Starting phenix.real_space_refine on Sun Aug 9 09:41:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbp_54734/08_2026/9sbp_54734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbp_54734/08_2026/9sbp_54734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sbp_54734/08_2026/9sbp_54734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbp_54734/08_2026/9sbp_54734.map" model { file = "/net/cci-nas-00/data/ceres_data/9sbp_54734/08_2026/9sbp_54734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbp_54734/08_2026/9sbp_54734.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 96 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20457 2.51 5 N 5734 2.21 5 O 6423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32901 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10859 Classifications: {'peptide': 1379} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1316} Chain breaks: 8 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ATP:plan-1': 1, 'ATP:plan-2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 108.024 69.269 95.010 1.00217.07 S ATOM 479 SG CYS A 70 107.692 65.964 93.104 1.00227.46 S ATOM 532 SG CYS A 77 104.899 68.489 93.110 1.00209.37 S ATOM 762 SG CYS A 107 82.594 74.791 135.586 1.00245.50 S ATOM 786 SG CYS A 110 83.999 71.431 136.131 1.00235.40 S ATOM 1091 SG CYS A 148 80.745 72.353 137.914 1.00249.52 S ATOM 1105 SG CYS A 167 84.088 73.979 138.946 1.00263.07 S ATOM 19520 SG CYS B1163 99.765 56.807 104.957 1.00206.51 S ATOM 19538 SG CYS B1166 98.323 60.255 105.183 1.00211.69 S ATOM 19663 SG CYS B1182 102.100 59.724 104.502 1.00217.73 S ATOM 19682 SG CYS B1185 100.553 58.993 107.940 1.00233.04 S ATOM 20670 SG CYS C 86 94.357 75.015 26.755 1.00248.18 S ATOM 20687 SG CYS C 88 96.546 76.997 28.972 1.00275.36 S ATOM 20720 SG CYS C 92 95.974 78.059 25.405 1.00232.99 S ATOM 20743 SG CYS C 95 93.214 78.528 28.036 1.00234.52 S ATOM 28328 SG CYS I 7 38.960 126.658 126.625 1.00376.08 S ATOM 28353 SG CYS I 10 42.651 126.346 126.611 1.00370.29 S ATOM 28519 SG CYS I 29 40.630 123.652 128.425 1.00400.11 S ATOM 28543 SG CYS I 32 40.757 127.040 129.936 1.00404.50 S ATOM 28870 SG CYS I 75 17.605 119.087 87.095 1.00441.84 S ATOM 28892 SG CYS I 78 17.600 122.674 86.137 1.00438.87 S ATOM 29108 SG CYS I 103 20.858 120.679 85.865 1.00426.14 S ATOM 29128 SG CYS I 106 19.540 121.439 89.289 1.00441.05 S ATOM 29230 SG CYS J 7 65.294 90.469 38.069 1.00179.42 S ATOM 29253 SG CYS J 10 65.018 88.364 34.963 1.00190.72 S ATOM 29533 SG CYS J 45 61.852 89.193 36.895 1.00183.79 S ATOM 29539 SG CYS J 46 63.701 91.609 34.624 1.00186.83 S ATOM 30662 SG CYS L 31 98.055 114.231 54.970 1.00322.83 S ATOM 30682 SG CYS L 34 99.260 116.211 51.991 1.00321.34 S ATOM 30786 SG CYS L 48 101.671 114.802 54.573 1.00332.06 S ATOM 30809 SG CYS L 51 99.596 117.799 55.463 1.00338.04 S Time building chain proxies: 5.93, per 1000 atoms: 0.18 Number of scatterers: 32901 At special positions: 0 Unit cell: (154.505, 156.681, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 96 15.00 Mg 1 11.99 O 6423 8.00 N 5734 7.00 C 20457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 46 sheets defined 39.5% alpha, 19.1% beta 42 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.517A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 144 removed outlier: 4.676A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.686A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.507A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.758A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.692A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.716A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.767A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.679A pdb=" N SER A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.571A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.852A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.585A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.630A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.962A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.872A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.665A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1271 removed outlier: 3.622A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.690A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.998A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.547A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.668A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1447 through 1452' Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.860A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.600A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.939A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.672A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.511A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.661A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.591A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.518A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.674A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.912A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.521A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.519A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.871A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 889 through 893 removed outlier: 4.033A pdb=" N LYS B 892 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.448A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.762A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.803A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1175 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.520A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.623A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.865A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 removed outlier: 4.142A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.528A pdb=" N THR D 26 " --> pdb=" O ASN D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.841A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.576A pdb=" N LEU D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.521A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.652A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.550A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.833A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.504A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.003A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.784A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.527A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.690A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.757A pdb=" N GLU A 16 " --> pdb=" O TYR B1217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 6.949A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.693A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.777A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.675A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.535A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 587 through 590 removed outlier: 7.058A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.880A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.508A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.197A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.373A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.263A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 71 removed outlier: 4.962A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 71 removed outlier: 4.962A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.004A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.272A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC8, first strand: chain 'B' and resid 585 through 590 removed outlier: 4.968A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.534A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.534A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 3.650A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.523A pdb=" N THR B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.819A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.797A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.485A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.593A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.324A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.746A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 85 through 87 removed outlier: 5.237A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.878A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.548A pdb=" N ASP I 19 " --> pdb=" O ARG I 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.907A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE I 100 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 21 through 23 1348 hydrogen bonds defined for protein. 3687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 10.32 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10158 1.33 - 1.45: 5107 1.45 - 1.57: 17930 1.57 - 1.69: 187 1.69 - 1.81: 292 Bond restraints: 33674 Sorted by residual: bond pdb=" O5' ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.579 1.509 0.070 1.10e-02 8.26e+03 4.11e+01 bond pdb=" C1' DC N 73 " pdb=" N1 DC N 73 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" C1' DC T 31 " pdb=" N1 DC T 31 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" C1' DC T 20 " pdb=" N1 DC T 20 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.91e+01 ... (remaining 33669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 45621 3.28 - 6.56: 195 6.56 - 9.85: 38 9.85 - 13.13: 1 13.13 - 16.41: 1 Bond angle restraints: 45856 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B1301 " pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " ideal model delta sigma weight residual 136.83 123.84 12.99 1.00e+00 1.00e+00 1.69e+02 angle pdb=" O4' DT N 50 " pdb=" C4' DT N 50 " pdb=" C3' DT N 50 " ideal model delta sigma weight residual 106.00 102.28 3.72 6.00e-01 2.78e+00 3.84e+01 angle pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " ideal model delta sigma weight residual 101.57 109.41 -7.84 1.54e+00 4.24e-01 2.61e+01 angle pdb=" O4' DC T 53 " pdb=" C4' DC T 53 " pdb=" C3' DC T 53 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.09e+01 ... (remaining 45851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 19803 35.21 - 70.42: 513 70.42 - 105.63: 28 105.63 - 140.84: 1 140.84 - 176.06: 3 Dihedral angle restraints: 20348 sinusoidal: 9046 harmonic: 11302 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN A 68 " pdb=" C GLN A 68 " pdb=" N THR A 69 " pdb=" CA THR A 69 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS A1093 " pdb=" C LYS A1093 " pdb=" N VAL A1094 " pdb=" CA VAL A1094 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 20345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4023 0.048 - 0.096: 867 0.096 - 0.143: 258 0.143 - 0.191: 7 0.191 - 0.239: 1 Chirality restraints: 5156 Sorted by residual: chirality pdb=" CB ILE A1148 " pdb=" CA ILE A1148 " pdb=" CG1 ILE A1148 " pdb=" CG2 ILE A1148 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" C3' DC T 39 " pdb=" C4' DC T 39 " pdb=" O3' DC T 39 " pdb=" C2' DC T 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 5153 not shown) Planarity restraints: 5608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.015 2.00e-02 2.50e+03 1.33e-02 3.51e+00 pdb=" CG TYR B 797 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO A1099 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 245 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.023 5.00e-02 4.00e+02 ... (remaining 5605 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 378 2.58 - 3.16: 28017 3.16 - 3.74: 52380 3.74 - 4.32: 71568 4.32 - 4.90: 116957 Nonbonded interactions: 269300 Sorted by model distance: nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1801 " model vdw 1.997 2.170 nonbonded pdb=" O2 DC N 39 " pdb=" N2 DG T 52 " model vdw 2.048 3.120 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1801 " model vdw 2.137 2.170 nonbonded pdb=" O ARG A1215 " pdb=" OG1 THR A1219 " model vdw 2.154 3.040 nonbonded pdb=" OE1 GLU A1256 " pdb=" ND1 HIS A1258 " model vdw 2.159 3.120 ... (remaining 269295 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.230 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.400 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.005 0.119 33706 Z= 0.299 Angle : 0.635 16.410 45901 Z= 0.414 Chirality : 0.042 0.239 5156 Planarity : 0.003 0.043 5608 Dihedral : 14.417 176.056 13028 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3839 helix: 1.90 (0.15), residues: 1313 sheet: 0.06 (0.22), residues: 597 loop : -0.39 (0.15), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1366 TYR 0.033 0.001 TYR B 797 PHE 0.018 0.001 PHE I 4 TRP 0.011 0.001 TRP A1228 HIS 0.015 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.30 (33674) covalent geometry : angle 0.62683 / 0.41 (45856) hydrogen bonds : bond 0.18476 / 12.40 ( 1429) hydrogen bonds : angle 7.08002 / 5.12 ( 3905) metal coordination : bond 0.00879 / 0.58 ( 32) metal coordination : angle 3.23344 / 2.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 627 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8217 (mtt) cc_final: 0.7804 (mtt) REVERT: A 122 MET cc_start: 0.9405 (tpp) cc_final: 0.9093 (tpp) REVERT: A 142 CYS cc_start: 0.9388 (m) cc_final: 0.9031 (p) REVERT: A 146 MET cc_start: 0.8203 (mmm) cc_final: 0.7960 (mmm) REVERT: A 226 GLU cc_start: 0.9438 (tt0) cc_final: 0.9066 (tp30) REVERT: A 277 GLU cc_start: 0.9681 (tt0) cc_final: 0.9461 (tm-30) REVERT: A 351 THR cc_start: 0.8970 (m) cc_final: 0.8650 (m) REVERT: A 456 MET cc_start: 0.9247 (mtm) cc_final: 0.8878 (mtp) REVERT: A 487 MET cc_start: 0.9195 (mtp) cc_final: 0.8367 (mtt) REVERT: A 605 MET cc_start: 0.9463 (tpt) cc_final: 0.9104 (tpp) REVERT: A 712 GLU cc_start: 0.8561 (pt0) cc_final: 0.8023 (pt0) REVERT: A 849 MET cc_start: 0.8751 (ttp) cc_final: 0.8297 (ttp) REVERT: A 873 MET cc_start: 0.9260 (mmt) cc_final: 0.8593 (mmp) REVERT: A 934 LYS cc_start: 0.9739 (tttm) cc_final: 0.9339 (tptt) REVERT: A 1062 GLU cc_start: 0.9117 (tp30) cc_final: 0.8908 (mm-30) REVERT: A 1063 MET cc_start: 0.9378 (mmm) cc_final: 0.8697 (mmm) REVERT: A 1079 MET cc_start: 0.8262 (tmm) cc_final: 0.7915 (tmm) REVERT: A 1168 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8241 (pm20) REVERT: A 1315 GLU cc_start: 0.9188 (tt0) cc_final: 0.8531 (tp30) REVERT: A 1368 MET cc_start: 0.9183 (mtm) cc_final: 0.8922 (mtt) REVERT: A 1398 MET cc_start: 0.9087 (ptm) cc_final: 0.8452 (ptp) REVERT: A 1417 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7724 (mp0) REVERT: A 1444 MET cc_start: 0.8926 (mmm) cc_final: 0.8361 (mmm) REVERT: B 43 LEU cc_start: 0.9388 (mt) cc_final: 0.9023 (mt) REVERT: B 173 MET cc_start: 0.9015 (ttm) cc_final: 0.8613 (ttp) REVERT: B 224 GLN cc_start: 0.8859 (mt0) cc_final: 0.8548 (mp10) REVERT: B 378 LEU cc_start: 0.9581 (tp) cc_final: 0.9364 (tt) REVERT: B 408 LEU cc_start: 0.8757 (mt) cc_final: 0.8444 (tp) REVERT: B 473 MET cc_start: 0.8523 (mmt) cc_final: 0.8039 (pmm) REVERT: B 498 THR cc_start: 0.9178 (m) cc_final: 0.8774 (p) REVERT: B 542 MET cc_start: 0.8585 (mtm) cc_final: 0.8128 (mtp) REVERT: B 563 MET cc_start: 0.9302 (ttp) cc_final: 0.8946 (tmm) REVERT: B 615 MET cc_start: 0.8875 (mtm) cc_final: 0.8606 (mtm) REVERT: B 622 LYS cc_start: 0.9369 (mttt) cc_final: 0.9161 (mtpp) REVERT: B 775 LYS cc_start: 0.9439 (mtmt) cc_final: 0.8908 (mtmm) REVERT: B 1032 SER cc_start: 0.9668 (m) cc_final: 0.9430 (p) REVERT: B 1072 MET cc_start: 0.8884 (mtp) cc_final: 0.8484 (mtp) REVERT: B 1120 GLU cc_start: 0.8488 (tt0) cc_final: 0.7958 (tp30) REVERT: B 1152 MET cc_start: 0.8771 (mmm) cc_final: 0.8543 (mmm) REVERT: B 1202 LEU cc_start: 0.9276 (tp) cc_final: 0.8738 (tp) REVERT: B 1206 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 1208 MET cc_start: 0.9493 (mtp) cc_final: 0.9176 (mtm) REVERT: C 29 MET cc_start: 0.8901 (ttm) cc_final: 0.8567 (tmm) REVERT: C 37 MET cc_start: 0.9437 (mtm) cc_final: 0.8561 (mtm) REVERT: C 47 ASP cc_start: 0.9333 (t70) cc_final: 0.8960 (t0) REVERT: C 125 MET cc_start: 0.9091 (mtp) cc_final: 0.8490 (mtm) REVERT: C 177 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8246 (tt0) REVERT: C 230 MET cc_start: 0.8879 (mtt) cc_final: 0.8599 (mtt) REVERT: D 1 MET cc_start: 0.2418 (ptm) cc_final: 0.1735 (ttp) REVERT: D 9 GLN cc_start: 0.2959 (mt0) cc_final: 0.2144 (mt0) REVERT: D 31 GLN cc_start: 0.7123 (mt0) cc_final: 0.6766 (mm-40) REVERT: D 58 VAL cc_start: 0.8928 (t) cc_final: 0.8722 (t) REVERT: D 70 PHE cc_start: 0.8087 (m-10) cc_final: 0.7817 (m-80) REVERT: E 8 ASN cc_start: 0.9345 (m110) cc_final: 0.8962 (m110) REVERT: E 22 MET cc_start: 0.9328 (ttp) cc_final: 0.9116 (ttp) REVERT: E 57 MET cc_start: 0.9316 (mtm) cc_final: 0.8470 (ptm) REVERT: E 93 MET cc_start: 0.8939 (tpp) cc_final: 0.8561 (tpp) REVERT: E 106 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8810 (mp10) REVERT: E 214 CYS cc_start: 0.8690 (t) cc_final: 0.8188 (t) REVERT: F 78 GLN cc_start: 0.9208 (mt0) cc_final: 0.9002 (mp10) REVERT: F 85 MET cc_start: 0.9667 (ttm) cc_final: 0.9306 (ttm) REVERT: F 112 GLU cc_start: 0.9035 (mp0) cc_final: 0.8746 (mp0) REVERT: F 119 ARG cc_start: 0.9365 (tpp80) cc_final: 0.8983 (mtm110) REVERT: F 123 LYS cc_start: 0.9323 (tttm) cc_final: 0.8602 (tptm) REVERT: F 127 GLU cc_start: 0.9429 (mt-10) cc_final: 0.8954 (mp0) REVERT: F 144 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8187 (mt-10) REVERT: G 6 ASP cc_start: 0.7022 (m-30) cc_final: 0.6750 (m-30) REVERT: G 24 GLN cc_start: 0.9284 (mt0) cc_final: 0.9066 (mp10) REVERT: G 33 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8066 (tp30) REVERT: G 58 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7698 (mmm-85) REVERT: G 70 PHE cc_start: 0.7908 (m-80) cc_final: 0.7569 (m-10) REVERT: G 74 TYR cc_start: 0.7240 (p90) cc_final: 0.6969 (p90) REVERT: G 82 PHE cc_start: 0.6037 (m-80) cc_final: 0.5830 (m-80) REVERT: G 99 PHE cc_start: 0.7345 (p90) cc_final: 0.7042 (p90) REVERT: G 101 VAL cc_start: 0.6651 (t) cc_final: 0.6056 (t) REVERT: G 115 MET cc_start: 0.6555 (mtp) cc_final: 0.6342 (ttm) REVERT: H 14 GLU cc_start: 0.8427 (tt0) cc_final: 0.7835 (tp30) REVERT: H 33 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8726 (mt0) REVERT: H 43 ASN cc_start: 0.9181 (t0) cc_final: 0.8875 (t0) REVERT: H 103 LYS cc_start: 0.8700 (tptt) cc_final: 0.8441 (tptp) REVERT: H 123 MET cc_start: 0.9004 (ttt) cc_final: 0.8613 (ttp) REVERT: H 137 GLN cc_start: 0.9063 (tt0) cc_final: 0.8761 (tt0) REVERT: I 45 ARG cc_start: 0.6966 (ttt90) cc_final: 0.6354 (ttt90) REVERT: I 51 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5274 (t0) REVERT: I 65 ASP cc_start: 0.8859 (t70) cc_final: 0.8537 (t0) REVERT: I 92 ARG cc_start: 0.6337 (mtt90) cc_final: 0.6016 (mtt180) REVERT: J 16 ASP cc_start: 0.9555 (p0) cc_final: 0.9037 (p0) REVERT: J 30 LEU cc_start: 0.8524 (mt) cc_final: 0.8010 (mp) REVERT: K 17 SER cc_start: 0.9313 (m) cc_final: 0.8868 (p) REVERT: K 33 ILE cc_start: 0.9091 (mt) cc_final: 0.8871 (tp) REVERT: K 106 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8712 (mt-10) REVERT: L 54 ARG cc_start: 0.6894 (mtt-85) cc_final: 0.6518 (mtt90) REVERT: L 56 LEU cc_start: 0.8680 (mt) cc_final: 0.8391 (mm) REVERT: L 58 LYS cc_start: 0.8267 (tttm) cc_final: 0.8039 (tttt) outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.2169 time to fit residues: 215.9181 Evaluate side-chains 396 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN B 110 HIS B 449 ASN B 538 ASN B 761 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 37 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN I 51 ASN I 87 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.076923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.052277 restraints weight = 115908.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053872 restraints weight = 60403.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.054926 restraints weight = 40196.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055590 restraints weight = 31218.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.055998 restraints weight = 26758.219| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33706 Z= 0.223 Angle : 0.693 18.225 45901 Z= 0.354 Chirality : 0.046 0.230 5156 Planarity : 0.005 0.048 5608 Dihedral : 16.524 176.419 5262 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 1.14 % Allowed : 7.12 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3839 helix: 1.53 (0.14), residues: 1343 sheet: 0.02 (0.21), residues: 611 loop : -0.43 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 73 TYR 0.024 0.001 TYR B 797 PHE 0.020 0.002 PHE A 219 TRP 0.011 0.001 TRP B 31 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (33674) covalent geometry : angle 0.66681 / 0.35 (45856) hydrogen bonds : bond 0.05020 / 3.35 ( 1429) hydrogen bonds : angle 5.40995 / 3.92 ( 3905) metal coordination : bond 0.01402 / 0.73 ( 32) metal coordination : angle 6.03889 / 4.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 441 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8502 (mtt) cc_final: 0.8095 (mtt) REVERT: A 146 MET cc_start: 0.8238 (mmm) cc_final: 0.7952 (mmm) REVERT: A 456 MET cc_start: 0.9146 (mtm) cc_final: 0.8758 (mtp) REVERT: A 654 ASN cc_start: 0.9190 (m110) cc_final: 0.8984 (m-40) REVERT: A 849 MET cc_start: 0.9288 (ttp) cc_final: 0.8884 (ttp) REVERT: A 873 MET cc_start: 0.9278 (mmt) cc_final: 0.8461 (mmp) REVERT: A 934 LYS cc_start: 0.9679 (tttm) cc_final: 0.9365 (tptt) REVERT: A 1063 MET cc_start: 0.9439 (mmm) cc_final: 0.9140 (mmm) REVERT: A 1079 MET cc_start: 0.8297 (tmm) cc_final: 0.8052 (tmm) REVERT: A 1285 MET cc_start: 0.9015 (mmm) cc_final: 0.8519 (tmm) REVERT: A 1315 GLU cc_start: 0.8863 (tt0) cc_final: 0.8347 (tp30) REVERT: A 1368 MET cc_start: 0.8856 (mtm) cc_final: 0.8434 (mtp) REVERT: A 1417 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8498 (mp0) REVERT: A 1444 MET cc_start: 0.9113 (mmm) cc_final: 0.8648 (mmm) REVERT: B 747 MET cc_start: 0.9347 (mmp) cc_final: 0.9137 (mmp) REVERT: B 816 GLU cc_start: 0.8827 (mp0) cc_final: 0.8606 (mp0) REVERT: B 999 MET cc_start: 0.9285 (tpp) cc_final: 0.9045 (tpp) REVERT: B 1072 MET cc_start: 0.8321 (mtp) cc_final: 0.8009 (mtp) REVERT: B 1152 MET cc_start: 0.9148 (mmm) cc_final: 0.8821 (mmm) REVERT: B 1202 LEU cc_start: 0.9467 (tp) cc_final: 0.8772 (tp) REVERT: B 1206 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8588 (mt-10) REVERT: B 1208 MET cc_start: 0.9270 (mtp) cc_final: 0.9007 (mtm) REVERT: C 37 MET cc_start: 0.9317 (mtm) cc_final: 0.8617 (mtm) REVERT: C 47 ASP cc_start: 0.8881 (t70) cc_final: 0.8653 (t0) REVERT: C 177 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7924 (tt0) REVERT: D 1 MET cc_start: 0.2620 (ptm) cc_final: 0.2076 (ttp) REVERT: D 67 ARG cc_start: 0.6336 (tpp80) cc_final: 0.6056 (tpp80) REVERT: D 70 PHE cc_start: 0.8331 (m-10) cc_final: 0.8030 (m-80) REVERT: D 151 PHE cc_start: 0.8040 (t80) cc_final: 0.7649 (t80) REVERT: E 8 ASN cc_start: 0.9279 (m110) cc_final: 0.8912 (m110) REVERT: G 3 PHE cc_start: 0.8037 (m-10) cc_final: 0.7781 (m-10) REVERT: G 32 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: G 33 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8137 (tp30) REVERT: G 58 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8362 (mmt90) REVERT: G 82 PHE cc_start: 0.6407 (m-80) cc_final: 0.5924 (m-80) REVERT: H 43 ASN cc_start: 0.9664 (t0) cc_final: 0.8825 (t0) REVERT: H 52 GLN cc_start: 0.9141 (mp10) cc_final: 0.8798 (mp10) REVERT: H 105 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6509 (tm-30) REVERT: H 123 MET cc_start: 0.9043 (ttt) cc_final: 0.8785 (ttp) REVERT: I 30 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7279 (mtm-85) REVERT: J 16 ASP cc_start: 0.9100 (p0) cc_final: 0.8685 (p0) REVERT: J 32 GLU cc_start: 0.9230 (mp0) cc_final: 0.8833 (mm-30) REVERT: K 16 GLU cc_start: 0.7929 (tt0) cc_final: 0.7487 (tp30) REVERT: K 17 SER cc_start: 0.9482 (m) cc_final: 0.9276 (p) REVERT: K 36 GLU cc_start: 0.8650 (mm-30) cc_final: 0.7985 (mm-30) REVERT: K 64 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8191 (mt-10) REVERT: K 106 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8536 (mt-10) REVERT: L 58 LYS cc_start: 0.8805 (tttm) cc_final: 0.8599 (ttmt) outliers start: 39 outliers final: 22 residues processed: 461 average time/residue: 0.2286 time to fit residues: 167.6845 Evaluate side-chains 392 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 369 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 296 optimal weight: 8.9990 chunk 335 optimal weight: 0.6980 chunk 310 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 251 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 0.0570 chunk 344 optimal weight: 3.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN D 9 GLN D 28 GLN D 37 GLN D 173 HIS E 101 GLN H 33 GLN H 131 ASN I 46 HIS J 53 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053812 restraints weight = 114395.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055460 restraints weight = 59019.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056526 restraints weight = 38929.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057232 restraints weight = 30208.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057643 restraints weight = 25712.495| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33706 Z= 0.121 Angle : 0.595 15.265 45901 Z= 0.310 Chirality : 0.044 0.240 5156 Planarity : 0.004 0.080 5608 Dihedral : 16.428 175.523 5260 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 1.17 % Allowed : 8.41 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3839 helix: 1.52 (0.14), residues: 1348 sheet: 0.02 (0.21), residues: 616 loop : -0.46 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 91 TYR 0.017 0.001 TYR G 51 PHE 0.027 0.001 PHE B 286 TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (33674) covalent geometry : angle 0.57896 / 0.31 (45856) hydrogen bonds : bond 0.04052 / 2.71 ( 1429) hydrogen bonds : angle 4.92441 / 3.56 ( 3905) metal coordination : bond 0.00730 / 0.51 ( 32) metal coordination : angle 4.45655 / 3.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 453 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8583 (mtt) cc_final: 0.8304 (mtt) REVERT: A 146 MET cc_start: 0.8238 (mmm) cc_final: 0.7996 (mmm) REVERT: A 287 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8336 (t70) REVERT: A 455 MET cc_start: 0.8945 (ttm) cc_final: 0.7692 (ttp) REVERT: A 456 MET cc_start: 0.9173 (mtm) cc_final: 0.8677 (mtp) REVERT: A 487 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7850 (mtp) REVERT: A 789 LYS cc_start: 0.9407 (mttt) cc_final: 0.9085 (mttm) REVERT: A 849 MET cc_start: 0.9308 (ttp) cc_final: 0.8739 (ttt) REVERT: A 873 MET cc_start: 0.9238 (mmt) cc_final: 0.8406 (mmp) REVERT: A 934 LYS cc_start: 0.9661 (tttm) cc_final: 0.9321 (tptt) REVERT: A 1062 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 1063 MET cc_start: 0.9370 (mmm) cc_final: 0.9143 (mmm) REVERT: A 1079 MET cc_start: 0.8233 (tmm) cc_final: 0.7914 (tmm) REVERT: A 1285 MET cc_start: 0.9007 (mmm) cc_final: 0.8639 (mmm) REVERT: A 1315 GLU cc_start: 0.8832 (tt0) cc_final: 0.8283 (tp30) REVERT: A 1368 MET cc_start: 0.8809 (mtm) cc_final: 0.8401 (mtp) REVERT: A 1375 MET cc_start: 0.9155 (mtp) cc_final: 0.8812 (ttm) REVERT: A 1417 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8436 (mp0) REVERT: A 1444 MET cc_start: 0.9056 (mmm) cc_final: 0.8394 (mmt) REVERT: B 529 GLU cc_start: 0.8282 (pm20) cc_final: 0.8074 (pm20) REVERT: B 775 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9114 (mtmm) REVERT: B 809 MET cc_start: 0.9170 (mtm) cc_final: 0.8876 (mtm) REVERT: B 816 GLU cc_start: 0.8800 (mp0) cc_final: 0.8593 (mp0) REVERT: B 885 MET cc_start: 0.4793 (tpp) cc_final: 0.4580 (tpp) REVERT: B 1072 MET cc_start: 0.8254 (mtp) cc_final: 0.7992 (mtp) REVERT: B 1111 MET cc_start: 0.8906 (mmm) cc_final: 0.8616 (mmm) REVERT: B 1152 MET cc_start: 0.9114 (mmm) cc_final: 0.8814 (mmm) REVERT: B 1202 LEU cc_start: 0.9419 (tp) cc_final: 0.8502 (tp) REVERT: B 1206 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8689 (mp0) REVERT: B 1208 MET cc_start: 0.9245 (mtp) cc_final: 0.8980 (mtm) REVERT: C 29 MET cc_start: 0.8495 (tmm) cc_final: 0.8005 (tmm) REVERT: C 157 CYS cc_start: 0.9016 (m) cc_final: 0.8671 (p) REVERT: C 177 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 34 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: D 37 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6436 (mm-40) REVERT: D 50 LEU cc_start: 0.8875 (tp) cc_final: 0.8350 (tp) REVERT: D 67 ARG cc_start: 0.6414 (tpp80) cc_final: 0.6146 (tpp80) REVERT: D 70 PHE cc_start: 0.8315 (m-10) cc_final: 0.8042 (m-80) REVERT: D 142 LYS cc_start: 0.8905 (tttt) cc_final: 0.8674 (mtpp) REVERT: D 146 GLN cc_start: 0.7741 (tp40) cc_final: 0.7521 (mm-40) REVERT: D 151 PHE cc_start: 0.8024 (t80) cc_final: 0.7659 (t80) REVERT: E 8 ASN cc_start: 0.9275 (m110) cc_final: 0.8944 (m-40) REVERT: F 81 THR cc_start: 0.9596 (m) cc_final: 0.9139 (p) REVERT: F 87 LYS cc_start: 0.9429 (ptmt) cc_final: 0.9038 (ptpp) REVERT: F 88 TYR cc_start: 0.9008 (m-80) cc_final: 0.8631 (m-80) REVERT: G 6 ASP cc_start: 0.7308 (m-30) cc_final: 0.6937 (t0) REVERT: G 21 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8163 (mtp-110) REVERT: G 29 LYS cc_start: 0.9094 (tppt) cc_final: 0.8772 (tptm) REVERT: G 32 GLU cc_start: 0.8435 (mp0) cc_final: 0.7953 (mp0) REVERT: G 33 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8038 (tp30) REVERT: G 115 MET cc_start: 0.6675 (mtp) cc_final: 0.6114 (ttm) REVERT: H 52 GLN cc_start: 0.9216 (mp10) cc_final: 0.8790 (mp10) REVERT: H 105 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6547 (tm-30) REVERT: H 123 MET cc_start: 0.9062 (ttt) cc_final: 0.8860 (ttp) REVERT: H 130 ARG cc_start: 0.8956 (ttm-80) cc_final: 0.8609 (mtm-85) REVERT: I 5 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6834 (mmm-85) REVERT: I 30 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7910 (mtt-85) REVERT: I 71 SER cc_start: 0.8173 (t) cc_final: 0.7848 (t) REVERT: I 95 THR cc_start: 0.8004 (m) cc_final: 0.7730 (p) REVERT: J 16 ASP cc_start: 0.9021 (p0) cc_final: 0.8650 (p0) REVERT: J 27 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8326 (mt-10) REVERT: K 16 GLU cc_start: 0.8037 (tt0) cc_final: 0.7278 (tp30) REVERT: K 36 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7858 (mm-30) REVERT: K 64 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8225 (mt-10) REVERT: K 106 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8497 (mt-10) outliers start: 40 outliers final: 17 residues processed: 475 average time/residue: 0.2223 time to fit residues: 168.5002 Evaluate side-chains 393 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 372 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 56 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 294 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 368 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN A1009 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 33 GLN H 131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.052842 restraints weight = 116548.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054451 restraints weight = 60723.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055499 restraints weight = 40360.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056165 restraints weight = 31316.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.056577 restraints weight = 26846.763| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33706 Z= 0.203 Angle : 0.620 13.351 45901 Z= 0.321 Chirality : 0.044 0.205 5156 Planarity : 0.004 0.053 5608 Dihedral : 16.422 175.991 5260 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.46 % Allowed : 10.16 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3839 helix: 1.57 (0.14), residues: 1340 sheet: -0.03 (0.21), residues: 615 loop : -0.46 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.019 0.001 TYR B 830 PHE 0.021 0.001 PHE A 219 TRP 0.011 0.001 TRP B 31 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (33674) covalent geometry : angle 0.60492 / 0.32 (45856) hydrogen bonds : bond 0.03897 / 2.61 ( 1429) hydrogen bonds : angle 4.87452 / 3.53 ( 3905) metal coordination : bond 0.00803 / 0.50 ( 32) metal coordination : angle 4.31332 / 2.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 379 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8518 (mtt) cc_final: 0.8138 (mtt) REVERT: A 146 MET cc_start: 0.8256 (mmm) cc_final: 0.7952 (mmm) REVERT: A 287 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8371 (t70) REVERT: A 456 MET cc_start: 0.9153 (mtm) cc_final: 0.8545 (mtp) REVERT: A 486 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8475 (pm20) REVERT: A 873 MET cc_start: 0.9203 (mmt) cc_final: 0.8392 (mmp) REVERT: A 934 LYS cc_start: 0.9665 (tttm) cc_final: 0.9338 (tptt) REVERT: A 1062 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8050 (tp30) REVERT: A 1063 MET cc_start: 0.9406 (mmm) cc_final: 0.9196 (mmm) REVERT: A 1079 MET cc_start: 0.8270 (tmm) cc_final: 0.7847 (tmm) REVERT: A 1144 LYS cc_start: 0.9495 (tppt) cc_final: 0.9284 (tppt) REVERT: A 1285 MET cc_start: 0.9061 (mmm) cc_final: 0.8673 (mmm) REVERT: A 1315 GLU cc_start: 0.8856 (tt0) cc_final: 0.8376 (tp30) REVERT: A 1368 MET cc_start: 0.8809 (mtm) cc_final: 0.8349 (mtp) REVERT: A 1375 MET cc_start: 0.9140 (mtp) cc_final: 0.8844 (ttm) REVERT: A 1444 MET cc_start: 0.9067 (mmm) cc_final: 0.8368 (mmt) REVERT: B 312 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: B 775 LYS cc_start: 0.9431 (mtmt) cc_final: 0.9165 (mtmm) REVERT: B 809 MET cc_start: 0.9228 (mtm) cc_final: 0.8917 (mtm) REVERT: B 885 MET cc_start: 0.4999 (tpp) cc_final: 0.4699 (tpp) REVERT: B 1072 MET cc_start: 0.8319 (mtp) cc_final: 0.8049 (mtp) REVERT: B 1111 MET cc_start: 0.8888 (mmm) cc_final: 0.8281 (mmm) REVERT: B 1152 MET cc_start: 0.9123 (mmm) cc_final: 0.8776 (mmm) REVERT: B 1202 LEU cc_start: 0.9472 (tp) cc_final: 0.8513 (tp) REVERT: B 1206 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8716 (mp0) REVERT: B 1208 MET cc_start: 0.9266 (mtp) cc_final: 0.9006 (mtm) REVERT: C 29 MET cc_start: 0.8630 (tmm) cc_final: 0.8077 (tmm) REVERT: C 177 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 34 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8271 (mp10) REVERT: D 67 ARG cc_start: 0.6427 (tpp80) cc_final: 0.6176 (tpp80) REVERT: D 70 PHE cc_start: 0.8332 (m-10) cc_final: 0.8015 (m-80) REVERT: D 151 PHE cc_start: 0.8068 (t80) cc_final: 0.7728 (t80) REVERT: E 8 ASN cc_start: 0.9267 (m110) cc_final: 0.8940 (m110) REVERT: F 81 THR cc_start: 0.9580 (m) cc_final: 0.9146 (p) REVERT: F 87 LYS cc_start: 0.9431 (ptmt) cc_final: 0.9106 (ptpp) REVERT: F 88 TYR cc_start: 0.9029 (m-80) cc_final: 0.7960 (m-80) REVERT: G 6 ASP cc_start: 0.7416 (m-30) cc_final: 0.7065 (t0) REVERT: G 21 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.8100 (mtp-110) REVERT: G 32 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: G 33 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8185 (tp30) REVERT: G 58 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8267 (mmm-85) REVERT: G 115 MET cc_start: 0.6551 (mtp) cc_final: 0.6089 (ttm) REVERT: H 42 ILE cc_start: 0.9423 (mm) cc_final: 0.9184 (tp) REVERT: H 52 GLN cc_start: 0.9244 (mp10) cc_final: 0.8781 (mp10) REVERT: H 103 LYS cc_start: 0.9269 (tppp) cc_final: 0.8876 (tptp) REVERT: H 130 ARG cc_start: 0.8979 (ttm-80) cc_final: 0.8547 (mtm-85) REVERT: I 5 ARG cc_start: 0.7311 (mmm-85) cc_final: 0.6958 (mmm-85) REVERT: I 30 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7969 (mtt-85) REVERT: I 81 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7855 (mmm-85) REVERT: I 95 THR cc_start: 0.7907 (m) cc_final: 0.7663 (p) REVERT: J 16 ASP cc_start: 0.8965 (p0) cc_final: 0.8537 (p0) REVERT: J 32 GLU cc_start: 0.9191 (mp0) cc_final: 0.8845 (mm-30) REVERT: K 16 GLU cc_start: 0.7983 (tt0) cc_final: 0.7277 (tp30) REVERT: K 36 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7786 (mm-30) REVERT: K 64 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8189 (mt-10) REVERT: K 106 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8559 (mt-10) outliers start: 50 outliers final: 30 residues processed: 413 average time/residue: 0.2047 time to fit residues: 136.1692 Evaluate side-chains 391 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 293 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 331 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 0.0770 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 33 GLN H 137 GLN J 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052793 restraints weight = 115375.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054389 restraints weight = 60500.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055429 restraints weight = 40278.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056090 restraints weight = 31303.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056496 restraints weight = 26889.856| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33706 Z= 0.189 Angle : 0.606 14.547 45901 Z= 0.313 Chirality : 0.044 0.238 5156 Planarity : 0.004 0.048 5608 Dihedral : 16.444 175.986 5260 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 1.66 % Allowed : 10.65 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3839 helix: 1.56 (0.14), residues: 1348 sheet: -0.09 (0.21), residues: 616 loop : -0.50 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 144 TYR 0.018 0.001 TYR G 51 PHE 0.023 0.001 PHE G 3 TRP 0.011 0.001 TRP B 31 HIS 0.008 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (33674) covalent geometry : angle 0.58729 / 0.31 (45856) hydrogen bonds : bond 0.03742 / 2.50 ( 1429) hydrogen bonds : angle 4.76970 / 3.45 ( 3905) metal coordination : bond 0.00825 / 0.52 ( 32) metal coordination : angle 4.77982 / 3.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 382 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8491 (mtt) cc_final: 0.8112 (mtt) REVERT: A 146 MET cc_start: 0.8253 (mmm) cc_final: 0.7951 (mmm) REVERT: A 456 MET cc_start: 0.9148 (mtm) cc_final: 0.8544 (mtp) REVERT: A 487 MET cc_start: 0.8713 (mtp) cc_final: 0.8292 (mtp) REVERT: A 873 MET cc_start: 0.9225 (mmt) cc_final: 0.8433 (mmp) REVERT: A 934 LYS cc_start: 0.9660 (tttm) cc_final: 0.9352 (tptt) REVERT: A 1062 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8010 (tp30) REVERT: A 1063 MET cc_start: 0.9409 (mmm) cc_final: 0.9173 (mmm) REVERT: A 1079 MET cc_start: 0.8199 (tmm) cc_final: 0.7859 (tmm) REVERT: A 1285 MET cc_start: 0.9095 (mmm) cc_final: 0.8680 (mmm) REVERT: A 1315 GLU cc_start: 0.8835 (tt0) cc_final: 0.8363 (tp30) REVERT: A 1368 MET cc_start: 0.8766 (mtm) cc_final: 0.8322 (mtp) REVERT: A 1444 MET cc_start: 0.9046 (mmm) cc_final: 0.8318 (mmt) REVERT: B 101 MET cc_start: 0.8416 (mmm) cc_final: 0.8209 (tpp) REVERT: B 775 LYS cc_start: 0.9441 (mtmt) cc_final: 0.9178 (mtmm) REVERT: B 809 MET cc_start: 0.9181 (mtm) cc_final: 0.8907 (mtm) REVERT: B 1072 MET cc_start: 0.8371 (mtp) cc_final: 0.8019 (mtp) REVERT: B 1152 MET cc_start: 0.9089 (mmm) cc_final: 0.8687 (mmm) REVERT: B 1202 LEU cc_start: 0.9490 (tp) cc_final: 0.8515 (tp) REVERT: B 1206 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8720 (mp0) REVERT: B 1208 MET cc_start: 0.9238 (mtp) cc_final: 0.8964 (mtm) REVERT: C 29 MET cc_start: 0.8796 (tmm) cc_final: 0.8158 (tmm) REVERT: C 177 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7969 (tt0) REVERT: D 67 ARG cc_start: 0.6394 (tpp80) cc_final: 0.6174 (tpp80) REVERT: D 70 PHE cc_start: 0.8322 (m-10) cc_final: 0.8012 (m-80) REVERT: D 151 PHE cc_start: 0.8075 (t80) cc_final: 0.7738 (t80) REVERT: E 8 ASN cc_start: 0.9269 (m110) cc_final: 0.8936 (m110) REVERT: E 121 MET cc_start: 0.9215 (mmm) cc_final: 0.8953 (mmt) REVERT: F 81 THR cc_start: 0.9555 (m) cc_final: 0.9121 (p) REVERT: F 87 LYS cc_start: 0.9442 (ptmt) cc_final: 0.9116 (ptpp) REVERT: F 88 TYR cc_start: 0.9041 (m-80) cc_final: 0.7950 (m-80) REVERT: F 118 LEU cc_start: 0.9452 (tt) cc_final: 0.9195 (tp) REVERT: F 122 MET cc_start: 0.9403 (mtp) cc_final: 0.9004 (mtm) REVERT: G 3 PHE cc_start: 0.8157 (m-80) cc_final: 0.7654 (m-10) REVERT: G 6 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.7057 (t0) REVERT: G 21 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.7994 (ttm110) REVERT: G 24 GLN cc_start: 0.8892 (mp10) cc_final: 0.8632 (mp10) REVERT: G 58 ARG cc_start: 0.8937 (mmt90) cc_final: 0.8345 (mmm-85) REVERT: G 99 PHE cc_start: 0.6484 (p90) cc_final: 0.6191 (p90) REVERT: G 115 MET cc_start: 0.6563 (mtp) cc_final: 0.6043 (ttm) REVERT: H 42 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9206 (tp) REVERT: H 52 GLN cc_start: 0.9250 (mp10) cc_final: 0.8766 (mp10) REVERT: H 105 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6566 (tm-30) REVERT: H 123 MET cc_start: 0.9028 (ttt) cc_final: 0.8677 (ttm) REVERT: H 126 GLU cc_start: 0.8843 (tt0) cc_final: 0.8491 (tt0) REVERT: H 130 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8632 (mtm-85) REVERT: I 5 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7081 (mmm-85) REVERT: I 30 ARG cc_start: 0.8217 (mtt-85) cc_final: 0.7988 (mtt-85) REVERT: J 16 ASP cc_start: 0.9018 (p0) cc_final: 0.8818 (p0) REVERT: J 32 GLU cc_start: 0.9213 (mp0) cc_final: 0.8841 (mm-30) REVERT: K 16 GLU cc_start: 0.8017 (tt0) cc_final: 0.7334 (tp30) REVERT: K 22 ASP cc_start: 0.8931 (t0) cc_final: 0.8648 (p0) REVERT: K 36 GLU cc_start: 0.8612 (mm-30) cc_final: 0.7733 (mm-30) REVERT: K 64 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8155 (mt-10) REVERT: K 106 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8581 (mt-10) outliers start: 57 outliers final: 31 residues processed: 419 average time/residue: 0.2025 time to fit residues: 136.9024 Evaluate side-chains 380 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 346 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 88 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 358 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.053829 restraints weight = 113981.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055452 restraints weight = 59297.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056507 restraints weight = 39221.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057174 restraints weight = 30327.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057594 restraints weight = 25943.045| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33706 Z= 0.129 Angle : 0.591 11.497 45901 Z= 0.305 Chirality : 0.043 0.250 5156 Planarity : 0.004 0.058 5608 Dihedral : 16.424 175.337 5260 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 1.49 % Allowed : 11.33 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3839 helix: 1.62 (0.14), residues: 1343 sheet: -0.09 (0.21), residues: 620 loop : -0.46 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 81 TYR 0.018 0.001 TYR I 44 PHE 0.021 0.001 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (33674) covalent geometry : angle 0.57622 / 0.30 (45856) hydrogen bonds : bond 0.03520 / 2.34 ( 1429) hydrogen bonds : angle 4.63236 / 3.34 ( 3905) metal coordination : bond 0.00642 / 0.42 ( 32) metal coordination : angle 4.26753 / 2.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 380 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8510 (mtt) cc_final: 0.8140 (mtt) REVERT: A 146 MET cc_start: 0.8238 (mmm) cc_final: 0.7986 (mmm) REVERT: A 437 MET cc_start: 0.8225 (mmm) cc_final: 0.8017 (mmt) REVERT: A 456 MET cc_start: 0.9154 (mtm) cc_final: 0.8530 (mtp) REVERT: A 849 MET cc_start: 0.9310 (ttp) cc_final: 0.8937 (ttt) REVERT: A 873 MET cc_start: 0.9191 (mmt) cc_final: 0.8408 (mmp) REVERT: A 934 LYS cc_start: 0.9617 (tttm) cc_final: 0.9314 (tptt) REVERT: A 1062 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7982 (tp30) REVERT: A 1079 MET cc_start: 0.8146 (tmm) cc_final: 0.7796 (tmm) REVERT: A 1144 LYS cc_start: 0.9454 (tppt) cc_final: 0.9238 (tppt) REVERT: A 1285 MET cc_start: 0.9095 (mmm) cc_final: 0.8726 (mmm) REVERT: A 1315 GLU cc_start: 0.8777 (tt0) cc_final: 0.8277 (tp30) REVERT: A 1368 MET cc_start: 0.8715 (mtm) cc_final: 0.8240 (mtp) REVERT: A 1417 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8458 (mp0) REVERT: A 1444 MET cc_start: 0.8989 (mmm) cc_final: 0.8258 (mmt) REVERT: B 173 MET cc_start: 0.8856 (ttp) cc_final: 0.8646 (ttp) REVERT: B 312 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: B 775 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9124 (mtmm) REVERT: B 816 GLU cc_start: 0.8728 (mp0) cc_final: 0.8527 (mp0) REVERT: B 1072 MET cc_start: 0.8339 (mtp) cc_final: 0.7986 (mtp) REVERT: B 1152 MET cc_start: 0.9084 (mmm) cc_final: 0.8727 (mmm) REVERT: B 1202 LEU cc_start: 0.9469 (tp) cc_final: 0.8521 (tp) REVERT: B 1206 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8704 (mp0) REVERT: C 29 MET cc_start: 0.8826 (tmm) cc_final: 0.8125 (tmm) REVERT: C 75 MET cc_start: 0.8900 (mmm) cc_final: 0.8646 (mmm) REVERT: C 177 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7960 (tt0) REVERT: D 67 ARG cc_start: 0.6445 (tpp80) cc_final: 0.6212 (tpp80) REVERT: D 70 PHE cc_start: 0.8337 (m-10) cc_final: 0.7990 (m-80) REVERT: D 151 PHE cc_start: 0.8129 (t80) cc_final: 0.7783 (t80) REVERT: E 8 ASN cc_start: 0.9262 (m110) cc_final: 0.8937 (m110) REVERT: F 81 THR cc_start: 0.9547 (m) cc_final: 0.9134 (p) REVERT: F 88 TYR cc_start: 0.9027 (m-80) cc_final: 0.8036 (m-80) REVERT: F 124 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8186 (tt0) REVERT: G 18 PHE cc_start: 0.9147 (m-10) cc_final: 0.8747 (m-10) REVERT: G 21 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8213 (ttm110) REVERT: G 24 GLN cc_start: 0.8874 (mp10) cc_final: 0.8671 (mp10) REVERT: G 33 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8823 (mm-30) REVERT: G 58 ARG cc_start: 0.8932 (mmt90) cc_final: 0.8341 (mmm-85) REVERT: G 99 PHE cc_start: 0.6483 (p90) cc_final: 0.6108 (p90) REVERT: G 115 MET cc_start: 0.6688 (mtp) cc_final: 0.6131 (ttm) REVERT: H 52 GLN cc_start: 0.9235 (mp10) cc_final: 0.8789 (mp10) REVERT: H 123 MET cc_start: 0.9007 (ttt) cc_final: 0.8663 (ttm) REVERT: H 126 GLU cc_start: 0.8815 (tt0) cc_final: 0.8481 (tt0) REVERT: H 130 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8581 (mtm-85) REVERT: I 30 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7991 (mtt-85) REVERT: I 81 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.7466 (tpp80) REVERT: J 16 ASP cc_start: 0.9002 (p0) cc_final: 0.8798 (p0) REVERT: J 26 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8110 (pp30) REVERT: K 16 GLU cc_start: 0.7989 (tt0) cc_final: 0.7314 (tp30) REVERT: K 22 ASP cc_start: 0.8892 (t0) cc_final: 0.8639 (p0) REVERT: K 36 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7710 (mm-30) REVERT: K 64 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8137 (mt-10) REVERT: K 106 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8579 (mt-10) REVERT: L 53 HIS cc_start: 0.7452 (t70) cc_final: 0.6830 (t70) REVERT: L 63 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7827 (ttp-170) outliers start: 51 outliers final: 36 residues processed: 414 average time/residue: 0.2076 time to fit residues: 139.5350 Evaluate side-chains 399 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 360 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 375 optimal weight: 0.0010 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 305 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 365 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 280 optimal weight: 20.0000 chunk 342 optimal weight: 8.9990 chunk 341 optimal weight: 6.9990 overall best weight: 3.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.076920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052756 restraints weight = 115469.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054319 restraints weight = 61600.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055321 restraints weight = 41404.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.055956 restraints weight = 32275.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056357 restraints weight = 27796.312| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33706 Z= 0.210 Angle : 0.637 17.532 45901 Z= 0.323 Chirality : 0.044 0.253 5156 Planarity : 0.004 0.051 5608 Dihedral : 16.441 175.959 5260 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 1.55 % Allowed : 12.05 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3839 helix: 1.62 (0.14), residues: 1346 sheet: -0.16 (0.21), residues: 638 loop : -0.46 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 73 TYR 0.012 0.001 TYR H 102 PHE 0.023 0.001 PHE D 33 TRP 0.012 0.001 TRP B 31 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (33674) covalent geometry : angle 0.61179 / 0.32 (45856) hydrogen bonds : bond 0.03615 / 2.40 ( 1429) hydrogen bonds : angle 4.69020 / 3.38 ( 3905) metal coordination : bond 0.01146 / 0.67 ( 32) metal coordination : angle 5.75479 / 3.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8581 (mtt) cc_final: 0.8169 (mtt) REVERT: A 146 MET cc_start: 0.8227 (mmm) cc_final: 0.7930 (mmm) REVERT: A 437 MET cc_start: 0.8236 (mmm) cc_final: 0.8001 (mmt) REVERT: A 456 MET cc_start: 0.9138 (mtm) cc_final: 0.8765 (mtp) REVERT: A 470 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9036 (pp) REVERT: A 846 GLU cc_start: 0.8193 (pt0) cc_final: 0.7724 (pt0) REVERT: A 849 MET cc_start: 0.9280 (ttp) cc_final: 0.9062 (ttt) REVERT: A 873 MET cc_start: 0.9203 (mmt) cc_final: 0.8464 (mmp) REVERT: A 934 LYS cc_start: 0.9637 (tttm) cc_final: 0.9342 (tptt) REVERT: A 1062 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 1063 MET cc_start: 0.9222 (mmm) cc_final: 0.8905 (mmm) REVERT: A 1079 MET cc_start: 0.8114 (tmm) cc_final: 0.7756 (tmm) REVERT: A 1285 MET cc_start: 0.9050 (mmm) cc_final: 0.8697 (mmm) REVERT: A 1315 GLU cc_start: 0.8778 (tt0) cc_final: 0.8373 (tp30) REVERT: A 1368 MET cc_start: 0.8649 (mtm) cc_final: 0.8210 (mtp) REVERT: A 1398 MET cc_start: 0.9095 (ttp) cc_final: 0.8566 (ttp) REVERT: A 1444 MET cc_start: 0.8923 (mmm) cc_final: 0.8197 (mmt) REVERT: B 101 MET cc_start: 0.8733 (tpp) cc_final: 0.8448 (tpp) REVERT: B 173 MET cc_start: 0.8900 (ttp) cc_final: 0.8698 (ttp) REVERT: B 312 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: B 775 LYS cc_start: 0.9416 (mtmt) cc_final: 0.9156 (mtmm) REVERT: B 1072 MET cc_start: 0.8306 (mtp) cc_final: 0.7961 (mtp) REVERT: B 1152 MET cc_start: 0.9083 (mmm) cc_final: 0.8655 (mmm) REVERT: B 1202 LEU cc_start: 0.9502 (tp) cc_final: 0.8523 (tp) REVERT: B 1206 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8714 (mp0) REVERT: C 29 MET cc_start: 0.8912 (tmm) cc_final: 0.8169 (tmm) REVERT: C 75 MET cc_start: 0.8859 (mmm) cc_final: 0.8627 (mmm) REVERT: D 67 ARG cc_start: 0.6516 (tpp80) cc_final: 0.6296 (tpp80) REVERT: D 70 PHE cc_start: 0.8337 (m-10) cc_final: 0.8013 (m-80) REVERT: D 151 PHE cc_start: 0.8135 (t80) cc_final: 0.7794 (t80) REVERT: E 8 ASN cc_start: 0.9250 (m110) cc_final: 0.8929 (m110) REVERT: F 81 THR cc_start: 0.9520 (m) cc_final: 0.9115 (p) REVERT: F 88 TYR cc_start: 0.9029 (m-80) cc_final: 0.8734 (m-80) REVERT: F 124 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8139 (tt0) REVERT: G 18 PHE cc_start: 0.9186 (m-10) cc_final: 0.8971 (m-10) REVERT: G 21 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.8235 (ttm110) REVERT: G 24 GLN cc_start: 0.8875 (mp10) cc_final: 0.8652 (mp10) REVERT: G 58 ARG cc_start: 0.9001 (mmt90) cc_final: 0.8668 (mmm-85) REVERT: G 79 PHE cc_start: 0.7616 (t80) cc_final: 0.7275 (t80) REVERT: G 99 PHE cc_start: 0.6504 (p90) cc_final: 0.6166 (p90) REVERT: G 115 MET cc_start: 0.6652 (mtp) cc_final: 0.6192 (ttm) REVERT: H 52 GLN cc_start: 0.9242 (mp10) cc_final: 0.8796 (mp10) REVERT: H 123 MET cc_start: 0.8945 (ttt) cc_final: 0.8624 (ttp) REVERT: H 126 GLU cc_start: 0.8820 (tt0) cc_final: 0.8473 (tt0) REVERT: H 130 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8473 (mtm-85) REVERT: I 81 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8048 (tpp-160) REVERT: K 36 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7611 (mm-30) REVERT: K 64 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8110 (mt-10) REVERT: K 106 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8522 (mt-10) REVERT: L 53 HIS cc_start: 0.7572 (t70) cc_final: 0.6979 (t70) REVERT: L 63 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7858 (ttp-170) outliers start: 53 outliers final: 39 residues processed: 402 average time/residue: 0.1996 time to fit residues: 131.7434 Evaluate side-chains 383 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 204 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN A1048 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051918 restraints weight = 116558.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053491 restraints weight = 61243.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054535 restraints weight = 40907.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055180 restraints weight = 31815.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.055565 restraints weight = 27365.618| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33706 Z= 0.240 Angle : 0.671 16.952 45901 Z= 0.339 Chirality : 0.044 0.219 5156 Planarity : 0.004 0.048 5608 Dihedral : 16.499 176.598 5260 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 1.49 % Allowed : 12.35 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3839 helix: 1.54 (0.14), residues: 1346 sheet: -0.21 (0.20), residues: 640 loop : -0.48 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.020 0.001 TYR G 51 PHE 0.020 0.001 PHE A 219 TRP 0.012 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (33674) covalent geometry : angle 0.64742 / 0.34 (45856) hydrogen bonds : bond 0.03724 / 2.46 ( 1429) hydrogen bonds : angle 4.73824 / 3.41 ( 3905) metal coordination : bond 0.01036 / 0.65 ( 32) metal coordination : angle 5.68747 / 3.90 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 361 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8518 (mtt) cc_final: 0.8083 (mtt) REVERT: A 146 MET cc_start: 0.8268 (mmm) cc_final: 0.7961 (mmm) REVERT: A 304 MET cc_start: 0.9326 (mmm) cc_final: 0.9123 (mmt) REVERT: A 437 MET cc_start: 0.8315 (mmm) cc_final: 0.8063 (mmt) REVERT: A 456 MET cc_start: 0.9134 (mtm) cc_final: 0.8915 (mtp) REVERT: A 470 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9024 (pp) REVERT: A 849 MET cc_start: 0.9263 (ttp) cc_final: 0.9017 (ttt) REVERT: A 873 MET cc_start: 0.9302 (mmt) cc_final: 0.8559 (mmp) REVERT: A 934 LYS cc_start: 0.9680 (tttm) cc_final: 0.9377 (tptt) REVERT: A 1063 MET cc_start: 0.9267 (mmm) cc_final: 0.8901 (mmm) REVERT: A 1079 MET cc_start: 0.8243 (tmm) cc_final: 0.7819 (tmm) REVERT: A 1285 MET cc_start: 0.9085 (mmm) cc_final: 0.8740 (mmm) REVERT: A 1315 GLU cc_start: 0.8850 (tt0) cc_final: 0.8391 (tp30) REVERT: A 1368 MET cc_start: 0.8708 (mtm) cc_final: 0.8277 (mtp) REVERT: A 1444 MET cc_start: 0.8869 (mmm) cc_final: 0.8165 (mmt) REVERT: A 1454 MET cc_start: 0.7330 (mpp) cc_final: 0.7114 (mpp) REVERT: B 101 MET cc_start: 0.8816 (tpp) cc_final: 0.8554 (mmm) REVERT: B 312 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: B 775 LYS cc_start: 0.9474 (mtmt) cc_final: 0.9209 (mtmm) REVERT: B 1111 MET cc_start: 0.8807 (mmm) cc_final: 0.8418 (mmm) REVERT: B 1152 MET cc_start: 0.9077 (mmm) cc_final: 0.8633 (mmm) REVERT: B 1202 LEU cc_start: 0.9537 (tp) cc_final: 0.8850 (tp) REVERT: B 1206 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 29 MET cc_start: 0.9019 (tmm) cc_final: 0.8141 (tmm) REVERT: C 75 MET cc_start: 0.8899 (mmm) cc_final: 0.8636 (mmm) REVERT: C 190 ASP cc_start: 0.8637 (t0) cc_final: 0.8421 (t0) REVERT: D 70 PHE cc_start: 0.8347 (m-10) cc_final: 0.8028 (m-80) REVERT: D 151 PHE cc_start: 0.7870 (t80) cc_final: 0.7517 (t80) REVERT: E 8 ASN cc_start: 0.9270 (m110) cc_final: 0.8933 (m110) REVERT: F 81 THR cc_start: 0.9520 (m) cc_final: 0.9093 (p) REVERT: F 122 MET cc_start: 0.9461 (mtp) cc_final: 0.9115 (mtm) REVERT: F 124 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8247 (tt0) REVERT: G 21 ARG cc_start: 0.8507 (mtp-110) cc_final: 0.8262 (ttm110) REVERT: G 24 GLN cc_start: 0.8871 (mp10) cc_final: 0.8637 (mp10) REVERT: G 58 ARG cc_start: 0.8985 (mmt90) cc_final: 0.8624 (mmm-85) REVERT: G 79 PHE cc_start: 0.7579 (t80) cc_final: 0.7235 (t80) REVERT: G 99 PHE cc_start: 0.6723 (p90) cc_final: 0.6429 (p90) REVERT: G 115 MET cc_start: 0.6767 (mtp) cc_final: 0.6401 (ttm) REVERT: H 123 MET cc_start: 0.8987 (ttt) cc_final: 0.8664 (ttm) REVERT: H 126 GLU cc_start: 0.8862 (tt0) cc_final: 0.8452 (tt0) REVERT: H 130 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8535 (mtm-85) REVERT: I 30 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7970 (mtt-85) REVERT: I 70 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7490 (mmm-85) REVERT: I 81 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8050 (tpp-160) REVERT: K 64 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8149 (mt-10) REVERT: K 106 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8542 (mt-10) outliers start: 51 outliers final: 38 residues processed: 396 average time/residue: 0.2146 time to fit residues: 136.1693 Evaluate side-chains 392 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 352 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 3 optimal weight: 5.9990 chunk 325 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 285 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053167 restraints weight = 112645.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054774 restraints weight = 58326.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.055834 restraints weight = 38699.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056504 restraints weight = 29943.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056852 restraints weight = 25676.929| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33706 Z= 0.143 Angle : 0.624 16.238 45901 Z= 0.317 Chirality : 0.043 0.219 5156 Planarity : 0.004 0.056 5608 Dihedral : 16.482 176.078 5260 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.94 % Rotamer: Outliers : 1.17 % Allowed : 12.90 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3839 helix: 1.60 (0.15), residues: 1345 sheet: -0.19 (0.21), residues: 640 loop : -0.45 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 63 TYR 0.020 0.001 TYR B1092 PHE 0.022 0.001 PHE A 219 TRP 0.010 0.001 TRP B 561 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (33674) covalent geometry : angle 0.60324 / 0.32 (45856) hydrogen bonds : bond 0.03463 / 2.30 ( 1429) hydrogen bonds : angle 4.58774 / 3.30 ( 3905) metal coordination : bond 0.00689 / 0.43 ( 32) metal coordination : angle 5.15292 / 3.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 375 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8575 (mtt) cc_final: 0.8165 (mtt) REVERT: A 146 MET cc_start: 0.8191 (mmm) cc_final: 0.7912 (mmm) REVERT: A 456 MET cc_start: 0.9143 (mtm) cc_final: 0.8607 (mtp) REVERT: A 470 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9145 (pp) REVERT: A 849 MET cc_start: 0.9301 (ttp) cc_final: 0.8928 (ttt) REVERT: A 873 MET cc_start: 0.9177 (mmt) cc_final: 0.8417 (mmp) REVERT: A 934 LYS cc_start: 0.9642 (tttm) cc_final: 0.9340 (tptt) REVERT: A 1062 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 1063 MET cc_start: 0.9297 (mmm) cc_final: 0.8817 (mmm) REVERT: A 1079 MET cc_start: 0.8159 (tmm) cc_final: 0.7741 (tmm) REVERT: A 1285 MET cc_start: 0.9016 (mmm) cc_final: 0.8693 (mmm) REVERT: A 1315 GLU cc_start: 0.8733 (tt0) cc_final: 0.8278 (tp30) REVERT: A 1368 MET cc_start: 0.8612 (mtm) cc_final: 0.8171 (mtp) REVERT: A 1444 MET cc_start: 0.8833 (mmm) cc_final: 0.8175 (mmt) REVERT: A 1454 MET cc_start: 0.7196 (mpp) cc_final: 0.6952 (mpp) REVERT: B 312 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: B 775 LYS cc_start: 0.9391 (mtmt) cc_final: 0.9135 (mtmm) REVERT: B 1111 MET cc_start: 0.8775 (mmm) cc_final: 0.8421 (mmm) REVERT: B 1152 MET cc_start: 0.9037 (mmm) cc_final: 0.8626 (mmm) REVERT: B 1202 LEU cc_start: 0.9491 (tp) cc_final: 0.8482 (tp) REVERT: B 1206 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8613 (mp0) REVERT: C 29 MET cc_start: 0.8953 (tmm) cc_final: 0.8087 (tmm) REVERT: C 75 MET cc_start: 0.8833 (mmm) cc_final: 0.8610 (mmm) REVERT: D 31 GLN cc_start: 0.6105 (mm-40) cc_final: 0.5795 (tt0) REVERT: D 67 ARG cc_start: 0.6576 (tpp80) cc_final: 0.6328 (tpp80) REVERT: D 70 PHE cc_start: 0.8379 (m-10) cc_final: 0.8025 (m-80) REVERT: D 166 LEU cc_start: 0.8967 (tp) cc_final: 0.8738 (pp) REVERT: E 8 ASN cc_start: 0.9239 (m110) cc_final: 0.8924 (m110) REVERT: F 81 THR cc_start: 0.9503 (m) cc_final: 0.9114 (p) REVERT: F 88 TYR cc_start: 0.8944 (m-80) cc_final: 0.8662 (m-80) REVERT: F 124 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8152 (tt0) REVERT: G 21 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.8214 (ttm110) REVERT: G 24 GLN cc_start: 0.8868 (mp10) cc_final: 0.8608 (mp10) REVERT: G 33 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8415 (tp30) REVERT: G 79 PHE cc_start: 0.7568 (t80) cc_final: 0.7208 (t80) REVERT: G 99 PHE cc_start: 0.6626 (p90) cc_final: 0.6287 (p90) REVERT: G 115 MET cc_start: 0.6770 (mtp) cc_final: 0.6384 (ttm) REVERT: H 123 MET cc_start: 0.8884 (ttt) cc_final: 0.8591 (ttm) REVERT: H 126 GLU cc_start: 0.8746 (tt0) cc_final: 0.8367 (tt0) REVERT: I 30 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7938 (mtt-85) REVERT: I 70 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7543 (mmm-85) REVERT: I 91 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7891 (tpp80) REVERT: K 64 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8079 (mt-10) REVERT: K 106 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8458 (mt-10) outliers start: 40 outliers final: 32 residues processed: 404 average time/residue: 0.2151 time to fit residues: 139.3010 Evaluate side-chains 389 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 355 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 4 optimal weight: 0.3980 chunk 236 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 370 optimal weight: 0.5980 chunk 367 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 381 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 312 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS C 188 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN H 33 GLN H 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.078125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.053703 restraints weight = 115786.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055339 restraints weight = 59879.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056392 restraints weight = 39673.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057067 restraints weight = 30762.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057472 restraints weight = 26389.206| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33706 Z= 0.121 Angle : 0.626 16.415 45901 Z= 0.316 Chirality : 0.043 0.220 5156 Planarity : 0.004 0.049 5608 Dihedral : 16.431 176.370 5260 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 0.99 % Allowed : 13.31 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3839 helix: 1.61 (0.15), residues: 1342 sheet: -0.20 (0.21), residues: 648 loop : -0.45 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 63 TYR 0.020 0.001 TYR B1092 PHE 0.023 0.001 PHE A 219 TRP 0.011 0.001 TRP B 31 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (33674) covalent geometry : angle 0.60843 / 0.32 (45856) hydrogen bonds : bond 0.03349 / 2.23 ( 1429) hydrogen bonds : angle 4.50174 / 3.24 ( 3905) metal coordination : bond 0.00568 / 0.34 ( 32) metal coordination : angle 4.80881 / 3.45 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 376 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8573 (mtt) cc_final: 0.8130 (mtt) REVERT: A 146 MET cc_start: 0.8228 (mmm) cc_final: 0.7937 (mmm) REVERT: A 456 MET cc_start: 0.9070 (mtm) cc_final: 0.8527 (mtp) REVERT: A 470 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8964 (pp) REVERT: A 849 MET cc_start: 0.9289 (ttp) cc_final: 0.8919 (ttt) REVERT: A 873 MET cc_start: 0.9191 (mmt) cc_final: 0.8426 (mmp) REVERT: A 934 LYS cc_start: 0.9619 (tttm) cc_final: 0.9312 (tptt) REVERT: A 1062 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7973 (mm-30) REVERT: A 1063 MET cc_start: 0.9313 (mmm) cc_final: 0.8840 (mmm) REVERT: A 1079 MET cc_start: 0.8181 (tmm) cc_final: 0.7729 (tmm) REVERT: A 1285 MET cc_start: 0.9113 (mmm) cc_final: 0.8756 (mmm) REVERT: A 1315 GLU cc_start: 0.8776 (tt0) cc_final: 0.8296 (tp30) REVERT: A 1368 MET cc_start: 0.8652 (mtm) cc_final: 0.8175 (mtp) REVERT: A 1444 MET cc_start: 0.8757 (mmm) cc_final: 0.8062 (mmt) REVERT: A 1454 MET cc_start: 0.7383 (mpp) cc_final: 0.7134 (mpp) REVERT: B 312 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: B 775 LYS cc_start: 0.9375 (mtmt) cc_final: 0.9024 (mtmm) REVERT: B 1111 MET cc_start: 0.8800 (mmm) cc_final: 0.8445 (mmm) REVERT: B 1152 MET cc_start: 0.9052 (mmm) cc_final: 0.8651 (mmm) REVERT: B 1202 LEU cc_start: 0.9501 (tp) cc_final: 0.8544 (tp) REVERT: B 1206 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8653 (mp0) REVERT: C 29 MET cc_start: 0.8990 (tmm) cc_final: 0.8083 (tmm) REVERT: C 75 MET cc_start: 0.8900 (mmm) cc_final: 0.8653 (mmm) REVERT: D 31 GLN cc_start: 0.6134 (mm-40) cc_final: 0.5795 (tt0) REVERT: D 50 LEU cc_start: 0.8765 (tp) cc_final: 0.8198 (tp) REVERT: D 67 ARG cc_start: 0.6583 (tpp80) cc_final: 0.6367 (tpp80) REVERT: D 70 PHE cc_start: 0.8345 (m-10) cc_final: 0.8012 (m-80) REVERT: D 146 GLN cc_start: 0.7900 (tp40) cc_final: 0.7459 (mm-40) REVERT: D 166 LEU cc_start: 0.8971 (tp) cc_final: 0.8702 (pp) REVERT: E 8 ASN cc_start: 0.9270 (m110) cc_final: 0.8940 (m110) REVERT: E 121 MET cc_start: 0.9241 (mmm) cc_final: 0.8943 (mmt) REVERT: F 81 THR cc_start: 0.9532 (m) cc_final: 0.9197 (p) REVERT: F 88 TYR cc_start: 0.8913 (m-80) cc_final: 0.7829 (m-80) REVERT: G 18 PHE cc_start: 0.9321 (m-10) cc_final: 0.8890 (m-10) REVERT: G 21 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.8249 (ttm110) REVERT: G 24 GLN cc_start: 0.8873 (mp10) cc_final: 0.8610 (mp10) REVERT: G 33 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8386 (tp30) REVERT: G 79 PHE cc_start: 0.7477 (t80) cc_final: 0.7074 (t80) REVERT: G 99 PHE cc_start: 0.6608 (p90) cc_final: 0.6320 (p90) REVERT: G 115 MET cc_start: 0.6582 (mtp) cc_final: 0.6266 (ttm) REVERT: H 123 MET cc_start: 0.8944 (ttt) cc_final: 0.8517 (ttm) REVERT: H 126 GLU cc_start: 0.8810 (tt0) cc_final: 0.8448 (tt0) REVERT: I 5 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6809 (mmm-85) REVERT: I 30 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.7957 (mtt-85) REVERT: I 70 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: K 64 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8132 (mt-10) REVERT: K 106 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8444 (mt-10) outliers start: 34 outliers final: 29 residues processed: 403 average time/residue: 0.2237 time to fit residues: 144.5473 Evaluate side-chains 392 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 198 optimal weight: 0.4980 chunk 213 optimal weight: 5.9990 chunk 385 optimal weight: 50.0000 chunk 208 optimal weight: 0.5980 chunk 230 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053347 restraints weight = 114936.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.054938 restraints weight = 59298.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.056006 restraints weight = 39288.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056676 restraints weight = 30444.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057013 restraints weight = 26112.748| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33706 Z= 0.117 Angle : 0.621 15.213 45901 Z= 0.312 Chirality : 0.043 0.220 5156 Planarity : 0.004 0.058 5608 Dihedral : 16.377 177.450 5260 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 0.90 % Allowed : 13.81 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3839 helix: 1.62 (0.15), residues: 1349 sheet: -0.13 (0.21), residues: 639 loop : -0.42 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 63 TYR 0.026 0.001 TYR B 830 PHE 0.023 0.001 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (33674) covalent geometry : angle 0.60502 / 0.31 (45856) hydrogen bonds : bond 0.03291 / 2.19 ( 1429) hydrogen bonds : angle 4.44329 / 3.20 ( 3905) metal coordination : bond 0.00522 / 0.32 ( 32) metal coordination : angle 4.44417 / 3.21 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5760.71 seconds wall clock time: 100 minutes 35.75 seconds (6035.75 seconds total)