 TRP A 336 HIS 0.004 0.001 HIS A1540 Details of bonding type rmsd covalent geometry : bond 0.00837 (17552) covalent geometry : angle 1.29996 (23822) SS BOND : bond 0.00479 ( 10) SS BOND : angle 0.97792 ( 20) hydrogen bonds : bond 0.23228 ( 830) hydrogen bonds : angle 8.85376 ( 2424) link_BETA1-4 : bond 0.00786 ( 8) link_BETA1-4 : angle 2.40316 ( 24) link_NAG-ASN : bond 0.01394 ( 7) link_NAG-ASN : angle 5.58628 ( 21) *********************** 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 : 0.748 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: 0.4044 (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: 0.1387 time to fit residues: 112.4603 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 : 0.678 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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 = 0.4630 r_free = 0.4630 target = 0.228285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.184060 restraints weight = 23929.480| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.76 r_work: 0.3702 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3262 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= 0.191 Angle : 0.921 35.457 23887 Z= 0.431 Chirality : 0.048 0.329 2761 Planarity : 0.006 0.085 2998 Dihedral : 15.234 147.313 2840 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.10 % Favored : 93.62 % 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 : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.18), residues: 2116 helix: -0.15 (0.16), residues: 1055 sheet: -1.09 (0.35), residues: 212 loop : -2.09 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 511 TYR 0.039 0.002 TYR A1169 PHE 0.049 0.002 PHE A 909 TRP 0.016 0.002 TRP A 382 HIS 0.008 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00423 (17552) covalent geometry : angle 0.90099 (23822) SS BOND : bond 0.00404 ( 10) SS BOND : angle 2.81174 ( 20) hydrogen bonds : bond 0.05790 ( 830) hydrogen bonds : angle 5.67261 ( 2424) link_BETA1-4 : bond 0.00756 ( 8) link_BETA1-4 : angle 3.06714 ( 24) link_NAG-ASN : bond 0.01071 ( 7) link_NAG-ASN : angle 4.98152 ( 21) *********************** 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 405 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 321 time to evaluate : 0.558 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 118 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5231 (mt) REVERT: A 259 ASN cc_start: 0.7775 (m110) cc_final: 0.7518 (m110) REVERT: A 263 LYS cc_start: 0.7316 (tptt) cc_final: 0.6551 (mmtp) REVERT: A 337 ASP cc_start: 0.5547 (OUTLIER) cc_final: 0.5340 (p0) REVERT: A 532 PHE cc_start: 0.7630 (t80) cc_final: 0.6466 (t80) REVERT: A 551 TRP cc_start: 0.6912 (t-100) cc_final: 0.6704 (t60) REVERT: A 620 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7765 (mtp85) REVERT: A 683 GLN cc_start: 0.5355 (tp40) cc_final: 0.5147 (mp10) REVERT: A 706 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6703 (tt0) REVERT: A 713 TYR cc_start: 0.6990 (m-10) cc_final: 0.6585 (m-80) REVERT: A 1117 ASP cc_start: 0.7508 (p0) cc_final: 0.7294 (p0) REVERT: A 1126 MET cc_start: 0.7945 (ptp) cc_final: 0.7725 (ptt) REVERT: A 1230 TYR cc_start: 0.7660 (t80) cc_final: 0.7308 (t80) REVERT: A 1239 THR cc_start: 0.6728 (OUTLIER) cc_final: 0.6521 (p) REVERT: A 1242 GLU cc_start: 0.7724 (mp0) cc_final: 0.7481 (mp0) REVERT: A 1509 MET cc_start: 0.7816 (mmt) cc_final: 0.7408 (mmt) REVERT: A 1544 GLU cc_start: 0.8223 (mp0) cc_final: 0.7953 (mp0) REVERT: A 1594 MET cc_start: 0.0058 (pmm) cc_final: -0.0150 (mpp) REVERT: A 1619 ARG cc_start: 0.5197 (OUTLIER) cc_final: 0.4164 (ptt90) REVERT: A 1646 MET cc_start: 0.4353 (pmm) cc_final: 0.3742 (pmm) REVERT: D 41 GLN cc_start: 0.7447 (tt0) cc_final: 0.6882 (tm-30) REVERT: D 578 MET cc_start: 0.8635 (mtp) cc_final: 0.8373 (mtp) REVERT: D 589 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7663 (ttm170) REVERT: D 678 GLU cc_start: 0.8574 (pt0) cc_final: 0.7849 (mm-30) REVERT: D 848 MET cc_start: 0.5575 (mmm) cc_final: 0.4675 (mmt) REVERT: D 869 ASN cc_start: 0.8911 (t0) cc_final: 0.8424 (t0) REVERT: D 875 PHE cc_start: 0.7995 (t80) cc_final: 0.7639 (t80) REVERT: D 886 LEU cc_start: 0.8945 (mt) cc_final: 0.8720 (mt) REVERT: D 1017 MET cc_start: 0.7367 (ttm) cc_final: 0.6632 (tpt) outliers start: 84 outliers final: 37 residues processed: 382 average time/residue: 0.1235 time to fit residues: 73.8786 Evaluate side-chains 308 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 337 ASP 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 731 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 1095 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1239 THR 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 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU 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 798 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1037 THR 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 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 A1113 ASN A1252 ASN ** A1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.222988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.179341 restraints weight = 23901.752| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.94 r_work: 0.3600 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17577 Z= 0.165 Angle : 0.770 14.813 23887 Z= 0.369 Chirality : 0.045 0.334 2761 Planarity : 0.005 0.079 2998 Dihedral : 12.924 158.006 2796 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.61 % Rotamer: Outliers : 5.23 % Allowed : 24.36 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.18), residues: 2116 helix: 0.31 (0.16), residues: 1057 sheet: -1.00 (0.35), residues: 207 loop : -1.91 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1547 TYR 0.019 0.002 TYR A1169 PHE 0.040 0.002 PHE A 909 TRP 0.019 0.001 TRP A 336 HIS 0.007 0.001 HIS A1260 Details of bonding type rmsd covalent geometry : bond 0.00366 (17552) covalent geometry : angle 0.74961 (23822) SS BOND : bond 0.00831 ( 10) SS BOND : angle 1.63381 ( 20) hydrogen bonds : bond 0.04555 ( 830) hydrogen bonds : angle 5.04819 ( 2424) link_BETA1-4 : bond 0.00926 ( 8) link_BETA1-4 : angle 3.26247 ( 24) link_NAG-ASN : bond 0.00988 ( 7) link_NAG-ASN : angle 4.76760 ( 21) *********************** 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 378 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.604 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: 0.5763 (OUTLIER) cc_final: 0.4500 (tp) REVERT: A 151 ASP cc_start: 0.7941 (p0) cc_final: 0.7596 (p0) REVERT: A 179 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7540 (tp) REVERT: A 263 LYS cc_start: 0.7264 (tptt) cc_final: 0.6494 (mmtp) REVERT: A 273 LEU cc_start: 0.8313 (tp) cc_final: 0.7995 (tp) REVERT: A 344 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8030 (p) REVERT: A 526 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5937 (p90) REVERT: A 532 PHE cc_start: 0.7780 (t80) cc_final: 0.6595 (t80) REVERT: A 533 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7822 (tp) REVERT: A 546 TYR cc_start: 0.7049 (t80) cc_final: 0.6693 (t80) REVERT: A 655 LEU cc_start: 0.8183 (mt) cc_final: 0.7795 (mp) REVERT: A 706 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6823 (tt0) REVERT: A 1063 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 1117 ASP cc_start: 0.7636 (p0) cc_final: 0.7405 (p0) REVERT: A 1125 MET cc_start: 0.8543 (mtt) cc_final: 0.8253 (mtp) REVERT: A 1126 MET cc_start: 0.7966 (ptp) cc_final: 0.7765 (ptt) REVERT: A 1230 TYR cc_start: 0.7626 (t80) cc_final: 0.7330 (t80) REVERT: A 1242 GLU cc_start: 0.7806 (mp0) cc_final: 0.7483 (mp0) REVERT: A 1276 MET cc_start: 0.7809 (mmm) cc_final: 0.7606 (mmm) REVERT: A 1509 MET cc_start: 0.7835 (mmt) cc_final: 0.7496 (mmt) REVERT: A 1594 MET cc_start: -0.0012 (pmm) cc_final: -0.0293 (mpp) REVERT: D 41 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: D 424 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8457 (pt0) REVERT: D 578 MET cc_start: 0.8561 (mtp) cc_final: 0.8301 (mtp) REVERT: D 678 GLU cc_start: 0.8409 (pt0) cc_final: 0.7695 (mm-30) REVERT: D 848 MET cc_start: 0.5745 (mmm) cc_final: 0.5297 (mmp) REVERT: D 869 ASN cc_start: 0.8909 (t0) cc_final: 0.8541 (t0) REVERT: D 875 PHE cc_start: 0.8084 (t80) cc_final: 0.7744 (t80) REVERT: D 1017 MET cc_start: 0.7421 (ttm) cc_final: 0.6746 (tpt) outliers start: 94 outliers final: 40 residues processed: 353 average time/residue: 0.1237 time to fit residues: 68.2282 Evaluate side-chains 294 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 320 THR 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 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 1063 PHE Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1411 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 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 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 366 GLU 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 585 GLU Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 798 VAL 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 90 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 526 ASN D 713 ASN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** 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 = 0.4546 r_free = 0.4546 target = 0.218509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.168690 restraints weight = 23391.740| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.75 r_work: 0.3551 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5059 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= 0.171 Angle : 0.720 9.624 23887 Z= 0.351 Chirality : 0.046 0.370 2761 Planarity : 0.005 0.083 2998 Dihedral : 11.752 160.427 2791 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 5.01 % Allowed : 24.36 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.18), residues: 2116 helix: 0.55 (0.16), residues: 1063 sheet: -0.93 (0.36), residues: 191 loop : -1.74 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 418 TYR 0.033 0.002 TYR A1169 PHE 0.038 0.002 PHE A1405 TRP 0.013 0.001 TRP D 185 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00397 (17552) covalent geometry : angle 0.69843 (23822) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.20518 ( 20) hydrogen bonds : bond 0.04259 ( 830) hydrogen bonds : angle 4.77141 ( 2424) link_BETA1-4 : bond 0.00842 ( 8) link_BETA1-4 : angle 3.36284 ( 24) link_NAG-ASN : bond 0.01072 ( 7) link_NAG-ASN : angle 4.63155 ( 21) *********************** 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 364 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 0.586 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 214 GLN cc_start: 0.6231 (tm-30) cc_final: 0.6003 (mt0) REVERT: A 263 LYS cc_start: 0.7352 (tptt) cc_final: 0.6905 (tppt) REVERT: A 273 LEU cc_start: 0.8637 (tp) cc_final: 0.8341 (tp) REVERT: A 281 ILE cc_start: 0.8411 (mt) cc_final: 0.8193 (tt) REVERT: A 290 PHE cc_start: 0.7721 (m-80) cc_final: 0.7393 (m-10) REVERT: A 526 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.6134 (p90) REVERT: A 532 PHE cc_start: 0.7834 (t80) cc_final: 0.6903 (t80) REVERT: A 655 LEU cc_start: 0.8185 (mt) cc_final: 0.7754 (mp) REVERT: A 672 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 706 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6915 (tt0) REVERT: A 921 ASP cc_start: 0.7323 (t0) cc_final: 0.7112 (t0) REVERT: A 1117 ASP cc_start: 0.7830 (p0) cc_final: 0.7518 (p0) REVERT: A 1125 MET cc_start: 0.8663 (mtt) cc_final: 0.8343 (mtp) REVERT: A 1126 MET cc_start: 0.8052 (ptp) cc_final: 0.7773 (ptt) REVERT: A 1230 TYR cc_start: 0.7568 (t80) cc_final: 0.7349 (t80) REVERT: A 1233 TRP cc_start: 0.8455 (t60) cc_final: 0.8034 (t60) REVERT: A 1276 MET cc_start: 0.8167 (mmm) cc_final: 0.7851 (mmm) REVERT: A 1417 MET cc_start: 0.8439 (mmm) cc_final: 0.8233 (mmp) REVERT: A 1470 MET cc_start: 0.7387 (tmm) cc_final: 0.6972 (ptm) REVERT: A 1509 MET cc_start: 0.7996 (mmt) cc_final: 0.7706 (mmt) REVERT: A 1619 ARG cc_start: 0.5202 (OUTLIER) cc_final: 0.4341 (ptt90) REVERT: A 1646 MET cc_start: 0.3810 (pmm) cc_final: 0.3412 (pmm) REVERT: D 41 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: D 171 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: D 424 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: D 578 MET cc_start: 0.8525 (mtp) cc_final: 0.8304 (mtp) REVERT: D 589 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7452 (ttm-80) REVERT: D 678 GLU cc_start: 0.8416 (pt0) cc_final: 0.7747 (mm-30) REVERT: D 713 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.7151 (t0) REVERT: D 848 MET cc_start: 0.5776 (mmm) cc_final: 0.4834 (mmp) REVERT: D 861 MET cc_start: 0.6915 (ptp) cc_final: 0.6218 (ptt) REVERT: D 869 ASN cc_start: 0.8851 (t0) cc_final: 0.8490 (t0) REVERT: D 875 PHE cc_start: 0.8007 (t80) cc_final: 0.7704 (t80) REVERT: D 1017 MET cc_start: 0.7340 (ttm) cc_final: 0.6664 (tpt) outliers start: 90 outliers final: 44 residues processed: 338 average time/residue: 0.1223 time to fit residues: 65.3322 Evaluate side-chains 291 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 337 ASP 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 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 672 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 1116 PHE Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1567 THR 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 41 GLN 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 366 GLU Chi-restraints excluded: chain D residue 419 ILE 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 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 781 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 142 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 166 optimal weight: 0.0020 chunk 165 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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** D 374 ASN D 526 ASN D 641 GLN D 652 ASN ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** 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 = 0.4531 r_free = 0.4531 target = 0.216741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.4024 r_free = 0.4024 target = 0.160731 restraints weight = 23227.486| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.64 r_work: 0.3546 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5561 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= 0.157 Angle : 0.688 14.745 23887 Z= 0.337 Chirality : 0.044 0.330 2761 Planarity : 0.005 0.089 2998 Dihedral : 11.159 165.373 2791 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 4.17 % Allowed : 25.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2116 helix: 0.69 (0.16), residues: 1059 sheet: -0.86 (0.37), residues: 191 loop : -1.73 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1547 TYR 0.018 0.001 TYR D 719 PHE 0.035 0.002 PHE A1405 TRP 0.014 0.001 TRP D 185 HIS 0.007 0.001 HIS D 885 Details of bonding type rmsd covalent geometry : bond 0.00366 (17552) covalent geometry : angle 0.66799 (23822) SS BOND : bond 0.00446 ( 10) SS BOND : angle 1.32275 ( 20) hydrogen bonds : bond 0.03891 ( 830) hydrogen bonds : angle 4.52206 ( 2424) link_BETA1-4 : bond 0.00837 ( 8) link_BETA1-4 : angle 3.29266 ( 24) link_NAG-ASN : bond 0.00930 ( 7) link_NAG-ASN : angle 4.31232 ( 21) *********************** 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 344 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 269 time to evaluate : 0.639 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 214 GLN cc_start: 0.6496 (tm-30) cc_final: 0.6085 (tt0) REVERT: A 263 LYS cc_start: 0.7656 (tptt) cc_final: 0.7120 (tppt) REVERT: A 273 LEU cc_start: 0.8771 (tp) cc_final: 0.8504 (tp) REVERT: A 281 ILE cc_start: 0.8562 (mt) cc_final: 0.8350 (tt) REVERT: A 401 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7459 (mt) REVERT: A 526 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.6028 (p90) REVERT: A 532 PHE cc_start: 0.7775 (t80) cc_final: 0.6837 (t80) REVERT: A 539 LEU cc_start: 0.7750 (mt) cc_final: 0.7143 (mt) REVERT: A 683 GLN cc_start: 0.5370 (tp40) cc_final: 0.4991 (mp10) REVERT: A 706 GLU cc_start: 0.7706 (mm-30) cc_final: 0.6875 (tt0) REVERT: A 921 ASP cc_start: 0.7627 (t0) cc_final: 0.7304 (t0) REVERT: A 924 GLN cc_start: 0.3553 (tm-30) cc_final: 0.3245 (tm-30) REVERT: A 1117 ASP cc_start: 0.8057 (p0) cc_final: 0.7717 (p0) REVERT: A 1125 MET cc_start: 0.8745 (mtt) cc_final: 0.8509 (mtp) REVERT: A 1126 MET cc_start: 0.8033 (ptp) cc_final: 0.7742 (ptt) REVERT: A 1230 TYR cc_start: 0.7729 (t80) cc_final: 0.7487 (t80) REVERT: A 1233 TRP cc_start: 0.8520 (t60) cc_final: 0.8088 (t60) REVERT: A 1276 MET cc_start: 0.8366 (mmm) cc_final: 0.8017 (mmm) REVERT: A 1420 PHE cc_start: 0.7507 (t80) cc_final: 0.7214 (t80) REVERT: A 1470 MET cc_start: 0.7396 (tmm) cc_final: 0.7092 (ptm) REVERT: A 1509 MET cc_start: 0.8234 (mmt) cc_final: 0.7950 (mmt) REVERT: A 1619 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.4659 (ptt90) REVERT: A 1646 MET cc_start: 0.4220 (pmm) cc_final: 0.3805 (pmm) REVERT: D 41 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: D 171 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: D 424 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: D 578 MET cc_start: 0.8540 (mtp) cc_final: 0.8338 (mtp) REVERT: D 589 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7756 (ttm-80) REVERT: D 678 GLU cc_start: 0.8590 (pt0) cc_final: 0.7905 (mm-30) REVERT: D 848 MET cc_start: 0.5607 (mmm) cc_final: 0.5097 (mmp) REVERT: D 854 ASP cc_start: 0.8315 (p0) cc_final: 0.7770 (p0) REVERT: D 855 ASP cc_start: 0.7925 (t0) cc_final: 0.7677 (t0) REVERT: D 869 ASN cc_start: 0.8924 (t0) cc_final: 0.8561 (t0) REVERT: D 891 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7963 (p) REVERT: D 1013 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7816 (mm) REVERT: D 1017 MET cc_start: 0.7365 (ttm) cc_final: 0.6752 (tpt) outliers start: 75 outliers final: 49 residues processed: 323 average time/residue: 0.1229 time to fit residues: 61.8840 Evaluate side-chains 304 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 401 LEU 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 556 GLN 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 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 1105 ILE Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1483 SER 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 31 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 41 GLN 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 366 GLU Chi-restraints excluded: chain D residue 419 ILE 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 647 THR Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 781 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 1013 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 69 optimal weight: 50.0000 chunk 160 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 556 GLN A1252 ASN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 ASN D 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.216613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161833 restraints weight = 23157.123| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.84 r_work: 0.3522 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17577 Z= 0.143 Angle : 0.667 12.676 23887 Z= 0.325 Chirality : 0.043 0.334 2761 Planarity : 0.005 0.079 2998 Dihedral : 10.698 168.487 2786 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.39 % Allowed : 25.86 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2116 helix: 0.78 (0.16), residues: 1067 sheet: -0.85 (0.38), residues: 178 loop : -1.70 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1547 TYR 0.033 0.001 TYR A 299 PHE 0.055 0.002 PHE A1405 TRP 0.014 0.001 TRP D 185 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00328 (17552) covalent geometry : angle 0.64692 (23822) SS BOND : bond 0.00280 ( 10) SS BOND : angle 0.92647 ( 20) hydrogen bonds : bond 0.03711 ( 830) hydrogen bonds : angle 4.41924 ( 2424) link_BETA1-4 : bond 0.00827 ( 8) link_BETA1-4 : angle 3.29036 ( 24) link_NAG-ASN : bond 0.00890 ( 7) link_NAG-ASN : angle 4.17139 ( 21) *********************** 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 329 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 0.722 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: A 214 GLN cc_start: 0.6566 (tm-30) cc_final: 0.6247 (mt0) REVERT: A 263 LYS cc_start: 0.7842 (tptt) cc_final: 0.7400 (tppt) REVERT: A 273 LEU cc_start: 0.8858 (tp) cc_final: 0.8583 (tp) REVERT: A 418 ARG cc_start: 0.7117 (mmp80) cc_final: 0.6687 (mmm-85) REVERT: A 526 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.6140 (p90) REVERT: A 532 PHE cc_start: 0.7698 (t80) cc_final: 0.6855 (t80) REVERT: A 727 MET cc_start: 0.7645 (mmm) cc_final: 0.7399 (mmm) REVERT: A 921 ASP cc_start: 0.7574 (t0) cc_final: 0.7355 (t0) REVERT: A 1117 ASP cc_start: 0.8007 (p0) cc_final: 0.7690 (p0) REVERT: A 1125 MET cc_start: 0.8818 (mtt) cc_final: 0.8584 (mtp) REVERT: A 1126 MET cc_start: 0.7943 (ptp) cc_final: 0.7723 (ptt) REVERT: A 1230 TYR cc_start: 0.7769 (t80) cc_final: 0.7488 (t80) REVERT: A 1233 TRP cc_start: 0.8529 (t60) cc_final: 0.8188 (t60) REVERT: A 1276 MET cc_start: 0.8365 (mmm) cc_final: 0.8034 (mmm) REVERT: A 1420 PHE cc_start: 0.7525 (t80) cc_final: 0.7302 (t80) REVERT: A 1470 MET cc_start: 0.7457 (tmm) cc_final: 0.7222 (ptm) REVERT: A 1509 MET cc_start: 0.8232 (mmt) cc_final: 0.7900 (mmt) REVERT: A 1619 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.4551 (ptt90) REVERT: A 1646 MET cc_start: 0.4377 (pmm) cc_final: 0.3725 (pmm) REVERT: D 41 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: D 171 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: D 366 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: D 424 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: D 589 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7525 (ttm-80) REVERT: D 678 GLU cc_start: 0.8483 (pt0) cc_final: 0.7867 (mm-30) REVERT: D 875 PHE cc_start: 0.7831 (t80) cc_final: 0.7414 (t80) REVERT: D 891 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7769 (p) REVERT: D 1013 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7893 (mm) REVERT: D 1017 MET cc_start: 0.7235 (ttm) cc_final: 0.6745 (tpt) outliers start: 79 outliers final: 53 residues processed: 308 average time/residue: 0.1253 time to fit residues: 60.6240 Evaluate side-chains 296 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 GLN 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 556 GLN 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 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 1158 TYR 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 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 41 GLN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 100 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 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 419 ILE 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 592 VAL 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 798 VAL Chi-restraints excluded: chain D residue 805 LYS 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 115 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.217185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163518 restraints weight = 23221.149| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.68 r_work: 0.3537 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17577 Z= 0.125 Angle : 0.662 11.803 23887 Z= 0.320 Chirality : 0.043 0.331 2761 Planarity : 0.005 0.084 2998 Dihedral : 10.295 171.103 2786 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.89 % Allowed : 26.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2116 helix: 0.88 (0.16), residues: 1073 sheet: -0.81 (0.37), residues: 188 loop : -1.70 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1547 TYR 0.028 0.001 TYR D 644 PHE 0.043 0.001 PHE A1405 TRP 0.014 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00279 (17552) covalent geometry : angle 0.64338 (23822) SS BOND : bond 0.00209 ( 10) SS BOND : angle 1.01476 ( 20) hydrogen bonds : bond 0.03488 ( 830) hydrogen bonds : angle 4.33210 ( 2424) link_BETA1-4 : bond 0.00858 ( 8) link_BETA1-4 : angle 3.26635 ( 24) link_NAG-ASN : bond 0.00878 ( 7) link_NAG-ASN : angle 4.01353 ( 21) *********************** 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 319 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 0.681 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 263 LYS cc_start: 0.7976 (tptt) cc_final: 0.7498 (tppt) REVERT: A 273 LEU cc_start: 0.8880 (tp) cc_final: 0.8602 (tp) REVERT: A 418 ARG cc_start: 0.7157 (mmp80) cc_final: 0.6736 (mmm-85) REVERT: A 526 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6139 (p90) REVERT: A 532 PHE cc_start: 0.7648 (t80) cc_final: 0.6794 (t80) REVERT: A 655 LEU cc_start: 0.8099 (mt) cc_final: 0.7710 (mp) REVERT: A 672 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 921 ASP cc_start: 0.7650 (t0) cc_final: 0.7351 (t0) REVERT: A 1117 ASP cc_start: 0.7993 (p0) cc_final: 0.7699 (p0) REVERT: A 1125 MET cc_start: 0.8837 (mtt) cc_final: 0.8634 (mtp) REVERT: A 1230 TYR cc_start: 0.7765 (t80) cc_final: 0.7480 (t80) REVERT: A 1233 TRP cc_start: 0.8547 (t60) cc_final: 0.8262 (t60) REVERT: A 1276 MET cc_start: 0.8383 (mmm) cc_final: 0.8158 (mmm) REVERT: A 1420 PHE cc_start: 0.7610 (t80) cc_final: 0.7350 (t80) REVERT: A 1470 MET cc_start: 0.7407 (tmm) cc_final: 0.7144 (ptm) REVERT: A 1474 MET cc_start: 0.6426 (mtm) cc_final: 0.5784 (mtm) REVERT: A 1509 MET cc_start: 0.8273 (mmt) cc_final: 0.7971 (mmt) REVERT: A 1619 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.4745 (ptt90) REVERT: A 1646 MET cc_start: 0.4308 (pmm) cc_final: 0.3728 (pmm) REVERT: D 41 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: D 366 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: D 424 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: D 589 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7550 (ttm-80) REVERT: D 665 ASP cc_start: 0.8421 (t0) cc_final: 0.8179 (t0) REVERT: D 678 GLU cc_start: 0.8525 (pt0) cc_final: 0.7908 (mm-30) REVERT: D 793 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7382 (ttm) REVERT: D 848 MET cc_start: 0.5693 (mmp) cc_final: 0.2458 (ptt) REVERT: D 875 PHE cc_start: 0.7784 (t80) cc_final: 0.7375 (t80) REVERT: D 1013 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7819 (mm) REVERT: D 1017 MET cc_start: 0.7181 (ttm) cc_final: 0.6894 (tpt) outliers start: 70 outliers final: 50 residues processed: 297 average time/residue: 0.1225 time to fit residues: 57.3979 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 : 0.702 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 248 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 546 TYR Chi-restraints excluded: chain A residue 556 GLN 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 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 1158 TYR Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1381 VAL 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 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 41 GLN 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 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 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 805 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 102 optimal weight: 0.0000 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 556 GLN D 682 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 = 0.4514 r_free = 0.4514 target = 0.214446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159656 restraints weight = 22948.938| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.72 r_work: 0.3489 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6341 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= 0.172 Angle : 0.688 10.971 23887 Z= 0.338 Chirality : 0.044 0.324 2761 Planarity : 0.005 0.078 2998 Dihedral : 10.058 171.974 2786 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.00 % Allowed : 26.36 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.18), residues: 2116 helix: 0.83 (0.16), residues: 1079 sheet: -0.83 (0.37), residues: 188 loop : -1.62 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1547 TYR 0.031 0.002 TYR D 719 PHE 0.022 0.002 PHE D 686 TRP 0.012 0.001 TRP A1641 HIS 0.003 0.001 HIS D 392 Details of bonding type rmsd covalent geometry : bond 0.00406 (17552) covalent geometry : angle 0.66894 (23822) SS BOND : bond 0.00308 ( 10) SS BOND : angle 1.00302 ( 20) hydrogen bonds : bond 0.03739 ( 830) hydrogen bonds : angle 4.38181 ( 2424) link_BETA1-4 : bond 0.00763 ( 8) link_BETA1-4 : angle 3.36991 ( 24) link_NAG-ASN : bond 0.00822 ( 7) link_NAG-ASN : angle 4.13208 ( 21) *********************** 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 319 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 247 time to evaluate : 0.663 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 263 LYS cc_start: 0.8076 (tptt) cc_final: 0.7610 (tppt) REVERT: A 273 LEU cc_start: 0.8987 (tp) cc_final: 0.8706 (tp) REVERT: A 339 PRO cc_start: 0.8147 (Cg_endo) cc_final: 0.7818 (Cg_exo) REVERT: A 418 ARG cc_start: 0.7083 (mmp80) cc_final: 0.6647 (mmm-85) REVERT: A 526 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6153 (p90) REVERT: A 532 PHE cc_start: 0.7666 (t80) cc_final: 0.6806 (t80) REVERT: A 672 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 727 MET cc_start: 0.7921 (mmm) cc_final: 0.7720 (mmm) REVERT: A 917 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6713 (pt) REVERT: A 921 ASP cc_start: 0.7750 (t0) cc_final: 0.7428 (t0) REVERT: A 1117 ASP cc_start: 0.8053 (p0) cc_final: 0.7707 (p0) REVERT: A 1122 LEU cc_start: 0.8715 (tp) cc_final: 0.8444 (mp) REVERT: A 1125 MET cc_start: 0.8893 (mtt) cc_final: 0.8679 (mtp) REVERT: A 1230 TYR cc_start: 0.7811 (t80) cc_final: 0.7458 (t80) REVERT: A 1259 GLN cc_start: 0.7713 (mt0) cc_final: 0.7457 (mt0) REVERT: A 1420 PHE cc_start: 0.8082 (t80) cc_final: 0.7862 (t80) REVERT: A 1474 MET cc_start: 0.6515 (mtm) cc_final: 0.6003 (mtm) REVERT: A 1509 MET cc_start: 0.8339 (mmt) cc_final: 0.8077 (mmt) REVERT: A 1619 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.4780 (ptt90) REVERT: A 1646 MET cc_start: 0.4272 (pmm) cc_final: 0.3764 (pmm) REVERT: D 366 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: D 424 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: D 589 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7469 (ttm-80) REVERT: D 665 ASP cc_start: 0.8454 (t0) cc_final: 0.8200 (t0) REVERT: D 678 GLU cc_start: 0.8594 (pt0) cc_final: 0.7982 (mm-30) REVERT: D 793 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: D 848 MET cc_start: 0.5926 (mmp) cc_final: 0.2802 (ptt) REVERT: D 854 ASP cc_start: 0.8306 (p0) cc_final: 0.7750 (p0) REVERT: D 875 PHE cc_start: 0.7824 (t80) cc_final: 0.7434 (t80) REVERT: D 1013 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7826 (mm) outliers start: 72 outliers final: 52 residues processed: 299 average time/residue: 0.1198 time to fit residues: 56.9037 Evaluate side-chains 297 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 248 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 546 TYR Chi-restraints excluded: chain A residue 563 LEU 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 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 1158 TYR Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1427 MET 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 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 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 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 583 SER 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 805 LYS 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 83 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- 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 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN ** D 694 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 = 0.4371 r_free = 0.4371 target = 0.205399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155688 restraints weight = 22404.499| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.74 r_work: 0.3309 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6576 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= 0.154 Angle : 0.681 11.082 23887 Z= 0.332 Chirality : 0.043 0.333 2761 Planarity : 0.005 0.080 2998 Dihedral : 9.693 171.425 2786 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.89 % Allowed : 26.47 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.18), residues: 2116 helix: 0.92 (0.16), residues: 1076 sheet: -0.80 (0.37), residues: 191 loop : -1.74 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1547 TYR 0.038 0.001 TYR D 719 PHE 0.068 0.002 PHE A1405 TRP 0.014 0.001 TRP D 720 HIS 0.004 0.001 HIS A 545 Details of bonding type rmsd covalent geometry : bond 0.00360 (17552) covalent geometry : angle 0.66140 (23822) SS BOND : bond 0.00127 ( 10) SS BOND : angle 0.99948 ( 20) hydrogen bonds : bond 0.03604 ( 830) hydrogen bonds : angle 4.34592 ( 2424) link_BETA1-4 : bond 0.00801 ( 8) link_BETA1-4 : angle 3.33315 ( 24) link_NAG-ASN : bond 0.00813 ( 7) link_NAG-ASN : angle 4.23458 ( 21) *********************** 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 309 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 239 time to evaluate : 0.658 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 263 LYS cc_start: 0.8044 (tptt) cc_final: 0.7685 (tppt) REVERT: A 273 LEU cc_start: 0.8983 (tp) cc_final: 0.8739 (tp) REVERT: A 418 ARG cc_start: 0.7047 (mmp80) cc_final: 0.6720 (mmm-85) REVERT: A 526 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6109 (p90) REVERT: A 532 PHE cc_start: 0.7676 (t80) cc_final: 0.6836 (t80) REVERT: A 672 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 917 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6833 (pt) REVERT: A 1117 ASP cc_start: 0.8201 (p0) cc_final: 0.7894 (p0) REVERT: A 1122 LEU cc_start: 0.8739 (tp) cc_final: 0.8450 (mp) REVERT: A 1230 TYR cc_start: 0.7635 (t80) cc_final: 0.7326 (t80) REVERT: A 1286 MET cc_start: 0.7746 (ttp) cc_final: 0.7354 (ttt) REVERT: A 1428 GLN cc_start: 0.7899 (mm110) cc_final: 0.7641 (mm110) REVERT: A 1474 MET cc_start: 0.6466 (mtm) cc_final: 0.6126 (mtm) REVERT: A 1619 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4134 (ptt90) REVERT: A 1646 MET cc_start: 0.3852 (pmm) cc_final: 0.3647 (pmm) REVERT: D 41 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 114 ARG cc_start: 0.7923 (ptt90) cc_final: 0.7604 (ptt90) REVERT: D 366 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: D 424 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: D 589 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7546 (ttm-80) REVERT: D 665 ASP cc_start: 0.8416 (t0) cc_final: 0.8180 (t0) REVERT: D 678 GLU cc_start: 0.8348 (pt0) cc_final: 0.7950 (mm-30) REVERT: D 793 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7740 (ttm) REVERT: D 848 MET cc_start: 0.6203 (mmp) cc_final: 0.3050 (ptt) REVERT: D 854 ASP cc_start: 0.8193 (p0) cc_final: 0.7625 (p0) REVERT: D 875 PHE cc_start: 0.7899 (t80) cc_final: 0.7542 (t80) REVERT: D 1013 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7911 (mm) REVERT: D 1017 MET cc_start: 0.7315 (tpt) cc_final: 0.6760 (ttm) outliers start: 70 outliers final: 53 residues processed: 289 average time/residue: 0.1280 time to fit residues: 57.4208 Evaluate side-chains 296 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 248 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 546 TYR 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 672 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 1158 TYR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1427 MET 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 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 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 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 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 805 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 128 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 209 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN D 526 ASN ** D 684 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 = 0.4372 r_free = 0.4372 target = 0.205706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156724 restraints weight = 22118.954| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.58 r_work: 0.3320 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17577 Z= 0.141 Angle : 0.680 11.385 23887 Z= 0.330 Chirality : 0.043 0.333 2761 Planarity : 0.004 0.077 2998 Dihedral : 9.435 172.934 2786 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.67 % Allowed : 26.92 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2116 helix: 0.98 (0.16), residues: 1078 sheet: -0.67 (0.39), residues: 180 loop : -1.67 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1547 TYR 0.028 0.001 TYR D 719 PHE 0.022 0.001 PHE A1071 TRP 0.015 0.001 TRP D 185 HIS 0.002 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00325 (17552) covalent geometry : angle 0.66119 (23822) SS BOND : bond 0.00115 ( 10) SS BOND : angle 0.96717 ( 20) hydrogen bonds : bond 0.03466 ( 830) hydrogen bonds : angle 4.31283 ( 2424) link_BETA1-4 : bond 0.00789 ( 8) link_BETA1-4 : angle 3.31994 ( 24) link_NAG-ASN : bond 0.00792 ( 7) link_NAG-ASN : angle 4.14885 ( 21) ********************** 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 307 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 0.673 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 263 LYS cc_start: 0.8069 (tptt) cc_final: 0.7678 (tppt) REVERT: A 273 LEU cc_start: 0.8921 (tp) cc_final: 0.8681 (tp) REVERT: A 418 ARG cc_start: 0.7043 (mmp80) cc_final: 0.6739 (mmm-85) REVERT: A 526 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6011 (p90) REVERT: A 532 PHE cc_start: 0.7741 (t80) cc_final: 0.6844 (t80) REVERT: A 672 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.7895 (tp) REVERT: A 917 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6773 (pt) REVERT: A 1117 ASP cc_start: 0.8175 (p0) cc_final: 0.7861 (p0) REVERT: A 1122 LEU cc_start: 0.8770 (tp) cc_final: 0.8487 (mp) REVERT: A 1230 TYR cc_start: 0.7703 (t80) cc_final: 0.7355 (t80) REVERT: A 1286 MET cc_start: 0.7831 (ttp) cc_final: 0.7444 (ttt) REVERT: A 1470 MET cc_start: 0.7881 (ppp) cc_final: 0.7675 (ppp) REVERT: A 1596 MET cc_start: -0.1241 (mmp) cc_final: -0.1532 (tpp) REVERT: A 1619 ARG cc_start: 0.5104 (OUTLIER) cc_final: 0.4304 (ptt90) REVERT: D 41 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7025 (tm-30) REVERT: D 114 ARG cc_start: 0.7888 (ptt90) cc_final: 0.7576 (ptt90) REVERT: D 366 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: D 424 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: D 589 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7522 (ttm-80) REVERT: D 665 ASP cc_start: 0.8427 (t0) cc_final: 0.8201 (t0) REVERT: D 678 GLU cc_start: 0.8399 (pt0) cc_final: 0.8014 (mm-30) REVERT: D 793 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7752 (ttm) REVERT: D 817 ASP cc_start: 0.6093 (p0) cc_final: 0.5821 (p0) REVERT: D 848 MET cc_start: 0.6251 (mmp) cc_final: 0.3159 (ptt) REVERT: D 875 PHE cc_start: 0.7867 (t80) cc_final: 0.7489 (t80) REVERT: D 1013 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7900 (mm) outliers start: 66 outliers final: 53 residues processed: 287 average time/residue: 0.1320 time to fit residues: 58.1726 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 : 0.700 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 248 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 546 TYR 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 672 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 1105 ILE Chi-restraints excluded: chain A residue 1158 TYR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1427 MET Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1531 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 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 284 SER Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 391 GLN Chi-restraints excluded: chain D residue 407 LYS 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 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 805 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 131 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 173 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 0.0670 chunk 158 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN ** 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 = 0.4374 r_free = 0.4374 target = 0.205679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153906 restraints weight = 22428.972| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.66 r_work: 0.3320 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17577 Z= 0.126 Angle : 0.677 11.403 23887 Z= 0.327 Chirality : 0.043 0.333 2761 Planarity : 0.004 0.077 2998 Dihedral : 9.217 174.205 2785 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.17 % Allowed : 27.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.18), residues: 2116 helix: 1.04 (0.16), residues: 1083 sheet: -0.63 (0.39), residues: 180 loop : -1.60 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1547 TYR 0.027 0.001 TYR D 719 PHE 0.032 0.001 PHE D 686 TRP 0.017 0.001 TRP D 185 HIS 0.005 0.001 HIS D 524 Details of bonding type rmsd covalent geometry : bond 0.00286 (17552) covalent geometry : angle 0.65857 (23822) SS BOND : bond 0.00215 ( 10) SS BOND : angle 0.90108 ( 20) hydrogen bonds : bond 0.03368 ( 830) hydrogen bonds : angle 4.28103 ( 2424) link_BETA1-4 : bond 0.00788 ( 8) link_BETA1-4 : angle 3.28552 ( 24) link_NAG-ASN : bond 0.00800 ( 7) link_NAG-ASN : angle 3.93714 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5281.78 seconds wall clock time: 90 minutes 50.17 seconds (5450.17 seconds total)