Starting phenix.real_space_refine on Wed Jul 30 10:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f7f_31487/07_2025/7f7f_31487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f7f_31487/07_2025/7f7f_31487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2025/7f7f_31487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2025/7f7f_31487.map" model { file = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2025/7f7f_31487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2025/7f7f_31487.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 60 5.16 5 C 7766 2.51 5 N 1996 2.21 5 O 2253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 9046 Classifications: {'peptide': 1135} Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 1096} Chain breaks: 3 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.96, per 1000 atoms: 0.66 Number of scatterers: 12076 At special positions: 0 Unit cell: (148.755, 109.72, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 1 11.99 O 2253 8.00 N 1996 7.00 C 7766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 12 sheets defined 32.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 221 through 232 removed outlier: 4.596A pdb=" N PHE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.958A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.512A pdb=" N ASP A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.937A pdb=" N GLY A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.510A pdb=" N THR A 455 " --> pdb=" O CYS A 452 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 548 through 576 removed outlier: 3.799A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.760A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 629 removed outlier: 3.509A pdb=" N GLU A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.685A pdb=" N LEU A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.004A pdb=" N PHE A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.663A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 removed outlier: 4.226A pdb=" N LYS A 925 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 943 through 951 removed outlier: 4.500A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.717A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 3.997A pdb=" N ALA A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 3.754A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.693A pdb=" N LEU A1092 " --> pdb=" O ARG A1088 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1121 removed outlier: 3.614A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.672A pdb=" N MET A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A1158 " --> pdb=" O GLN A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1173 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.590A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 3.628A pdb=" N PHE A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 4.192A pdb=" N LEU A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1255 removed outlier: 3.756A pdb=" N LEU A1255 " --> pdb=" O VAL A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1252 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.666A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1261' Processing helix chain 'A' and resid 1266 through 1287 removed outlier: 3.567A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A1273 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1275 " --> pdb=" O LEU A1271 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A1276 " --> pdb=" O TRP A1272 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1285 " --> pdb=" O SER A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 removed outlier: 3.738A pdb=" N ILE A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 3.507A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.604A pdb=" N VAL A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1395 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1395 through 1404 removed outlier: 3.528A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1418 removed outlier: 3.550A pdb=" N ARG A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 97 removed outlier: 4.126A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.673A pdb=" N ASP B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.660A pdb=" N ASP B 269 " --> pdb=" O TRP B 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.713A pdb=" N GLN B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.667A pdb=" N PHE B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 377 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.610A pdb=" N ILE A 409 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 8.227A pdb=" N CYS A1102 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 987 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 683 removed outlier: 7.829A pdb=" N MET A 677 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 966 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE A 679 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU A 964 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 681 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 960 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 823 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 836 through 839 removed outlier: 3.851A pdb=" N ILE A 852 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.769A pdb=" N VAL B 173 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.021A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.612A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 247 hydrogen bonds defined for protein. 690 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: 3.75 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3684 1.34 - 1.46: 2798 1.46 - 1.58: 5781 1.58 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 12353 Sorted by residual: bond pdb=" N GLU A1409 " pdb=" CA GLU A1409 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.64e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.488 -0.039 1.45e-02 4.76e+03 7.26e+00 bond pdb=" C VAL A1408 " pdb=" N GLU A1409 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.50e-02 4.44e+03 5.88e+00 bond pdb=" CD LYS A 542 " pdb=" CE LYS A 542 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.30e+00 bond pdb=" CG LYS A 542 " pdb=" CD LYS A 542 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.79e+00 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 15956 2.37 - 4.74: 658 4.74 - 7.11: 100 7.11 - 9.48: 31 9.48 - 11.84: 7 Bond angle restraints: 16752 Sorted by residual: angle pdb=" N VAL A 604 " pdb=" CA VAL A 604 " pdb=" C VAL A 604 " ideal model delta sigma weight residual 112.29 105.99 6.30 9.40e-01 1.13e+00 4.49e+01 angle pdb=" N PHE A1366 " pdb=" CA PHE A1366 " pdb=" C PHE A1366 " ideal model delta sigma weight residual 114.56 107.61 6.95 1.27e+00 6.20e-01 3.00e+01 angle pdb=" C TYR A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C ARG A1363 " pdb=" N GLU A1364 " pdb=" CA GLU A1364 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C CYS A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 16747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 7018 21.39 - 42.78: 348 42.78 - 64.17: 31 64.17 - 85.56: 8 85.56 - 106.94: 12 Dihedral angle restraints: 7417 sinusoidal: 3053 harmonic: 4364 Sorted by residual: dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N TYR A1219 " pdb=" CA TYR A1219 " ideal model delta harmonic sigma weight residual -180.00 -137.75 -42.25 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N LYS A 542 " pdb=" CA LYS A 542 " ideal model delta harmonic sigma weight residual -180.00 -138.58 -41.42 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLN A 233 " pdb=" C GLN A 233 " pdb=" N ILE A 234 " pdb=" CA ILE A 234 " ideal model delta harmonic sigma weight residual 180.00 -138.98 -41.02 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 7414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1246 0.058 - 0.116: 482 0.116 - 0.174: 121 0.174 - 0.231: 18 0.231 - 0.289: 6 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CB VAL A 245 " pdb=" CA VAL A 245 " pdb=" CG1 VAL A 245 " pdb=" CG2 VAL A 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1870 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C PHE B 398 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.030 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C VAL A1408 " -0.100 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1287 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A1288 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1288 " -0.047 5.00e-02 4.00e+02 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 292 2.68 - 3.23: 11016 3.23 - 3.79: 18973 3.79 - 4.34: 25164 4.34 - 4.90: 40361 Nonbonded interactions: 95806 Sorted by model distance: nonbonded pdb=" O THR A 669 " pdb="MG MG A1601 " model vdw 2.121 2.170 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.184 3.040 nonbonded pdb=" O ASP A 667 " pdb=" OG1 THR A 671 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A1221 " pdb=" OG1 THR A1353 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1601 " model vdw 2.262 2.170 ... (remaining 95801 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 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.410 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 0.102 12364 Z= 0.326 Angle : 1.136 12.979 16777 Z= 0.596 Chirality : 0.064 0.289 1873 Planarity : 0.008 0.084 2123 Dihedral : 13.552 106.944 4613 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.16), residues: 1487 helix: -4.70 (0.10), residues: 493 sheet: -3.22 (0.37), residues: 128 loop : -3.29 (0.17), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A1415 HIS 0.012 0.002 HIS B 186 PHE 0.036 0.004 PHE A1287 TYR 0.045 0.003 TYR A1273 ARG 0.014 0.001 ARG A1412 Details of bonding type rmsd link_NAG-ASN : bond 0.00847 ( 3) link_NAG-ASN : angle 5.11886 ( 9) link_BETA1-4 : bond 0.00820 ( 3) link_BETA1-4 : angle 4.56100 ( 9) hydrogen bonds : bond 0.31708 ( 243) hydrogen bonds : angle 11.62823 ( 690) link_BETA1-6 : bond 0.00567 ( 1) link_BETA1-6 : angle 2.47684 ( 3) SS BOND : bond 0.00380 ( 2) SS BOND : angle 1.48052 ( 4) covalent geometry : bond 0.00760 (12353) covalent geometry : angle 1.12455 (16752) Misc. bond : bond 0.00220 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.5546 (mpm) cc_final: 0.4399 (mtt) REVERT: A 519 MET cc_start: -0.0530 (mtt) cc_final: -0.0964 (ttm) REVERT: A 633 TYR cc_start: 0.8188 (t80) cc_final: 0.7971 (t80) REVERT: A 652 TRP cc_start: 0.7261 (m100) cc_final: 0.7015 (m-10) REVERT: A 848 ARG cc_start: 0.4870 (mtt90) cc_final: 0.3017 (mtm110) REVERT: A 992 LYS cc_start: 0.6964 (pptt) cc_final: 0.6753 (ptmm) REVERT: B 123 SER cc_start: 0.8729 (m) cc_final: 0.8036 (p) REVERT: B 142 TRP cc_start: 0.7858 (m-10) cc_final: 0.7143 (m-10) REVERT: B 370 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7934 (ttt90) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.3056 time to fit residues: 80.3040 Evaluate side-chains 115 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 71 optimal weight: 0.0070 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 484 ASN A 556 ASN A 674 GLN A1061 HIS A1067 ASN A1209 ASN A1226 ASN A1301 ASN A1307 HIS A1330 HIS B 125 HIS B 171 ASN B 209 HIS B 330 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.197485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175375 restraints weight = 14412.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168441 restraints weight = 20986.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.166172 restraints weight = 31636.944| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12364 Z= 0.150 Angle : 0.720 8.705 16777 Z= 0.375 Chirality : 0.047 0.388 1873 Planarity : 0.005 0.063 2123 Dihedral : 10.724 82.762 1780 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 2.38 % Allowed : 9.46 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.17), residues: 1487 helix: -3.87 (0.15), residues: 506 sheet: -2.88 (0.40), residues: 133 loop : -2.87 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1415 HIS 0.005 0.001 HIS B 186 PHE 0.032 0.002 PHE A 565 TYR 0.017 0.002 TYR A1256 ARG 0.013 0.001 ARG B 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 3) link_NAG-ASN : angle 3.89624 ( 9) link_BETA1-4 : bond 0.00608 ( 3) link_BETA1-4 : angle 3.54608 ( 9) hydrogen bonds : bond 0.04958 ( 243) hydrogen bonds : angle 6.89730 ( 690) link_BETA1-6 : bond 0.00740 ( 1) link_BETA1-6 : angle 2.32110 ( 3) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.42911 ( 4) covalent geometry : bond 0.00335 (12353) covalent geometry : angle 0.70967 (16752) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1665 (OUTLIER) cc_final: 0.1462 (mp) REVERT: A 189 MET cc_start: 0.5197 (mpm) cc_final: 0.4543 (mtt) REVERT: A 519 MET cc_start: 0.0142 (mtt) cc_final: -0.0720 (ttm) REVERT: A 643 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6997 (tt) REVERT: A 677 MET cc_start: 0.5151 (mmm) cc_final: 0.4570 (mtt) REVERT: A 848 ARG cc_start: 0.4655 (mtt90) cc_final: 0.3295 (mtm110) REVERT: A 1039 LYS cc_start: 0.7273 (ttpt) cc_final: 0.7019 (ttpt) REVERT: A 1330 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6404 (m-70) REVERT: B 123 SER cc_start: 0.8566 (m) cc_final: 0.7977 (p) REVERT: B 238 MET cc_start: 0.7465 (ttt) cc_final: 0.7216 (ttt) REVERT: B 321 ASP cc_start: 0.7137 (t0) cc_final: 0.6875 (t70) REVERT: B 359 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 370 ARG cc_start: 0.8295 (ptm-80) cc_final: 0.8059 (ttt180) outliers start: 31 outliers final: 13 residues processed: 163 average time/residue: 0.3171 time to fit residues: 74.8329 Evaluate side-chains 133 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 115 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A1330 HIS B 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.195677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174056 restraints weight = 14712.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.160144 restraints weight = 26161.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157557 restraints weight = 24478.732| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12364 Z= 0.125 Angle : 0.678 12.931 16777 Z= 0.345 Chirality : 0.046 0.357 1873 Planarity : 0.004 0.056 2123 Dihedral : 9.113 69.941 1780 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.00 % Allowed : 10.85 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.19), residues: 1487 helix: -3.27 (0.18), residues: 497 sheet: -2.56 (0.41), residues: 140 loop : -2.61 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 652 HIS 0.015 0.001 HIS A1330 PHE 0.023 0.001 PHE A 565 TYR 0.013 0.001 TYR A 633 ARG 0.004 0.000 ARG A 916 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 3) link_NAG-ASN : angle 3.61492 ( 9) link_BETA1-4 : bond 0.00701 ( 3) link_BETA1-4 : angle 3.37957 ( 9) hydrogen bonds : bond 0.04176 ( 243) hydrogen bonds : angle 6.20686 ( 690) link_BETA1-6 : bond 0.00587 ( 1) link_BETA1-6 : angle 1.76828 ( 3) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.65316 ( 4) covalent geometry : bond 0.00280 (12353) covalent geometry : angle 0.66843 (16752) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2165 (OUTLIER) cc_final: 0.1551 (mp) REVERT: A 189 MET cc_start: 0.5748 (mpm) cc_final: 0.4382 (mtt) REVERT: A 519 MET cc_start: -0.1099 (mtt) cc_final: -0.1833 (ttm) REVERT: A 643 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6968 (tt) REVERT: A 677 MET cc_start: 0.5756 (mmm) cc_final: 0.4947 (mtt) REVERT: A 684 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.5127 (pt) REVERT: A 706 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6249 (pp) REVERT: A 710 THR cc_start: 0.6444 (m) cc_final: 0.6209 (p) REVERT: A 1039 LYS cc_start: 0.7355 (ttpt) cc_final: 0.7045 (ttpt) REVERT: A 1040 TYR cc_start: 0.3902 (t80) cc_final: 0.3027 (t80) REVERT: A 1072 ILE cc_start: 0.7560 (tp) cc_final: 0.7335 (tp) REVERT: A 1186 GLU cc_start: 0.7426 (tp30) cc_final: 0.7155 (tp30) REVERT: B 66 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6880 (pt) REVERT: B 123 SER cc_start: 0.8378 (m) cc_final: 0.8036 (p) REVERT: B 238 MET cc_start: 0.7394 (ttt) cc_final: 0.7127 (ttt) REVERT: B 321 ASP cc_start: 0.6949 (t0) cc_final: 0.6668 (t70) outliers start: 39 outliers final: 18 residues processed: 158 average time/residue: 0.3523 time to fit residues: 82.9676 Evaluate side-chains 148 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 33 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN A1417 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.195682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.173863 restraints weight = 14580.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166550 restraints weight = 25683.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163830 restraints weight = 34686.211| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12364 Z= 0.117 Angle : 0.645 9.542 16777 Z= 0.327 Chirality : 0.045 0.348 1873 Planarity : 0.004 0.062 2123 Dihedral : 7.909 55.931 1780 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.92 % Allowed : 11.77 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.20), residues: 1487 helix: -2.84 (0.19), residues: 501 sheet: -2.63 (0.41), residues: 135 loop : -2.41 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 652 HIS 0.002 0.001 HIS A1293 PHE 0.022 0.001 PHE A 565 TYR 0.013 0.001 TYR B 293 ARG 0.004 0.000 ARG A 916 Details of bonding type rmsd link_NAG-ASN : bond 0.00722 ( 3) link_NAG-ASN : angle 3.41066 ( 9) link_BETA1-4 : bond 0.00599 ( 3) link_BETA1-4 : angle 3.23346 ( 9) hydrogen bonds : bond 0.03554 ( 243) hydrogen bonds : angle 5.67620 ( 690) link_BETA1-6 : bond 0.00437 ( 1) link_BETA1-6 : angle 1.69603 ( 3) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.73677 ( 4) covalent geometry : bond 0.00268 (12353) covalent geometry : angle 0.63565 (16752) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1755 (OUTLIER) cc_final: 0.1453 (mp) REVERT: A 189 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.4391 (mtt) REVERT: A 224 LEU cc_start: 0.4178 (OUTLIER) cc_final: 0.3065 (pp) REVERT: A 229 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.3934 (mm) REVERT: A 519 MET cc_start: 0.0104 (mtt) cc_final: -0.0982 (ttm) REVERT: A 643 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7038 (tt) REVERT: A 677 MET cc_start: 0.5292 (mmm) cc_final: 0.4795 (mtt) REVERT: A 684 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.5224 (pt) REVERT: A 706 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6405 (pp) REVERT: A 1040 TYR cc_start: 0.3851 (t80) cc_final: 0.2827 (t80) REVERT: A 1108 SER cc_start: 0.7945 (p) cc_final: 0.7519 (t) REVERT: A 1186 GLU cc_start: 0.7246 (tp30) cc_final: 0.7010 (tp30) REVERT: B 321 ASP cc_start: 0.7042 (t0) cc_final: 0.6728 (t70) REVERT: B 354 ASN cc_start: 0.7572 (t0) cc_final: 0.7358 (t0) outliers start: 38 outliers final: 22 residues processed: 160 average time/residue: 0.3097 time to fit residues: 74.2734 Evaluate side-chains 146 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 105 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 628 GLN A 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.189525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165375 restraints weight = 14818.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162461 restraints weight = 30025.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161643 restraints weight = 30370.621| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12364 Z= 0.233 Angle : 0.739 8.691 16777 Z= 0.378 Chirality : 0.050 0.422 1873 Planarity : 0.005 0.063 2123 Dihedral : 7.830 53.782 1780 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.54 % Allowed : 13.15 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.19), residues: 1487 helix: -2.85 (0.19), residues: 505 sheet: -2.66 (0.41), residues: 121 loop : -2.46 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1415 HIS 0.006 0.001 HIS A1293 PHE 0.025 0.002 PHE A 565 TYR 0.024 0.002 TYR A 585 ARG 0.006 0.001 ARG A1393 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 3) link_NAG-ASN : angle 3.77532 ( 9) link_BETA1-4 : bond 0.00489 ( 3) link_BETA1-4 : angle 3.46850 ( 9) hydrogen bonds : bond 0.04039 ( 243) hydrogen bonds : angle 5.81564 ( 690) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.78745 ( 3) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.97737 ( 4) covalent geometry : bond 0.00549 (12353) covalent geometry : angle 0.72915 (16752) Misc. bond : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2236 (OUTLIER) cc_final: 0.1891 (mp) REVERT: A 189 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4477 (mtp) REVERT: A 196 ILE cc_start: 0.0911 (OUTLIER) cc_final: 0.0174 (tp) REVERT: A 224 LEU cc_start: 0.4564 (OUTLIER) cc_final: 0.3071 (pp) REVERT: A 229 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3636 (mm) REVERT: A 519 MET cc_start: 0.0208 (mtt) cc_final: -0.0948 (ttm) REVERT: A 643 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7003 (tt) REVERT: A 652 TRP cc_start: 0.7369 (m100) cc_final: 0.7127 (m100) REVERT: A 677 MET cc_start: 0.5374 (mmm) cc_final: 0.4857 (mtt) REVERT: A 684 ILE cc_start: 0.5373 (OUTLIER) cc_final: 0.5121 (pt) REVERT: A 706 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6432 (pp) REVERT: A 1040 TYR cc_start: 0.4153 (t80) cc_final: 0.2661 (t80) REVERT: A 1108 SER cc_start: 0.7895 (p) cc_final: 0.7521 (t) REVERT: A 1186 GLU cc_start: 0.7583 (tp30) cc_final: 0.7333 (tp30) REVERT: B 238 MET cc_start: 0.7377 (ttt) cc_final: 0.7036 (ttt) REVERT: B 321 ASP cc_start: 0.7104 (t0) cc_final: 0.6759 (t70) outliers start: 46 outliers final: 25 residues processed: 164 average time/residue: 0.2416 time to fit residues: 58.6380 Evaluate side-chains 154 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 3 optimal weight: 0.0040 chunk 2 optimal weight: 0.0060 chunk 142 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN A1067 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.194566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171133 restraints weight = 14826.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165564 restraints weight = 27950.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.162920 restraints weight = 32257.302| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12364 Z= 0.115 Angle : 0.641 9.336 16777 Z= 0.325 Chirality : 0.044 0.355 1873 Planarity : 0.004 0.064 2123 Dihedral : 7.142 54.944 1780 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.38 % Allowed : 14.38 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1487 helix: -2.47 (0.21), residues: 500 sheet: -2.45 (0.41), residues: 134 loop : -2.28 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1415 HIS 0.004 0.001 HIS A1417 PHE 0.010 0.001 PHE A 467 TYR 0.013 0.001 TYR A1040 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 3) link_NAG-ASN : angle 3.32477 ( 9) link_BETA1-4 : bond 0.00443 ( 3) link_BETA1-4 : angle 2.94622 ( 9) hydrogen bonds : bond 0.03213 ( 243) hydrogen bonds : angle 5.41993 ( 690) link_BETA1-6 : bond 0.00273 ( 1) link_BETA1-6 : angle 1.58494 ( 3) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.68960 ( 4) covalent geometry : bond 0.00263 (12353) covalent geometry : angle 0.63248 (16752) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2157 (OUTLIER) cc_final: 0.1804 (mp) REVERT: A 189 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4505 (mtp) REVERT: A 224 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.3164 (pp) REVERT: A 229 LEU cc_start: 0.4223 (OUTLIER) cc_final: 0.3916 (mm) REVERT: A 519 MET cc_start: -0.0111 (mtt) cc_final: -0.1048 (ttm) REVERT: A 643 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7042 (tt) REVERT: A 677 MET cc_start: 0.5286 (mmm) cc_final: 0.4765 (mtt) REVERT: A 684 ILE cc_start: 0.5521 (OUTLIER) cc_final: 0.5284 (pt) REVERT: A 706 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6320 (pp) REVERT: A 1040 TYR cc_start: 0.4055 (t80) cc_final: 0.2848 (t80) REVERT: A 1058 LYS cc_start: 0.3178 (OUTLIER) cc_final: 0.2453 (tmtt) REVERT: A 1108 SER cc_start: 0.7959 (p) cc_final: 0.7543 (t) REVERT: A 1186 GLU cc_start: 0.7400 (tp30) cc_final: 0.7155 (tp30) REVERT: A 1270 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 238 MET cc_start: 0.7155 (ttt) cc_final: 0.6777 (ttt) REVERT: B 321 ASP cc_start: 0.6912 (t0) cc_final: 0.6607 (t70) REVERT: B 348 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.8512 (t60) outliers start: 44 outliers final: 26 residues processed: 155 average time/residue: 0.2418 time to fit residues: 55.4566 Evaluate side-chains 148 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 142 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170250 restraints weight = 14730.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.165908 restraints weight = 26318.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.164117 restraints weight = 34199.802| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12364 Z= 0.142 Angle : 0.647 9.220 16777 Z= 0.329 Chirality : 0.045 0.362 1873 Planarity : 0.004 0.064 2123 Dihedral : 7.074 54.294 1780 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.85 % Allowed : 14.31 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.20), residues: 1487 helix: -2.33 (0.21), residues: 502 sheet: -2.47 (0.41), residues: 127 loop : -2.25 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1336 HIS 0.004 0.001 HIS B 186 PHE 0.014 0.002 PHE A1366 TYR 0.018 0.001 TYR A1040 ARG 0.004 0.000 ARG A1393 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 3) link_NAG-ASN : angle 3.39250 ( 9) link_BETA1-4 : bond 0.00500 ( 3) link_BETA1-4 : angle 3.04416 ( 9) hydrogen bonds : bond 0.03249 ( 243) hydrogen bonds : angle 5.32635 ( 690) link_BETA1-6 : bond 0.00375 ( 1) link_BETA1-6 : angle 1.55208 ( 3) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.75120 ( 4) covalent geometry : bond 0.00334 (12353) covalent geometry : angle 0.63815 (16752) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2200 (OUTLIER) cc_final: 0.1954 (mp) REVERT: A 189 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4389 (mtp) REVERT: A 224 LEU cc_start: 0.4334 (OUTLIER) cc_final: 0.3106 (pp) REVERT: A 229 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3620 (mm) REVERT: A 519 MET cc_start: 0.0182 (mtt) cc_final: -0.0862 (ttm) REVERT: A 643 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6968 (tt) REVERT: A 684 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5329 (pt) REVERT: A 706 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6174 (pp) REVERT: A 965 ASP cc_start: 0.7445 (t0) cc_final: 0.6974 (m-30) REVERT: A 1037 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5834 (pt) REVERT: A 1040 TYR cc_start: 0.4313 (t80) cc_final: 0.2910 (t80) REVERT: A 1058 LYS cc_start: 0.3066 (OUTLIER) cc_final: 0.2454 (tmtt) REVERT: A 1108 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7467 (t) REVERT: A 1186 GLU cc_start: 0.7410 (tp30) cc_final: 0.7200 (tp30) REVERT: A 1270 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7786 (t80) REVERT: B 238 MET cc_start: 0.7231 (ttt) cc_final: 0.6870 (ttt) REVERT: B 321 ASP cc_start: 0.6805 (t0) cc_final: 0.6547 (t70) REVERT: B 343 ASP cc_start: 0.7220 (m-30) cc_final: 0.6689 (p0) REVERT: B 348 TRP cc_start: 0.9175 (OUTLIER) cc_final: 0.8562 (t60) outliers start: 50 outliers final: 31 residues processed: 153 average time/residue: 0.2264 time to fit residues: 51.6578 Evaluate side-chains 156 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 63 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.193399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169312 restraints weight = 14755.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.164883 restraints weight = 29225.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164474 restraints weight = 33301.452| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12364 Z= 0.139 Angle : 0.648 9.298 16777 Z= 0.329 Chirality : 0.045 0.359 1873 Planarity : 0.004 0.077 2123 Dihedral : 7.019 57.996 1780 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.85 % Allowed : 14.77 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.20), residues: 1487 helix: -2.21 (0.21), residues: 505 sheet: -2.29 (0.41), residues: 134 loop : -2.27 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1336 HIS 0.016 0.001 HIS A1330 PHE 0.013 0.001 PHE A1366 TYR 0.017 0.001 TYR A1040 ARG 0.004 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 3) link_NAG-ASN : angle 3.37660 ( 9) link_BETA1-4 : bond 0.00524 ( 3) link_BETA1-4 : angle 2.98814 ( 9) hydrogen bonds : bond 0.03258 ( 243) hydrogen bonds : angle 5.28641 ( 690) link_BETA1-6 : bond 0.00382 ( 1) link_BETA1-6 : angle 1.49659 ( 3) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.77101 ( 4) covalent geometry : bond 0.00329 (12353) covalent geometry : angle 0.63936 (16752) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2191 (OUTLIER) cc_final: 0.1954 (mp) REVERT: A 189 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4404 (mtp) REVERT: A 224 LEU cc_start: 0.4295 (OUTLIER) cc_final: 0.3115 (pp) REVERT: A 229 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3652 (mm) REVERT: A 519 MET cc_start: 0.0201 (mtt) cc_final: -0.0855 (ttm) REVERT: A 684 ILE cc_start: 0.5536 (OUTLIER) cc_final: 0.5292 (pt) REVERT: A 706 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6166 (pp) REVERT: A 965 ASP cc_start: 0.7169 (t0) cc_final: 0.6947 (m-30) REVERT: A 1037 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5719 (pt) REVERT: A 1040 TYR cc_start: 0.4161 (t80) cc_final: 0.2887 (t80) REVERT: A 1058 LYS cc_start: 0.3100 (OUTLIER) cc_final: 0.2484 (tmtt) REVERT: A 1108 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7455 (t) REVERT: A 1186 GLU cc_start: 0.7357 (tp30) cc_final: 0.7137 (tp30) REVERT: A 1270 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 238 MET cc_start: 0.7180 (ttt) cc_final: 0.6850 (ttt) REVERT: B 321 ASP cc_start: 0.6815 (t0) cc_final: 0.6553 (t70) REVERT: B 343 ASP cc_start: 0.7168 (m-30) cc_final: 0.6623 (p0) REVERT: B 348 TRP cc_start: 0.9152 (OUTLIER) cc_final: 0.8535 (t60) outliers start: 50 outliers final: 28 residues processed: 157 average time/residue: 0.2434 time to fit residues: 57.2971 Evaluate side-chains 154 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 95 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 59 optimal weight: 0.0040 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN A1330 HIS A1422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.194158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170685 restraints weight = 14745.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.166721 restraints weight = 27035.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165179 restraints weight = 32082.920| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12364 Z= 0.119 Angle : 0.655 15.069 16777 Z= 0.328 Chirality : 0.045 0.338 1873 Planarity : 0.004 0.067 2123 Dihedral : 6.794 54.593 1780 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.54 % Allowed : 15.62 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.20), residues: 1487 helix: -2.08 (0.21), residues: 507 sheet: -2.12 (0.40), residues: 144 loop : -2.27 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.013 0.001 HIS A1330 PHE 0.012 0.001 PHE A 561 TYR 0.015 0.001 TYR A1040 ARG 0.009 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 3) link_NAG-ASN : angle 3.21820 ( 9) link_BETA1-4 : bond 0.00559 ( 3) link_BETA1-4 : angle 2.87572 ( 9) hydrogen bonds : bond 0.03167 ( 243) hydrogen bonds : angle 5.18209 ( 690) link_BETA1-6 : bond 0.00369 ( 1) link_BETA1-6 : angle 1.51541 ( 3) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.72489 ( 4) covalent geometry : bond 0.00279 (12353) covalent geometry : angle 0.64753 (16752) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2183 (OUTLIER) cc_final: 0.1941 (mp) REVERT: A 189 MET cc_start: 0.5142 (OUTLIER) cc_final: 0.4550 (mtp) REVERT: A 196 ILE cc_start: 0.1016 (OUTLIER) cc_final: 0.0231 (tp) REVERT: A 224 LEU cc_start: 0.4128 (OUTLIER) cc_final: 0.3085 (pp) REVERT: A 229 LEU cc_start: 0.4008 (OUTLIER) cc_final: 0.3668 (mm) REVERT: A 519 MET cc_start: 0.0087 (mtt) cc_final: -0.0848 (ttm) REVERT: A 684 ILE cc_start: 0.5527 (OUTLIER) cc_final: 0.5291 (pt) REVERT: A 706 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.6065 (pp) REVERT: A 1040 TYR cc_start: 0.4121 (t80) cc_final: 0.2950 (t80) REVERT: A 1058 LYS cc_start: 0.3095 (OUTLIER) cc_final: 0.2464 (tmtt) REVERT: A 1108 SER cc_start: 0.7854 (p) cc_final: 0.7477 (t) REVERT: A 1270 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7987 (t80) REVERT: B 238 MET cc_start: 0.7053 (ttt) cc_final: 0.6808 (ttt) REVERT: B 321 ASP cc_start: 0.6827 (t0) cc_final: 0.6601 (t70) REVERT: B 343 ASP cc_start: 0.7151 (m-30) cc_final: 0.6665 (p0) REVERT: B 348 TRP cc_start: 0.9126 (OUTLIER) cc_final: 0.8587 (t60) outliers start: 46 outliers final: 29 residues processed: 156 average time/residue: 0.2742 time to fit residues: 65.5027 Evaluate side-chains 154 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.193485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170124 restraints weight = 14629.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164701 restraints weight = 29339.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162441 restraints weight = 40414.536| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12364 Z= 0.157 Angle : 0.683 14.263 16777 Z= 0.344 Chirality : 0.046 0.358 1873 Planarity : 0.004 0.074 2123 Dihedral : 6.787 54.181 1780 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.31 % Allowed : 16.31 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.20), residues: 1487 helix: -2.05 (0.21), residues: 512 sheet: -2.12 (0.40), residues: 145 loop : -2.25 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1415 HIS 0.014 0.001 HIS A1330 PHE 0.014 0.002 PHE A1365 TYR 0.019 0.001 TYR A1040 ARG 0.010 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 3) link_NAG-ASN : angle 3.36854 ( 9) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 2.97324 ( 9) hydrogen bonds : bond 0.03298 ( 243) hydrogen bonds : angle 5.22517 ( 690) link_BETA1-6 : bond 0.00423 ( 1) link_BETA1-6 : angle 1.53396 ( 3) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.87557 ( 4) covalent geometry : bond 0.00373 (12353) covalent geometry : angle 0.67535 (16752) Misc. bond : bond 0.00065 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2258 (OUTLIER) cc_final: 0.1986 (mp) REVERT: A 189 MET cc_start: 0.5101 (OUTLIER) cc_final: 0.4383 (mtp) REVERT: A 196 ILE cc_start: 0.0977 (OUTLIER) cc_final: 0.0222 (tp) REVERT: A 224 LEU cc_start: 0.4306 (OUTLIER) cc_final: 0.3129 (pp) REVERT: A 229 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3823 (mm) REVERT: A 258 ASP cc_start: 0.6724 (p0) cc_final: 0.6516 (p0) REVERT: A 519 MET cc_start: -0.0058 (mtt) cc_final: -0.0962 (ttm) REVERT: A 684 ILE cc_start: 0.5481 (OUTLIER) cc_final: 0.5238 (pt) REVERT: A 706 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6113 (pp) REVERT: A 1040 TYR cc_start: 0.4197 (t80) cc_final: 0.2933 (t80) REVERT: A 1058 LYS cc_start: 0.2982 (OUTLIER) cc_final: 0.2338 (tmtt) REVERT: A 1108 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 1256 TYR cc_start: 0.8894 (t80) cc_final: 0.8626 (t80) REVERT: A 1270 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7963 (t80) REVERT: B 238 MET cc_start: 0.7223 (ttt) cc_final: 0.6934 (ttt) REVERT: B 321 ASP cc_start: 0.6851 (t0) cc_final: 0.6567 (t70) REVERT: B 343 ASP cc_start: 0.7212 (m-30) cc_final: 0.6709 (p0) REVERT: B 348 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8573 (t60) outliers start: 43 outliers final: 28 residues processed: 147 average time/residue: 0.2348 time to fit residues: 51.7473 Evaluate side-chains 154 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.193590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170255 restraints weight = 14597.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166026 restraints weight = 29660.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164354 restraints weight = 37362.991| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12364 Z= 0.150 Angle : 0.680 14.272 16777 Z= 0.342 Chirality : 0.046 0.358 1873 Planarity : 0.004 0.085 2123 Dihedral : 6.720 54.129 1780 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.31 % Allowed : 16.31 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1487 helix: -1.98 (0.22), residues: 509 sheet: -2.12 (0.40), residues: 147 loop : -2.26 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.015 0.002 HIS A1330 PHE 0.013 0.002 PHE A1366 TYR 0.018 0.001 TYR A1040 ARG 0.009 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 3) link_NAG-ASN : angle 3.35028 ( 9) link_BETA1-4 : bond 0.00493 ( 3) link_BETA1-4 : angle 2.96596 ( 9) hydrogen bonds : bond 0.03276 ( 243) hydrogen bonds : angle 5.19124 ( 690) link_BETA1-6 : bond 0.00475 ( 1) link_BETA1-6 : angle 1.49690 ( 3) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.83131 ( 4) covalent geometry : bond 0.00357 (12353) covalent geometry : angle 0.67212 (16752) Misc. bond : bond 0.00062 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4504.61 seconds wall clock time: 82 minutes 53.92 seconds (4973.92 seconds total)