Starting phenix.real_space_refine on Sun Aug 9 09:41:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbo_54733/08_2026/9sbo_54733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbo_54733/08_2026/9sbo_54733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sbo_54733/08_2026/9sbo_54733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbo_54733/08_2026/9sbo_54733.map" model { file = "/net/cci-nas-00/data/ceres_data/9sbo_54733/08_2026/9sbo_54733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbo_54733/08_2026/9sbo_54733.cif" } resolution = 3.97 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= 0.023 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 7 residue(s): 0.03s 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: 9 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 16 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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 67 108.115 68.933 95.094 1.00243.45 S ATOM 479 SG CYS A 70 107.701 65.785 93.005 1.00250.57 S ATOM 532 SG CYS A 77 104.897 68.405 93.156 1.00219.96 S ATOM 762 SG CYS A 107 82.841 74.640 135.296 1.00255.30 S ATOM 786 SG CYS A 110 84.387 71.563 136.657 1.00249.81 S ATOM 1091 SG CYS A 148 80.820 72.456 137.687 1.00301.65 S ATOM 1105 SG CYS A 167 83.722 74.639 138.934 1.00276.50 S ATOM 19520 SG CYS B1163 99.818 56.684 104.858 1.00229.11 S ATOM 19538 SG CYS B1166 98.228 60.059 105.169 1.00239.04 S ATOM 19663 SG CYS B1182 102.039 59.718 104.772 1.00251.80 S ATOM 19682 SG CYS B1185 100.311 58.738 108.057 1.00245.97 S ATOM 20670 SG CYS C 86 94.413 74.463 26.613 1.00297.95 S ATOM 20687 SG CYS C 88 96.336 76.687 28.802 1.00291.45 S ATOM 20720 SG CYS C 92 95.596 77.928 25.390 1.00259.56 S ATOM 20743 SG CYS C 95 92.790 77.729 27.999 1.00253.36 S ATOM 28328 SG CYS I 7 38.414 126.449 126.818 1.00407.39 S ATOM 28353 SG CYS I 10 42.159 125.889 126.328 1.00405.64 S ATOM 28519 SG CYS I 29 40.274 123.301 128.336 1.00418.22 S ATOM 28543 SG CYS I 32 40.502 126.835 129.708 1.00421.59 S ATOM 28870 SG CYS I 75 17.051 119.327 86.535 1.00456.72 S ATOM 28892 SG CYS I 78 17.434 122.762 85.464 1.00452.84 S ATOM 29108 SG CYS I 103 20.579 120.578 85.384 1.00440.74 S ATOM 29128 SG CYS I 106 19.119 121.631 88.724 1.00437.23 S ATOM 29230 SG CYS J 7 65.133 90.025 37.689 1.00193.13 S ATOM 29253 SG CYS J 10 64.248 87.786 34.228 1.00203.63 S ATOM 29533 SG CYS J 45 61.716 89.079 36.688 1.00202.10 S ATOM 29539 SG CYS J 46 63.758 91.381 34.478 1.00217.22 S ATOM 30662 SG CYS L 31 98.136 113.985 55.061 1.00351.25 S ATOM 30682 SG CYS L 34 99.079 115.704 51.804 1.00349.75 S ATOM 30786 SG CYS L 48 101.697 114.746 54.415 1.00347.54 S ATOM 30809 SG CYS L 51 99.355 117.663 55.076 1.00349.29 S Time building chain proxies: 5.66, per 1000 atoms: 0.17 Number of scatterers: 32901 At special positions: 0 Unit cell: (153.417, 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 70 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " 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 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " 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 J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 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: 140 helices and 50 sheets defined 39.0% alpha, 19.2% beta 42 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 3.79 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 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.577A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.657A 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: 3.592A 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: 3.716A 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 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.770A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.630A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 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 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.506A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.811A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.107A 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: 3.630A 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: 3.623A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.711A 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 1056 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 1146 removed outlier: 4.126A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1173 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.739A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.727A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1357 removed outlier: 7.853A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.950A 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: 3.512A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.946A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.653A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.576A 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: 3.547A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.500A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) 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: 3.638A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.772A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.518A 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 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.729A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.903A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 3.770A pdb=" N TYR B 785 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.586A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.339A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.879A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.788A 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 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.597A 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 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.658A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.515A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.722A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.751A pdb=" N ALA D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) 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 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.645A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.542A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) 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 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.506A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.061A 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 40 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.981A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.557A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.536A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU K 51 " --> pdb=" O ARG K 47 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (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 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 9.977A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.786A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.721A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.782A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.795A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.341A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.125A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.518A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB6, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.523A pdb=" N LEU A1306 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.114A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 6 removed outlier: 5.432A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.381A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 46 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.723A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS B 99 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N SER B 125 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 111 removed outlier: 4.723A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS B 99 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N SER B 125 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) 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: 6.079A 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: 4.215A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 272 " --> pdb=" O GLN B 255 " (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 585 through 590 removed outlier: 6.998A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 Processing sheet with id=AC9, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.615A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.615A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 825 removed outlier: 8.701A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.546A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.522A pdb=" N PHE B1001 " --> pdb=" O TYR B1073 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.975A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.789A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE5, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.998A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.403A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.717A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 151 through 152 removed outlier: 4.739A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 143 " --> pdb=" O GLY G 89 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.614A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.554A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 83 through 86 removed outlier: 3.568A pdb=" N PHE I 100 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.504A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE K 71 " --> pdb=" O PHE K 35 " (cutoff:3.500A) 1355 hydrogen bonds defined for protein. 3705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 9.68 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10439 1.34 - 1.46: 5342 1.46 - 1.58: 17413 1.58 - 1.70: 187 1.70 - 1.82: 292 Bond restraints: 33673 Sorted by residual: bond pdb=" O5' ATP A1801 " pdb=" PA ATP A1801 " ideal model delta sigma weight residual 1.579 1.509 0.070 1.10e-02 8.26e+03 4.02e+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 32 " pdb=" N1 DC T 32 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.97e+01 bond pdb=" C1' DT T 25 " pdb=" N1 DT T 25 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" C1' DT T 30 " pdb=" N1 DT T 30 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 ... (remaining 33668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 45625 3.21 - 6.43: 186 6.43 - 9.64: 38 9.64 - 12.86: 2 12.86 - 16.07: 2 Bond angle restraints: 45853 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 123.80 16.07 1.00e+00 1.00e+00 2.58e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 123.78 13.05 1.00e+00 1.00e+00 1.70e+02 angle pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " ideal model delta sigma weight residual 101.57 109.67 -8.10 1.54e+00 4.24e-01 2.78e+01 angle pdb=" O4' DC T 53 " pdb=" C4' DC T 53 " pdb=" C3' DC T 53 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O4' DG T 51 " pdb=" C4' DG T 51 " pdb=" C3' DG T 51 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 ... (remaining 45848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 19749 33.78 - 67.57: 556 67.57 - 101.35: 36 101.35 - 135.13: 5 135.13 - 168.91: 1 Dihedral angle restraints: 20347 sinusoidal: 9046 harmonic: 11301 Sorted by residual: dihedral pdb=" CA MET A 708 " pdb=" C MET A 708 " pdb=" N THR A 709 " pdb=" CA THR A 709 " ideal model delta harmonic sigma weight residual 180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 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 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA THR A 709 " pdb=" C THR A 709 " pdb=" N LEU A 710 " pdb=" CA LEU A 710 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 20344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3956 0.045 - 0.090: 846 0.090 - 0.134: 343 0.134 - 0.179: 9 0.179 - 0.224: 2 Chirality restraints: 5156 Sorted by residual: 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 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE A1152 " pdb=" CA ILE A1152 " pdb=" CG1 ILE A1152 " pdb=" CG2 ILE A1152 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 5153 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 635 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO B 636 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 636 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 636 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 550 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO B 551 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1434 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1435 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1435 " 0.024 5.00e-02 4.00e+02 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 601 2.66 - 3.22: 30875 3.22 - 3.78: 52083 3.78 - 4.34: 70906 4.34 - 4.90: 113580 Nonbonded interactions: 268045 Sorted by model distance: nonbonded pdb=" O HIS A 286 " pdb=" ND1 HIS A 287 " model vdw 2.096 3.120 nonbonded pdb=" O PHE B 322 " pdb=" NE2 GLN B 325 " model vdw 2.154 3.120 nonbonded pdb=" O HIS A 706 " pdb=" NH2 ARG A1281 " model vdw 2.176 3.120 nonbonded pdb=" O VAL A 216 " pdb=" OG1 THR A 220 " model vdw 2.184 3.040 nonbonded pdb=" O LEU D 148 " pdb=" OG SER D 152 " model vdw 2.198 3.040 ... (remaining 268040 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.610 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.003 0.119 33705 Z= 0.254 Angle : 0.618 17.896 45898 Z= 0.406 Chirality : 0.042 0.224 5156 Planarity : 0.003 0.052 5607 Dihedral : 14.687 168.913 13027 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.91 (0.14), residues: 3837 helix: 2.01 (0.15), residues: 1295 sheet: 0.11 (0.21), residues: 637 loop : -0.15 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 30 TYR 0.015 0.001 TYR B 351 PHE 0.015 0.001 PHE A 646 TRP 0.019 0.001 TRP C 170 HIS 0.009 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.25 (33673) covalent geometry : angle 0.60374 / 0.41 (45853) hydrogen bonds : bond 0.18966 / 12.68 ( 1421) hydrogen bonds : angle 7.04738 / 4.93 ( 3925) metal coordination : bond 0.00744 / 0.52 ( 32) metal coordination : angle 4.19382 / 3.09 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 1.273 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: 0.8434 (mtt) cc_final: 0.8131 (mmm) REVERT: A 103 CYS cc_start: 0.9606 (m) cc_final: 0.9285 (m) REVERT: A 105 CYS cc_start: 0.9657 (m) cc_final: 0.9223 (m) REVERT: A 133 LYS cc_start: 0.9729 (mttm) cc_final: 0.9449 (mtmm) REVERT: A 205 GLU cc_start: 0.9443 (tt0) cc_final: 0.9178 (tm-30) REVERT: A 229 SER cc_start: 0.9372 (t) cc_final: 0.8988 (p) REVERT: A 250 ILE cc_start: 0.8663 (mm) cc_final: 0.8362 (tt) REVERT: A 345 VAL cc_start: 0.9517 (m) cc_final: 0.9195 (p) REVERT: A 449 SER cc_start: 0.9069 (m) cc_final: 0.8668 (p) REVERT: A 487 MET cc_start: 0.9093 (mtp) cc_final: 0.8807 (mtt) REVERT: A 511 ILE cc_start: 0.9222 (mt) cc_final: 0.8818 (mm) REVERT: A 521 MET cc_start: 0.9351 (mtt) cc_final: 0.8876 (mtm) REVERT: A 542 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8142 (pt0) REVERT: A 605 MET cc_start: 0.9368 (tpt) cc_final: 0.8904 (tpp) REVERT: A 826 ASP cc_start: 0.9357 (t70) cc_final: 0.9056 (t0) REVERT: A 873 MET cc_start: 0.8521 (mmt) cc_final: 0.7801 (mmt) REVERT: A 939 ASP cc_start: 0.9458 (m-30) cc_final: 0.8992 (m-30) REVERT: A 997 LEU cc_start: 0.9040 (mt) cc_final: 0.8818 (mt) REVERT: A 1062 GLU cc_start: 0.9428 (tt0) cc_final: 0.9197 (mt-10) REVERT: A 1063 MET cc_start: 0.8975 (mmm) cc_final: 0.8656 (mmm) REVERT: A 1205 LYS cc_start: 0.9483 (mtpp) cc_final: 0.9248 (mttt) REVERT: A 1259 MET cc_start: 0.8946 (mmm) cc_final: 0.8378 (tmm) REVERT: A 1269 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8634 (mt-10) REVERT: A 1280 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8652 (mp0) REVERT: A 1315 GLU cc_start: 0.9260 (tt0) cc_final: 0.8875 (tp30) REVERT: A 1333 ILE cc_start: 0.9084 (mt) cc_final: 0.8799 (mm) REVERT: A 1417 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 115 GLN cc_start: 0.9010 (tp40) cc_final: 0.8709 (tp-100) REVERT: B 360 PHE cc_start: 0.9049 (t80) cc_final: 0.8684 (t80) REVERT: B 427 ASP cc_start: 0.8955 (m-30) cc_final: 0.8704 (m-30) REVERT: B 498 THR cc_start: 0.9530 (m) cc_final: 0.9271 (t) REVERT: B 542 MET cc_start: 0.8718 (mtm) cc_final: 0.7845 (mmm) REVERT: B 608 ASP cc_start: 0.9230 (m-30) cc_final: 0.8994 (p0) REVERT: B 615 MET cc_start: 0.9190 (mtm) cc_final: 0.8363 (mtm) REVERT: B 616 ILE cc_start: 0.9118 (tt) cc_final: 0.8803 (pt) REVERT: B 629 ASP cc_start: 0.9322 (t0) cc_final: 0.8911 (p0) REVERT: B 778 MET cc_start: 0.9333 (ttm) cc_final: 0.9122 (ttm) REVERT: B 792 MET cc_start: 0.9224 (mtm) cc_final: 0.8998 (mtt) REVERT: B 894 ASP cc_start: 0.6380 (m-30) cc_final: 0.6075 (p0) REVERT: B 999 MET cc_start: 0.9584 (mmt) cc_final: 0.9261 (mmm) REVERT: B 1082 MET cc_start: 0.8470 (tpp) cc_final: 0.8102 (tpp) REVERT: B 1090 THR cc_start: 0.7808 (m) cc_final: 0.7407 (p) REVERT: B 1111 MET cc_start: 0.9169 (mmm) cc_final: 0.8934 (mmm) REVERT: B 1133 MET cc_start: 0.8205 (mtp) cc_final: 0.7446 (mtt) REVERT: B 1134 GLU cc_start: 0.9115 (mp0) cc_final: 0.8896 (mp0) REVERT: B 1137 CYS cc_start: 0.9336 (m) cc_final: 0.9096 (m) REVERT: C 26 ASP cc_start: 0.8388 (p0) cc_final: 0.8061 (p0) REVERT: C 37 MET cc_start: 0.9245 (mtm) cc_final: 0.8898 (mtm) REVERT: C 75 MET cc_start: 0.9045 (mmm) cc_final: 0.8379 (tpp) REVERT: C 125 MET cc_start: 0.9387 (mtp) cc_final: 0.8995 (mpp) REVERT: C 230 MET cc_start: 0.9011 (mtt) cc_final: 0.8778 (mpp) REVERT: D 1 MET cc_start: 0.4187 (ptm) cc_final: 0.3422 (mmt) REVERT: D 50 LEU cc_start: 0.7182 (mt) cc_final: 0.6534 (mt) REVERT: D 54 GLU cc_start: 0.9080 (tt0) cc_final: 0.8650 (tp30) REVERT: D 57 LEU cc_start: 0.8811 (mt) cc_final: 0.8343 (pp) REVERT: D 58 VAL cc_start: 0.8547 (t) cc_final: 0.8156 (p) REVERT: D 167 LEU cc_start: 0.7842 (mt) cc_final: 0.7442 (pp) REVERT: E 32 GLN cc_start: 0.9325 (tt0) cc_final: 0.9043 (tp-100) REVERT: E 57 MET cc_start: 0.8669 (mtm) cc_final: 0.8242 (ptp) REVERT: E 58 MET cc_start: 0.9124 (mtp) cc_final: 0.8818 (mtm) REVERT: E 61 GLN cc_start: 0.9162 (tt0) cc_final: 0.8794 (tm-30) REVERT: E 112 TYR cc_start: 0.9288 (p90) cc_final: 0.8767 (p90) REVERT: E 136 ASN cc_start: 0.9551 (t0) cc_final: 0.9297 (t0) REVERT: E 174 GLN cc_start: 0.8752 (mt0) cc_final: 0.8302 (mp10) REVERT: E 192 ARG cc_start: 0.9368 (ttt180) cc_final: 0.9088 (ttp80) REVERT: E 201 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8732 (ttmm) REVERT: E 214 CYS cc_start: 0.9518 (t) cc_final: 0.9250 (t) REVERT: E 215 MET cc_start: 0.8534 (ptt) cc_final: 0.7964 (mmm) REVERT: F 85 MET cc_start: 0.9485 (ttm) cc_final: 0.9240 (ttm) REVERT: F 89 GLU cc_start: 0.9267 (mt-10) cc_final: 0.9046 (mp0) REVERT: F 104 ASN cc_start: 0.9142 (m-40) cc_final: 0.8832 (t0) REVERT: F 108 PHE cc_start: 0.8779 (m-80) cc_final: 0.8059 (m-80) REVERT: F 110 ASP cc_start: 0.9153 (m-30) cc_final: 0.8309 (p0) REVERT: F 111 LEU cc_start: 0.9298 (mt) cc_final: 0.8908 (mm) REVERT: F 112 GLU cc_start: 0.9074 (mp0) cc_final: 0.8508 (mp0) REVERT: F 114 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8204 (mp0) REVERT: F 116 ASP cc_start: 0.9076 (t70) cc_final: 0.8715 (t0) REVERT: F 119 ARG cc_start: 0.9393 (tpp80) cc_final: 0.9191 (mmm-85) REVERT: F 124 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9260 (mt-10) REVERT: F 129 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8632 (mmmm) REVERT: F 144 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7813 (mt-10) REVERT: G 1 MET cc_start: 0.8328 (mmm) cc_final: 0.7606 (mmt) REVERT: G 3 PHE cc_start: 0.7622 (m-10) cc_final: 0.7380 (m-10) REVERT: G 42 PHE cc_start: 0.7803 (m-80) cc_final: 0.7491 (m-80) REVERT: G 51 TYR cc_start: 0.7949 (t80) cc_final: 0.7685 (t80) REVERT: G 69 GLU cc_start: 0.8161 (tt0) cc_final: 0.7914 (tt0) REVERT: H 14 GLU cc_start: 0.8745 (tt0) cc_final: 0.7371 (tm-30) REVERT: H 21 ASN cc_start: 0.9368 (m-40) cc_final: 0.8900 (m-40) REVERT: H 27 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8717 (mp0) REVERT: H 103 LYS cc_start: 0.9040 (tptt) cc_final: 0.8640 (tptp) REVERT: H 105 GLU cc_start: 0.8685 (tt0) cc_final: 0.8355 (tm-30) REVERT: H 112 ILE cc_start: 0.8798 (tt) cc_final: 0.8428 (tt) REVERT: H 116 TYR cc_start: 0.9303 (m-80) cc_final: 0.9097 (m-80) REVERT: H 123 MET cc_start: 0.9448 (ttt) cc_final: 0.8997 (tmm) REVERT: H 126 GLU cc_start: 0.9145 (tt0) cc_final: 0.8575 (tp30) REVERT: I 13 MET cc_start: 0.6839 (ptt) cc_final: 0.6147 (ppp) REVERT: I 15 TYR cc_start: 0.6285 (m-80) cc_final: 0.5844 (m-80) REVERT: I 19 ASP cc_start: 0.7220 (t0) cc_final: 0.6451 (t0) REVERT: I 27 PHE cc_start: 0.7778 (m-80) cc_final: 0.7342 (m-10) REVERT: I 44 TYR cc_start: 0.8155 (t80) cc_final: 0.7855 (t80) REVERT: I 45 ARG cc_start: 0.7059 (ttt90) cc_final: 0.6716 (ttm-80) REVERT: I 80 SER cc_start: 0.5786 (t) cc_final: 0.5326 (p) REVERT: I 91 ARG cc_start: 0.8780 (tpm170) cc_final: 0.8477 (mmt180) REVERT: K 10 PHE cc_start: 0.8211 (p90) cc_final: 0.7731 (p90) REVERT: K 17 SER cc_start: 0.9374 (m) cc_final: 0.9036 (t) REVERT: K 36 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8468 (tp30) REVERT: K 38 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8909 (mm-30) REVERT: K 54 ARG cc_start: 0.9285 (mtm180) cc_final: 0.8772 (mmm160) REVERT: K 55 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8991 (mtmm) REVERT: K 64 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8895 (mt-10) REVERT: K 72 LYS cc_start: 0.9240 (mttt) cc_final: 0.8806 (mttp) REVERT: L 29 TYR cc_start: 0.7889 (m-80) cc_final: 0.7035 (m-80) REVERT: L 58 LYS cc_start: 0.8428 (tttm) cc_final: 0.8139 (mtpt) REVERT: L 66 GLN cc_start: 0.8534 (tt0) cc_final: 0.7856 (pp30) REVERT: L 67 PHE cc_start: 0.8428 (m-80) cc_final: 0.8144 (m-80) outliers start: 0 outliers final: 0 residues processed: 686 average time/residue: 0.2160 time to fit residues: 234.4907 Evaluate side-chains 433 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN ** A1330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 862 GLN B1093 GLN F 100 GLN I 46 HIS K 44 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.078953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053905 restraints weight = 113669.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055553 restraints weight = 58509.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.056648 restraints weight = 38659.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.057335 restraints weight = 29729.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057755 restraints weight = 25378.812| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33705 Z= 0.173 Angle : 0.661 16.206 45898 Z= 0.341 Chirality : 0.046 0.275 5156 Planarity : 0.005 0.081 5607 Dihedral : 16.683 162.786 5259 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 1.34 % Allowed : 7.24 % Favored : 91.42 % 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: 0.70 (0.14), residues: 3837 helix: 1.75 (0.14), residues: 1330 sheet: -0.04 (0.21), residues: 614 loop : -0.23 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 857 TYR 0.026 0.001 TYR D 147 PHE 0.020 0.001 PHE A1402 TRP 0.008 0.001 TRP A 556 HIS 0.013 0.001 HIS G 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (33673) covalent geometry : angle 0.65019 / 0.34 (45853) hydrogen bonds : bond 0.04648 / 3.13 ( 1421) hydrogen bonds : angle 5.35465 / 3.77 ( 3925) metal coordination : bond 0.00661 / 0.42 ( 32) metal coordination : angle 3.83157 / 2.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 472 time to evaluate : 1.137 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: A 108 MET cc_start: 0.8805 (mmm) cc_final: 0.8196 (mmm) REVERT: A 250 ILE cc_start: 0.9067 (mm) cc_final: 0.8649 (pt) REVERT: A 345 VAL cc_start: 0.9505 (m) cc_final: 0.9281 (p) REVERT: A 449 SER cc_start: 0.8974 (m) cc_final: 0.8688 (p) REVERT: A 511 ILE cc_start: 0.9302 (mt) cc_final: 0.9009 (mm) REVERT: A 605 MET cc_start: 0.8988 (tpt) cc_final: 0.8640 (tpp) REVERT: A 826 ASP cc_start: 0.9078 (t70) cc_final: 0.8797 (t0) REVERT: A 873 MET cc_start: 0.8992 (mmt) cc_final: 0.7902 (mmt) REVERT: A 939 ASP cc_start: 0.8946 (m-30) cc_final: 0.8513 (m-30) REVERT: A 1063 MET cc_start: 0.9234 (mmm) cc_final: 0.9022 (mmm) REVERT: A 1093 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (tppp) REVERT: A 1111 MET cc_start: 0.8218 (mtp) cc_final: 0.7971 (mtm) REVERT: A 1240 CYS cc_start: 0.8884 (m) cc_final: 0.8280 (p) REVERT: A 1259 MET cc_start: 0.9171 (mmm) cc_final: 0.8237 (tmm) REVERT: A 1269 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8790 (mt-10) REVERT: A 1308 THR cc_start: 0.8937 (m) cc_final: 0.8483 (p) REVERT: A 1315 GLU cc_start: 0.8971 (tt0) cc_final: 0.8559 (tp30) REVERT: B 115 GLN cc_start: 0.8795 (tp40) cc_final: 0.8522 (tp-100) REVERT: B 194 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 427 ASP cc_start: 0.8936 (m-30) cc_final: 0.8660 (m-30) REVERT: B 563 MET cc_start: 0.9149 (tmm) cc_final: 0.8889 (tmm) REVERT: B 615 MET cc_start: 0.8441 (mtm) cc_final: 0.8222 (mtm) REVERT: B 616 ILE cc_start: 0.9462 (tt) cc_final: 0.9216 (pt) REVERT: B 778 MET cc_start: 0.9221 (ttm) cc_final: 0.8973 (ttm) REVERT: B 894 ASP cc_start: 0.7467 (m-30) cc_final: 0.6951 (p0) REVERT: B 999 MET cc_start: 0.9186 (mmt) cc_final: 0.8872 (mmm) REVERT: B 1090 THR cc_start: 0.8594 (m) cc_final: 0.7975 (p) REVERT: B 1133 MET cc_start: 0.8583 (mtp) cc_final: 0.7776 (mtt) REVERT: B 1137 CYS cc_start: 0.9022 (m) cc_final: 0.8810 (m) REVERT: B 1210 MET cc_start: 0.9215 (tpp) cc_final: 0.8731 (tpp) REVERT: C 37 MET cc_start: 0.9159 (mtm) cc_final: 0.8926 (mtm) REVERT: C 75 MET cc_start: 0.8500 (mmm) cc_final: 0.7976 (tpp) REVERT: C 125 MET cc_start: 0.9008 (mtp) cc_final: 0.8762 (mpp) REVERT: D 1 MET cc_start: 0.3042 (ptm) cc_final: 0.2776 (mmt) REVERT: D 50 LEU cc_start: 0.7280 (mt) cc_final: 0.6939 (mt) REVERT: D 54 GLU cc_start: 0.8999 (tt0) cc_final: 0.8461 (tp30) REVERT: D 56 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7558 (ttp80) REVERT: D 57 LEU cc_start: 0.8830 (mt) cc_final: 0.8323 (pp) REVERT: D 58 VAL cc_start: 0.8656 (t) cc_final: 0.8245 (p) REVERT: E 58 MET cc_start: 0.8661 (mtp) cc_final: 0.8415 (mtm) REVERT: E 61 GLN cc_start: 0.9102 (tt0) cc_final: 0.8884 (tm-30) REVERT: E 93 MET cc_start: 0.8730 (mmm) cc_final: 0.8255 (mmm) REVERT: E 112 TYR cc_start: 0.9172 (p90) cc_final: 0.8630 (p90) REVERT: E 179 GLN cc_start: 0.8661 (mt0) cc_final: 0.8305 (mt0) REVERT: F 104 ASN cc_start: 0.8957 (m-40) cc_final: 0.8556 (t0) REVERT: F 108 PHE cc_start: 0.8823 (m-80) cc_final: 0.8492 (m-80) REVERT: F 110 ASP cc_start: 0.9039 (m-30) cc_final: 0.8359 (p0) REVERT: F 111 LEU cc_start: 0.9374 (mt) cc_final: 0.9040 (mm) REVERT: F 112 GLU cc_start: 0.8935 (mp0) cc_final: 0.8467 (mp0) REVERT: F 128 LYS cc_start: 0.9502 (mmtp) cc_final: 0.9267 (mmmm) REVERT: F 144 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7845 (mt-10) REVERT: F 148 VAL cc_start: 0.9571 (t) cc_final: 0.9133 (p) REVERT: G 69 GLU cc_start: 0.8622 (tt0) cc_final: 0.8126 (tt0) REVERT: H 14 GLU cc_start: 0.8344 (tt0) cc_final: 0.7794 (tm-30) REVERT: H 45 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7873 (mp0) REVERT: H 55 LEU cc_start: 0.9428 (mt) cc_final: 0.9218 (mp) REVERT: H 103 LYS cc_start: 0.9490 (tptt) cc_final: 0.9009 (tptp) REVERT: H 116 TYR cc_start: 0.9005 (m-80) cc_final: 0.8553 (m-80) REVERT: I 13 MET cc_start: 0.7521 (ptt) cc_final: 0.6784 (ppp) REVERT: I 15 TYR cc_start: 0.7311 (m-80) cc_final: 0.6915 (m-80) REVERT: I 44 TYR cc_start: 0.8234 (t80) cc_final: 0.7862 (t80) REVERT: I 45 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7489 (ttm-80) REVERT: I 80 SER cc_start: 0.7157 (t) cc_final: 0.6446 (p) REVERT: K 36 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8464 (tp30) REVERT: K 37 LYS cc_start: 0.9592 (OUTLIER) cc_final: 0.9075 (mmmt) REVERT: L 28 LYS cc_start: 0.8102 (mptt) cc_final: 0.7682 (mttt) REVERT: L 66 GLN cc_start: 0.8553 (tt0) cc_final: 0.7962 (pp30) REVERT: L 67 PHE cc_start: 0.8640 (m-80) cc_final: 0.8306 (m-80) outliers start: 46 outliers final: 23 residues processed: 498 average time/residue: 0.2058 time to fit residues: 166.3219 Evaluate side-chains 435 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 410 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1093 LYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 46 HIS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 296 optimal weight: 5.9990 chunk 335 optimal weight: 20.0000 chunk 310 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B1141 HIS D 143 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN I 46 HIS K 44 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.052088 restraints weight = 115242.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053660 restraints weight = 61068.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.054671 restraints weight = 40825.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055328 restraints weight = 31763.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.055727 restraints weight = 27190.135| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 33705 Z= 0.322 Angle : 0.730 17.316 45898 Z= 0.373 Chirality : 0.046 0.238 5156 Planarity : 0.005 0.050 5607 Dihedral : 16.696 160.144 5259 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 1.90 % Allowed : 10.13 % Favored : 87.97 % 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: 0.36 (0.14), residues: 3837 helix: 1.49 (0.14), residues: 1331 sheet: -0.28 (0.21), residues: 595 loop : -0.43 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 344 TYR 0.020 0.002 TYR D 147 PHE 0.018 0.002 PHE B 360 TRP 0.008 0.001 TRP A 954 HIS 0.013 0.002 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.32 (33673) covalent geometry : angle 0.71749 / 0.37 (45853) hydrogen bonds : bond 0.04627 / 3.09 ( 1421) hydrogen bonds : angle 5.24555 / 3.71 ( 3925) metal coordination : bond 0.00914 / 0.55 ( 32) metal coordination : angle 4.42365 / 3.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 417 time to evaluate : 1.335 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: A 250 ILE cc_start: 0.9050 (mm) cc_final: 0.8614 (pt) REVERT: A 345 VAL cc_start: 0.9527 (m) cc_final: 0.9303 (p) REVERT: A 449 SER cc_start: 0.8978 (m) cc_final: 0.8747 (p) REVERT: A 605 MET cc_start: 0.8944 (tpt) cc_final: 0.8665 (tpp) REVERT: A 826 ASP cc_start: 0.9025 (t70) cc_final: 0.8786 (t0) REVERT: A 873 MET cc_start: 0.9209 (mmt) cc_final: 0.7850 (mmt) REVERT: A 939 ASP cc_start: 0.8909 (m-30) cc_final: 0.8434 (m-30) REVERT: A 1111 MET cc_start: 0.8342 (mtp) cc_final: 0.7907 (mtm) REVERT: A 1209 MET cc_start: 0.8363 (tpp) cc_final: 0.8082 (tpt) REVERT: A 1240 CYS cc_start: 0.8949 (m) cc_final: 0.8439 (p) REVERT: A 1315 GLU cc_start: 0.8879 (tt0) cc_final: 0.8547 (tp30) REVERT: A 1336 MET cc_start: 0.8940 (tmm) cc_final: 0.8664 (tmm) REVERT: B 101 MET cc_start: 0.8711 (mtt) cc_final: 0.8487 (mmm) REVERT: B 313 MET cc_start: 0.9608 (mmm) cc_final: 0.9343 (mmm) REVERT: B 314 LEU cc_start: 0.9779 (OUTLIER) cc_final: 0.9572 (mt) REVERT: B 427 ASP cc_start: 0.8998 (m-30) cc_final: 0.8702 (m-30) REVERT: B 563 MET cc_start: 0.9194 (tmm) cc_final: 0.8942 (tmm) REVERT: B 778 MET cc_start: 0.9167 (ttm) cc_final: 0.8936 (ttm) REVERT: B 1128 LEU cc_start: 0.9412 (mt) cc_final: 0.9140 (mt) REVERT: B 1133 MET cc_start: 0.8702 (mtp) cc_final: 0.7813 (mtt) REVERT: B 1210 MET cc_start: 0.9434 (tpp) cc_final: 0.9225 (tpp) REVERT: C 75 MET cc_start: 0.8429 (mmm) cc_final: 0.8206 (tpp) REVERT: C 125 MET cc_start: 0.8935 (mtp) cc_final: 0.8714 (mpp) REVERT: D 1 MET cc_start: 0.2837 (ptm) cc_final: 0.2442 (mmt) REVERT: D 50 LEU cc_start: 0.7617 (mt) cc_final: 0.7409 (mt) REVERT: D 54 GLU cc_start: 0.8927 (tt0) cc_final: 0.8355 (tp30) REVERT: D 56 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7485 (ttp80) REVERT: D 57 LEU cc_start: 0.8790 (mt) cc_final: 0.8294 (pp) REVERT: D 58 VAL cc_start: 0.8646 (t) cc_final: 0.8207 (p) REVERT: D 153 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.4803 (mmp-170) REVERT: D 156 ASP cc_start: 0.7342 (t70) cc_final: 0.7138 (t0) REVERT: E 58 MET cc_start: 0.8668 (mtp) cc_final: 0.8333 (mtm) REVERT: E 93 MET cc_start: 0.8700 (mmm) cc_final: 0.8442 (mmm) REVERT: E 112 TYR cc_start: 0.9219 (p90) cc_final: 0.8587 (p90) REVERT: F 104 ASN cc_start: 0.8887 (m-40) cc_final: 0.8523 (t0) REVERT: F 108 PHE cc_start: 0.8804 (m-80) cc_final: 0.8432 (m-80) REVERT: F 110 ASP cc_start: 0.9032 (m-30) cc_final: 0.8460 (p0) REVERT: F 122 MET cc_start: 0.9560 (ttm) cc_final: 0.9041 (mtm) REVERT: F 144 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7783 (mt-10) REVERT: G 69 GLU cc_start: 0.8659 (tt0) cc_final: 0.8084 (tt0) REVERT: H 14 GLU cc_start: 0.8360 (tt0) cc_final: 0.7771 (tm-30) REVERT: H 27 GLU cc_start: 0.7892 (mp0) cc_final: 0.5980 (mp0) REVERT: H 103 LYS cc_start: 0.9496 (tptt) cc_final: 0.9087 (tptp) REVERT: H 116 TYR cc_start: 0.8988 (m-80) cc_final: 0.8669 (m-80) REVERT: I 13 MET cc_start: 0.7546 (ptt) cc_final: 0.6786 (ppp) REVERT: I 15 TYR cc_start: 0.7361 (m-80) cc_final: 0.6822 (m-80) REVERT: I 19 ASP cc_start: 0.5397 (t0) cc_final: 0.5085 (t0) REVERT: I 21 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7097 (mp0) REVERT: I 24 ARG cc_start: 0.5883 (tmt-80) cc_final: 0.5615 (tpt170) REVERT: I 44 TYR cc_start: 0.8302 (t80) cc_final: 0.7996 (t80) REVERT: I 45 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7545 (ttm-80) REVERT: I 80 SER cc_start: 0.7226 (t) cc_final: 0.6625 (p) REVERT: L 28 LYS cc_start: 0.8068 (mptt) cc_final: 0.7660 (mttt) REVERT: L 66 GLN cc_start: 0.8512 (tt0) cc_final: 0.8060 (tm-30) outliers start: 65 outliers final: 40 residues processed: 450 average time/residue: 0.2104 time to fit residues: 153.9278 Evaluate side-chains 426 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 384 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1012 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 46 HIS Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 294 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 281 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 ASN B 46 GLN B1093 GLN C 112 ASN D 40 HIS E 61 GLN E 146 HIS I 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054407 restraints weight = 110766.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.056061 restraints weight = 57486.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057107 restraints weight = 37849.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057777 restraints weight = 29262.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058117 restraints weight = 25021.823| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33705 Z= 0.130 Angle : 0.620 15.413 45898 Z= 0.313 Chirality : 0.044 0.244 5156 Planarity : 0.004 0.063 5607 Dihedral : 16.682 160.716 5259 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 1.69 % Allowed : 11.56 % Favored : 86.75 % 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: 3837 helix: 1.60 (0.14), residues: 1344 sheet: -0.27 (0.21), residues: 598 loop : -0.38 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 192 TYR 0.024 0.001 TYR D 147 PHE 0.023 0.001 PHE A 219 TRP 0.007 0.001 TRP A 656 HIS 0.010 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (33673) covalent geometry : angle 0.60520 / 0.31 (45853) hydrogen bonds : bond 0.03819 / 2.57 ( 1421) hydrogen bonds : angle 4.83799 / 3.42 ( 3925) metal coordination : bond 0.00661 / 0.44 ( 32) metal coordination : angle 4.28116 / 2.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 434 time to evaluate : 1.228 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: A 250 ILE cc_start: 0.9020 (mm) cc_final: 0.8576 (pt) REVERT: A 345 VAL cc_start: 0.9496 (m) cc_final: 0.9250 (p) REVERT: A 455 MET cc_start: 0.8834 (ttp) cc_final: 0.7917 (ttp) REVERT: A 605 MET cc_start: 0.8934 (tpt) cc_final: 0.8655 (tpp) REVERT: A 826 ASP cc_start: 0.8946 (t70) cc_final: 0.8720 (t0) REVERT: A 873 MET cc_start: 0.9086 (mmt) cc_final: 0.7716 (mmt) REVERT: A 939 ASP cc_start: 0.8848 (m-30) cc_final: 0.8483 (m-30) REVERT: A 1111 MET cc_start: 0.8176 (mtp) cc_final: 0.7889 (mtm) REVERT: A 1240 CYS cc_start: 0.9000 (m) cc_final: 0.8417 (p) REVERT: A 1259 MET cc_start: 0.9012 (mmt) cc_final: 0.8089 (tmm) REVERT: A 1269 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8851 (mt-10) REVERT: A 1308 THR cc_start: 0.9052 (m) cc_final: 0.8599 (p) REVERT: A 1315 GLU cc_start: 0.8782 (tt0) cc_final: 0.8442 (tp30) REVERT: A 1336 MET cc_start: 0.8946 (tmm) cc_final: 0.8720 (tmm) REVERT: B 194 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 314 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9522 (mt) REVERT: B 427 ASP cc_start: 0.8980 (m-30) cc_final: 0.8670 (m-30) REVERT: B 563 MET cc_start: 0.9214 (tmm) cc_final: 0.8942 (tmm) REVERT: B 616 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9349 (pt) REVERT: B 778 MET cc_start: 0.9195 (ttm) cc_final: 0.8946 (ttm) REVERT: B 1169 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8643 (mtm) REVERT: C 37 MET cc_start: 0.9004 (mtp) cc_final: 0.8774 (mtm) REVERT: D 1 MET cc_start: 0.2772 (ptm) cc_final: 0.2406 (mmt) REVERT: D 50 LEU cc_start: 0.7589 (mt) cc_final: 0.7355 (mt) REVERT: D 54 GLU cc_start: 0.8951 (tt0) cc_final: 0.8408 (tp30) REVERT: D 57 LEU cc_start: 0.8770 (mt) cc_final: 0.8297 (pp) REVERT: D 58 VAL cc_start: 0.8609 (t) cc_final: 0.8183 (p) REVERT: E 8 ASN cc_start: 0.9364 (m110) cc_final: 0.8938 (m110) REVERT: E 58 MET cc_start: 0.8569 (mtp) cc_final: 0.8219 (mtp) REVERT: E 112 TYR cc_start: 0.9135 (p90) cc_final: 0.8485 (p90) REVERT: F 104 ASN cc_start: 0.8891 (m-40) cc_final: 0.8502 (t0) REVERT: F 108 PHE cc_start: 0.8691 (m-80) cc_final: 0.8314 (m-80) REVERT: F 110 ASP cc_start: 0.8933 (m-30) cc_final: 0.8499 (p0) REVERT: F 124 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8766 (mt-10) REVERT: F 144 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7797 (mt-10) REVERT: G 6 ASP cc_start: 0.6926 (t0) cc_final: 0.6214 (t0) REVERT: G 7 LEU cc_start: 0.9199 (mp) cc_final: 0.8973 (mt) REVERT: G 69 GLU cc_start: 0.8674 (tt0) cc_final: 0.8136 (tt0) REVERT: G 115 MET cc_start: 0.4689 (mtp) cc_final: 0.4425 (mtp) REVERT: H 14 GLU cc_start: 0.8214 (tt0) cc_final: 0.7703 (tm-30) REVERT: H 27 GLU cc_start: 0.7840 (mp0) cc_final: 0.5886 (mp0) REVERT: H 45 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7841 (mp0) REVERT: H 103 LYS cc_start: 0.9497 (tptt) cc_final: 0.9087 (tptp) REVERT: H 116 TYR cc_start: 0.8913 (m-80) cc_final: 0.8569 (m-80) REVERT: I 13 MET cc_start: 0.7528 (ptt) cc_final: 0.6757 (ppp) REVERT: I 15 TYR cc_start: 0.7321 (m-80) cc_final: 0.6759 (m-80) REVERT: I 24 ARG cc_start: 0.5660 (tmt-80) cc_final: 0.5403 (tpt170) REVERT: I 44 TYR cc_start: 0.8237 (t80) cc_final: 0.7821 (t80) REVERT: I 45 ARG cc_start: 0.7806 (ttt90) cc_final: 0.7463 (ttm-80) REVERT: I 46 HIS cc_start: 0.6840 (t-90) cc_final: 0.6571 (t-90) REVERT: I 73 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7768 (ptm160) REVERT: I 80 SER cc_start: 0.7337 (t) cc_final: 0.6602 (p) REVERT: K 85 ASP cc_start: 0.8906 (m-30) cc_final: 0.8685 (m-30) REVERT: L 28 LYS cc_start: 0.7990 (mptt) cc_final: 0.7606 (mttt) REVERT: L 38 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8452 (pt) outliers start: 58 outliers final: 35 residues processed: 464 average time/residue: 0.2197 time to fit residues: 165.4152 Evaluate side-chains 437 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 293 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 331 optimal weight: 0.1980 chunk 237 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 0.0370 chunk 74 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 overall best weight: 3.6464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS A 358 ASN A 698 GLN B 761 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052705 restraints weight = 113675.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.054262 restraints weight = 60349.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055267 restraints weight = 40529.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055909 restraints weight = 31531.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.056293 restraints weight = 27032.046| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33705 Z= 0.235 Angle : 0.663 15.449 45898 Z= 0.336 Chirality : 0.045 0.239 5156 Planarity : 0.004 0.066 5607 Dihedral : 16.693 160.912 5259 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 1.90 % Allowed : 12.46 % Favored : 85.64 % 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: 0.33 (0.14), residues: 3837 helix: 1.48 (0.14), residues: 1358 sheet: -0.38 (0.21), residues: 600 loop : -0.46 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 192 TYR 0.029 0.001 TYR G 130 PHE 0.019 0.001 PHE A 219 TRP 0.007 0.001 TRP A 572 HIS 0.012 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (33673) covalent geometry : angle 0.64985 / 0.34 (45853) hydrogen bonds : bond 0.03864 / 2.59 ( 1421) hydrogen bonds : angle 4.88645 / 3.46 ( 3925) metal coordination : bond 0.00739 / 0.46 ( 32) metal coordination : angle 4.25548 / 2.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 399 time to evaluate : 1.275 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: A 250 ILE cc_start: 0.9019 (mm) cc_final: 0.8548 (pt) REVERT: A 345 VAL cc_start: 0.9540 (m) cc_final: 0.9293 (p) REVERT: A 605 MET cc_start: 0.8993 (tpt) cc_final: 0.8693 (tpp) REVERT: A 826 ASP cc_start: 0.9036 (t70) cc_final: 0.8806 (t0) REVERT: A 838 GLN cc_start: 0.9322 (tp40) cc_final: 0.8542 (tm-30) REVERT: A 873 MET cc_start: 0.9186 (mmt) cc_final: 0.7816 (mmt) REVERT: A 939 ASP cc_start: 0.8934 (m-30) cc_final: 0.8595 (m-30) REVERT: A 1111 MET cc_start: 0.8340 (mtp) cc_final: 0.7996 (mtm) REVERT: A 1202 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: A 1240 CYS cc_start: 0.9002 (m) cc_final: 0.8402 (p) REVERT: A 1259 MET cc_start: 0.8994 (mmt) cc_final: 0.8087 (tmm) REVERT: A 1269 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8873 (mt-10) REVERT: A 1315 GLU cc_start: 0.8902 (tt0) cc_final: 0.8531 (tp30) REVERT: A 1336 MET cc_start: 0.9089 (tmm) cc_final: 0.8756 (tmm) REVERT: B 101 MET cc_start: 0.8780 (mmm) cc_final: 0.8319 (mmm) REVERT: B 313 MET cc_start: 0.9666 (mmm) cc_final: 0.9394 (mmm) REVERT: B 314 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9564 (mt) REVERT: B 427 ASP cc_start: 0.8950 (m-30) cc_final: 0.8682 (m-30) REVERT: B 563 MET cc_start: 0.9237 (tmm) cc_final: 0.8930 (tmm) REVERT: B 616 ILE cc_start: 0.9579 (OUTLIER) cc_final: 0.9342 (pt) REVERT: B 778 MET cc_start: 0.9253 (ttm) cc_final: 0.8941 (ttm) REVERT: B 1169 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8754 (mtm) REVERT: C 55 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9219 (p) REVERT: C 125 MET cc_start: 0.8678 (mpp) cc_final: 0.8169 (mpp) REVERT: D 1 MET cc_start: 0.2995 (ptm) cc_final: 0.2437 (mmt) REVERT: D 46 GLU cc_start: 0.7273 (tp30) cc_final: 0.6921 (tp30) REVERT: D 50 LEU cc_start: 0.7548 (mt) cc_final: 0.7257 (mt) REVERT: D 54 GLU cc_start: 0.8942 (tt0) cc_final: 0.8400 (tp30) REVERT: D 57 LEU cc_start: 0.8747 (mt) cc_final: 0.8256 (pp) REVERT: D 58 VAL cc_start: 0.8706 (t) cc_final: 0.8264 (p) REVERT: E 8 ASN cc_start: 0.9416 (m110) cc_final: 0.8968 (m110) REVERT: E 58 MET cc_start: 0.8626 (mtp) cc_final: 0.8272 (mtp) REVERT: F 89 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8812 (mp0) REVERT: F 104 ASN cc_start: 0.8923 (m-40) cc_final: 0.8508 (t0) REVERT: F 108 PHE cc_start: 0.8803 (m-80) cc_final: 0.8340 (m-80) REVERT: F 110 ASP cc_start: 0.9015 (m-30) cc_final: 0.8544 (p0) REVERT: F 124 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8846 (mt-10) REVERT: F 128 LYS cc_start: 0.9539 (mmtp) cc_final: 0.9259 (mmmm) REVERT: F 144 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7703 (mt-10) REVERT: G 69 GLU cc_start: 0.8680 (tt0) cc_final: 0.8149 (tt0) REVERT: G 115 MET cc_start: 0.4853 (mtp) cc_final: 0.4550 (mtp) REVERT: G 130 TYR cc_start: 0.7291 (m-80) cc_final: 0.7005 (t80) REVERT: H 103 LYS cc_start: 0.9461 (tptt) cc_final: 0.9019 (tptp) REVERT: I 13 MET cc_start: 0.7492 (ptt) cc_final: 0.6741 (ppp) REVERT: I 15 TYR cc_start: 0.7322 (m-80) cc_final: 0.6811 (m-80) REVERT: I 44 TYR cc_start: 0.8284 (t80) cc_final: 0.7892 (t80) REVERT: I 45 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7410 (ttm-80) REVERT: I 80 SER cc_start: 0.7298 (t) cc_final: 0.6596 (p) REVERT: I 91 ARG cc_start: 0.8541 (mmt-90) cc_final: 0.8269 (mpt180) REVERT: L 28 LYS cc_start: 0.7962 (mptt) cc_final: 0.7589 (mttt) REVERT: L 38 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8500 (pt) REVERT: L 56 LEU cc_start: 0.9048 (tp) cc_final: 0.8757 (tp) outliers start: 65 outliers final: 40 residues processed: 433 average time/residue: 0.2049 time to fit residues: 143.6378 Evaluate side-chains 425 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 378 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1012 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 88 optimal weight: 9.9990 chunk 368 optimal weight: 0.7980 chunk 358 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B1093 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.053177 restraints weight = 112993.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054797 restraints weight = 58203.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055853 restraints weight = 38527.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056516 restraints weight = 29748.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.056906 restraints weight = 25436.792| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33705 Z= 0.156 Angle : 0.623 14.567 45898 Z= 0.314 Chirality : 0.044 0.258 5156 Planarity : 0.004 0.059 5607 Dihedral : 16.688 161.541 5259 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 13.49 % Favored : 84.71 % 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: 0.40 (0.14), residues: 3837 helix: 1.58 (0.14), residues: 1344 sheet: -0.37 (0.20), residues: 612 loop : -0.43 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 192 TYR 0.024 0.001 TYR G 74 PHE 0.022 0.001 PHE A 219 TRP 0.008 0.001 TRP A 656 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (33673) covalent geometry : angle 0.60998 / 0.31 (45853) hydrogen bonds : bond 0.03580 / 2.40 ( 1421) hydrogen bonds : angle 4.73429 / 3.36 ( 3925) metal coordination : bond 0.00640 / 0.41 ( 32) metal coordination : angle 4.16734 / 2.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 400 time to evaluate : 1.283 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: A 22 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: A 250 ILE cc_start: 0.8996 (mm) cc_final: 0.8536 (pt) REVERT: A 345 VAL cc_start: 0.9520 (m) cc_final: 0.9268 (p) REVERT: A 605 MET cc_start: 0.9049 (tpt) cc_final: 0.8765 (tpp) REVERT: A 826 ASP cc_start: 0.9027 (t70) cc_final: 0.8797 (t0) REVERT: A 849 MET cc_start: 0.8624 (ttm) cc_final: 0.8148 (ttm) REVERT: A 939 ASP cc_start: 0.8914 (m-30) cc_final: 0.8587 (m-30) REVERT: A 1093 LYS cc_start: 0.8656 (tptm) cc_final: 0.8395 (tptm) REVERT: A 1111 MET cc_start: 0.8283 (mtp) cc_final: 0.7960 (mtm) REVERT: A 1259 MET cc_start: 0.9000 (mmt) cc_final: 0.8107 (tmm) REVERT: A 1315 GLU cc_start: 0.8893 (tt0) cc_final: 0.8510 (tp30) REVERT: A 1336 MET cc_start: 0.9134 (tmm) cc_final: 0.8852 (tmm) REVERT: A 1444 MET cc_start: 0.7993 (tpp) cc_final: 0.7719 (tpp) REVERT: B 101 MET cc_start: 0.8755 (mmm) cc_final: 0.8257 (mmm) REVERT: B 427 ASP cc_start: 0.8993 (m-30) cc_final: 0.8683 (m-30) REVERT: B 563 MET cc_start: 0.9274 (tmm) cc_final: 0.8957 (tmm) REVERT: B 616 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9363 (pt) REVERT: B 778 MET cc_start: 0.9245 (ttm) cc_final: 0.8951 (ttm) REVERT: B 1210 MET cc_start: 0.9548 (tpp) cc_final: 0.9182 (tpp) REVERT: C 55 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9191 (p) REVERT: C 75 MET cc_start: 0.8657 (mmm) cc_final: 0.8431 (tpp) REVERT: C 125 MET cc_start: 0.8670 (mpp) cc_final: 0.8241 (mpp) REVERT: D 1 MET cc_start: 0.2981 (ptm) cc_final: 0.2378 (mmt) REVERT: D 46 GLU cc_start: 0.7273 (tp30) cc_final: 0.6918 (tp30) REVERT: D 50 LEU cc_start: 0.7644 (mt) cc_final: 0.7397 (mt) REVERT: D 54 GLU cc_start: 0.8914 (tt0) cc_final: 0.8329 (tp30) REVERT: D 57 LEU cc_start: 0.8747 (mt) cc_final: 0.8256 (pp) REVERT: D 58 VAL cc_start: 0.8579 (t) cc_final: 0.8108 (p) REVERT: E 8 ASN cc_start: 0.9435 (m110) cc_final: 0.8977 (m-40) REVERT: E 58 MET cc_start: 0.8635 (mtp) cc_final: 0.8344 (mtp) REVERT: E 112 TYR cc_start: 0.9078 (p90) cc_final: 0.8440 (p90) REVERT: F 89 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8873 (mp0) REVERT: F 104 ASN cc_start: 0.8941 (m-40) cc_final: 0.8520 (t0) REVERT: F 108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8358 (m-80) REVERT: F 110 ASP cc_start: 0.9025 (m-30) cc_final: 0.8552 (p0) REVERT: F 124 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8811 (mt-10) REVERT: F 144 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7760 (mt-10) REVERT: G 69 GLU cc_start: 0.8662 (tt0) cc_final: 0.8149 (tt0) REVERT: G 115 MET cc_start: 0.4850 (mtp) cc_final: 0.4562 (mtp) REVERT: H 14 GLU cc_start: 0.8384 (tt0) cc_final: 0.7829 (tm-30) REVERT: H 27 GLU cc_start: 0.8298 (mp0) cc_final: 0.6447 (mp0) REVERT: H 37 LYS cc_start: 0.9405 (ptpp) cc_final: 0.9014 (pttp) REVERT: H 45 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7755 (mp0) REVERT: H 103 LYS cc_start: 0.9472 (tptt) cc_final: 0.9036 (tptp) REVERT: H 105 GLU cc_start: 0.8902 (tt0) cc_final: 0.8523 (tm-30) REVERT: H 123 MET cc_start: 0.8839 (ppp) cc_final: 0.8634 (ppp) REVERT: I 13 MET cc_start: 0.7637 (ptt) cc_final: 0.6851 (ppp) REVERT: I 15 TYR cc_start: 0.7333 (m-80) cc_final: 0.6759 (m-80) REVERT: I 44 TYR cc_start: 0.8270 (t80) cc_final: 0.7890 (t80) REVERT: I 45 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7429 (ttm-80) REVERT: I 80 SER cc_start: 0.7269 (t) cc_final: 0.6548 (p) REVERT: K 85 ASP cc_start: 0.9017 (m-30) cc_final: 0.8729 (m-30) REVERT: L 38 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8646 (pt) REVERT: L 56 LEU cc_start: 0.9023 (tp) cc_final: 0.8636 (tp) outliers start: 62 outliers final: 42 residues processed: 428 average time/residue: 0.2106 time to fit residues: 147.0236 Evaluate side-chains 428 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 381 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 375 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 305 optimal weight: 0.6980 chunk 283 optimal weight: 30.0000 chunk 365 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 341 optimal weight: 0.3980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 951 GLN B1093 GLN H 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.053825 restraints weight = 113116.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.055456 restraints weight = 57603.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.056515 restraints weight = 37736.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.057184 restraints weight = 28949.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.057588 restraints weight = 24626.704| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33705 Z= 0.179 Angle : 0.629 14.651 45898 Z= 0.316 Chirality : 0.044 0.298 5156 Planarity : 0.004 0.061 5607 Dihedral : 16.678 162.138 5259 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 1.81 % Allowed : 13.86 % Favored : 84.33 % 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: 0.41 (0.14), residues: 3837 helix: 1.57 (0.14), residues: 1346 sheet: -0.32 (0.20), residues: 616 loop : -0.43 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 192 TYR 0.023 0.001 TYR G 74 PHE 0.020 0.001 PHE A 219 TRP 0.006 0.001 TRP A 556 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (33673) covalent geometry : angle 0.61579 / 0.32 (45853) hydrogen bonds : bond 0.03554 / 2.38 ( 1421) hydrogen bonds : angle 4.69567 / 3.32 ( 3925) metal coordination : bond 0.00663 / 0.42 ( 32) metal coordination : angle 4.11408 / 2.69 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 389 time to evaluate : 1.276 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: A 22 PHE cc_start: 0.9478 (OUTLIER) cc_final: 0.8909 (m-10) REVERT: A 250 ILE cc_start: 0.8999 (mm) cc_final: 0.8530 (pt) REVERT: A 341 MET cc_start: 0.9327 (mmm) cc_final: 0.9057 (mmm) REVERT: A 345 VAL cc_start: 0.9530 (m) cc_final: 0.9280 (p) REVERT: A 470 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9065 (pp) REVERT: A 521 MET cc_start: 0.8956 (mtm) cc_final: 0.8545 (mpp) REVERT: A 605 MET cc_start: 0.9060 (tpt) cc_final: 0.8793 (tpp) REVERT: A 826 ASP cc_start: 0.9034 (t70) cc_final: 0.8809 (t0) REVERT: A 838 GLN cc_start: 0.9304 (tp40) cc_final: 0.8561 (tm-30) REVERT: A 849 MET cc_start: 0.8671 (ttm) cc_final: 0.8415 (ttp) REVERT: A 919 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9285 (mm) REVERT: A 939 ASP cc_start: 0.8920 (m-30) cc_final: 0.8588 (m-30) REVERT: A 1093 LYS cc_start: 0.8679 (tptm) cc_final: 0.8468 (tptm) REVERT: A 1111 MET cc_start: 0.8294 (mtp) cc_final: 0.7974 (mtm) REVERT: A 1259 MET cc_start: 0.9024 (mmt) cc_final: 0.8142 (tmm) REVERT: A 1315 GLU cc_start: 0.8902 (tt0) cc_final: 0.8518 (tp30) REVERT: A 1336 MET cc_start: 0.9159 (tmm) cc_final: 0.8854 (tmm) REVERT: A 1444 MET cc_start: 0.8009 (tpp) cc_final: 0.7777 (tpp) REVERT: B 101 MET cc_start: 0.8753 (mmm) cc_final: 0.8458 (mmm) REVERT: B 427 ASP cc_start: 0.9026 (m-30) cc_final: 0.8719 (m-30) REVERT: B 563 MET cc_start: 0.9268 (tmm) cc_final: 0.8806 (tmm) REVERT: B 616 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9363 (pt) REVERT: B 778 MET cc_start: 0.9239 (ttm) cc_final: 0.8963 (ttm) REVERT: B 1011 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 1093 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: B 1210 MET cc_start: 0.9580 (tpp) cc_final: 0.9297 (tpp) REVERT: C 55 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9234 (p) REVERT: C 75 MET cc_start: 0.8651 (mmm) cc_final: 0.8378 (tpp) REVERT: C 125 MET cc_start: 0.8672 (mpp) cc_final: 0.8237 (mpp) REVERT: D 1 MET cc_start: 0.2957 (ptm) cc_final: 0.2319 (mmt) REVERT: D 46 GLU cc_start: 0.7281 (tp30) cc_final: 0.6926 (tp30) REVERT: D 50 LEU cc_start: 0.7603 (mt) cc_final: 0.7378 (mt) REVERT: D 54 GLU cc_start: 0.8914 (tt0) cc_final: 0.8311 (tp30) REVERT: D 57 LEU cc_start: 0.8755 (mt) cc_final: 0.8269 (pp) REVERT: D 58 VAL cc_start: 0.8585 (t) cc_final: 0.8137 (p) REVERT: E 8 ASN cc_start: 0.9449 (m110) cc_final: 0.8988 (m-40) REVERT: E 57 MET cc_start: 0.8973 (pmm) cc_final: 0.8605 (pmm) REVERT: E 58 MET cc_start: 0.8677 (mtp) cc_final: 0.8379 (mtp) REVERT: E 112 TYR cc_start: 0.9132 (p90) cc_final: 0.8445 (p90) REVERT: F 89 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8747 (mp0) REVERT: F 104 ASN cc_start: 0.8950 (m-40) cc_final: 0.8527 (t0) REVERT: F 108 PHE cc_start: 0.8797 (m-80) cc_final: 0.8359 (m-80) REVERT: F 110 ASP cc_start: 0.9037 (m-30) cc_final: 0.8545 (p0) REVERT: F 124 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8833 (mt-10) REVERT: F 144 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7739 (mt-10) REVERT: G 69 GLU cc_start: 0.8705 (tt0) cc_final: 0.8226 (tt0) REVERT: G 115 MET cc_start: 0.4919 (mtp) cc_final: 0.4493 (mtp) REVERT: H 14 GLU cc_start: 0.8447 (tt0) cc_final: 0.7817 (tm-30) REVERT: H 27 GLU cc_start: 0.8331 (mp0) cc_final: 0.6631 (mp0) REVERT: H 37 LYS cc_start: 0.9416 (ptpp) cc_final: 0.9036 (pttp) REVERT: H 103 LYS cc_start: 0.9480 (tptt) cc_final: 0.9044 (tptp) REVERT: H 105 GLU cc_start: 0.8944 (tt0) cc_final: 0.8563 (tm-30) REVERT: H 123 MET cc_start: 0.8929 (ppp) cc_final: 0.8716 (ppp) REVERT: I 13 MET cc_start: 0.7656 (ptt) cc_final: 0.6878 (ppp) REVERT: I 15 TYR cc_start: 0.7309 (m-80) cc_final: 0.6761 (m-80) REVERT: I 44 TYR cc_start: 0.8279 (t80) cc_final: 0.7919 (t80) REVERT: I 45 ARG cc_start: 0.7787 (ttt90) cc_final: 0.7436 (ttm-80) REVERT: I 80 SER cc_start: 0.7214 (t) cc_final: 0.6491 (p) REVERT: I 91 ARG cc_start: 0.8445 (mpt180) cc_final: 0.8063 (mmp80) REVERT: K 85 ASP cc_start: 0.9026 (m-30) cc_final: 0.8716 (m-30) REVERT: L 28 LYS cc_start: 0.7885 (mptt) cc_final: 0.7530 (mttt) REVERT: L 33 GLU cc_start: 0.8465 (tt0) cc_final: 0.7944 (tm-30) REVERT: L 56 LEU cc_start: 0.9016 (tp) cc_final: 0.8716 (tp) outliers start: 62 outliers final: 42 residues processed: 422 average time/residue: 0.2022 time to fit residues: 139.3643 Evaluate side-chains 424 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 374 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 204 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN B 115 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054145 restraints weight = 110763.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055770 restraints weight = 57892.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056812 restraints weight = 38311.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.057479 restraints weight = 29642.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057867 restraints weight = 25330.222| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33705 Z= 0.141 Angle : 0.618 14.544 45898 Z= 0.310 Chirality : 0.043 0.238 5156 Planarity : 0.004 0.061 5607 Dihedral : 16.661 162.946 5259 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 1.81 % Allowed : 14.16 % Favored : 84.03 % 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: 3837 helix: 1.65 (0.14), residues: 1339 sheet: -0.31 (0.20), residues: 626 loop : -0.40 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1094 TYR 0.026 0.001 TYR G 74 PHE 0.021 0.001 PHE A 219 TRP 0.007 0.001 TRP A 656 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (33673) covalent geometry : angle 0.60552 / 0.31 (45853) hydrogen bonds : bond 0.03428 / 2.30 ( 1421) hydrogen bonds : angle 4.60643 / 3.26 ( 3925) metal coordination : bond 0.00596 / 0.38 ( 32) metal coordination : angle 3.92005 / 2.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 396 time to evaluate : 1.132 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: A 22 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.8934 (m-80) REVERT: A 250 ILE cc_start: 0.8973 (mm) cc_final: 0.8514 (pt) REVERT: A 345 VAL cc_start: 0.9524 (m) cc_final: 0.9277 (p) REVERT: A 455 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8415 (ptm) REVERT: A 605 MET cc_start: 0.9049 (tpt) cc_final: 0.8784 (tpp) REVERT: A 826 ASP cc_start: 0.8998 (t70) cc_final: 0.8780 (t0) REVERT: A 833 GLU cc_start: 0.8202 (pm20) cc_final: 0.7994 (pm20) REVERT: A 919 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9284 (mm) REVERT: A 939 ASP cc_start: 0.8865 (m-30) cc_final: 0.8543 (m-30) REVERT: A 1111 MET cc_start: 0.8197 (mtp) cc_final: 0.7971 (mtm) REVERT: A 1259 MET cc_start: 0.9105 (mmt) cc_final: 0.8201 (tmm) REVERT: A 1315 GLU cc_start: 0.8875 (tt0) cc_final: 0.8497 (tp30) REVERT: A 1336 MET cc_start: 0.9120 (tmm) cc_final: 0.8825 (tmm) REVERT: A 1444 MET cc_start: 0.8012 (tpp) cc_final: 0.7533 (tpp) REVERT: B 101 MET cc_start: 0.8707 (mmm) cc_final: 0.8434 (tpt) REVERT: B 427 ASP cc_start: 0.8932 (m-30) cc_final: 0.8660 (m-30) REVERT: B 432 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8000 (mmp) REVERT: B 563 MET cc_start: 0.9264 (tmm) cc_final: 0.8821 (tmm) REVERT: B 616 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9379 (pt) REVERT: B 778 MET cc_start: 0.9255 (ttm) cc_final: 0.8975 (ttm) REVERT: B 1011 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8921 (mm) REVERT: B 1093 GLN cc_start: 0.8942 (mp10) cc_final: 0.8741 (mp10) REVERT: B 1152 MET cc_start: 0.8802 (mmt) cc_final: 0.8199 (mmm) REVERT: B 1210 MET cc_start: 0.9583 (tpp) cc_final: 0.9198 (tpp) REVERT: C 75 MET cc_start: 0.8614 (mmm) cc_final: 0.8337 (tpp) REVERT: C 125 MET cc_start: 0.8640 (mpp) cc_final: 0.8203 (mpp) REVERT: D 1 MET cc_start: 0.3097 (ptm) cc_final: 0.2323 (mmt) REVERT: D 46 GLU cc_start: 0.7350 (tp30) cc_final: 0.7011 (tp30) REVERT: D 50 LEU cc_start: 0.7590 (mt) cc_final: 0.7363 (mt) REVERT: D 54 GLU cc_start: 0.8916 (tt0) cc_final: 0.8321 (tp30) REVERT: D 57 LEU cc_start: 0.8683 (mt) cc_final: 0.8218 (pp) REVERT: D 58 VAL cc_start: 0.8583 (t) cc_final: 0.8132 (p) REVERT: E 8 ASN cc_start: 0.9419 (m110) cc_final: 0.8964 (m-40) REVERT: E 57 MET cc_start: 0.8932 (pmm) cc_final: 0.8544 (pmm) REVERT: E 58 MET cc_start: 0.8680 (mtp) cc_final: 0.8366 (mtp) REVERT: E 112 TYR cc_start: 0.9078 (p90) cc_final: 0.8426 (p90) REVERT: F 89 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8801 (mp0) REVERT: F 104 ASN cc_start: 0.8930 (m-40) cc_final: 0.8496 (t0) REVERT: F 108 PHE cc_start: 0.8746 (m-80) cc_final: 0.8387 (m-80) REVERT: F 110 ASP cc_start: 0.8993 (m-30) cc_final: 0.8531 (p0) REVERT: F 124 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8814 (mt-10) REVERT: F 144 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7798 (mt-10) REVERT: G 69 GLU cc_start: 0.8700 (tt0) cc_final: 0.8377 (tt0) REVERT: G 115 MET cc_start: 0.4775 (mtp) cc_final: 0.4322 (mtp) REVERT: H 14 GLU cc_start: 0.8437 (tt0) cc_final: 0.7843 (tm-30) REVERT: H 27 GLU cc_start: 0.8388 (mp0) cc_final: 0.6756 (mp0) REVERT: H 37 LYS cc_start: 0.9414 (ptpp) cc_final: 0.9051 (pttp) REVERT: H 45 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7642 (mp0) REVERT: H 103 LYS cc_start: 0.9486 (tptt) cc_final: 0.9046 (tptp) REVERT: H 105 GLU cc_start: 0.8947 (tt0) cc_final: 0.8576 (tm-30) REVERT: H 123 MET cc_start: 0.8988 (ppp) cc_final: 0.8788 (ppp) REVERT: I 13 MET cc_start: 0.7655 (ptt) cc_final: 0.6866 (ppp) REVERT: I 15 TYR cc_start: 0.7309 (m-80) cc_final: 0.6765 (m-80) REVERT: I 44 TYR cc_start: 0.8278 (t80) cc_final: 0.7917 (t80) REVERT: I 80 SER cc_start: 0.7239 (t) cc_final: 0.6510 (p) REVERT: I 91 ARG cc_start: 0.8470 (mpt180) cc_final: 0.8048 (mmp80) REVERT: K 85 ASP cc_start: 0.9000 (m-30) cc_final: 0.8680 (m-30) REVERT: L 28 LYS cc_start: 0.7940 (mptt) cc_final: 0.7508 (mttt) REVERT: L 33 GLU cc_start: 0.8417 (tt0) cc_final: 0.7917 (tm-30) REVERT: L 56 LEU cc_start: 0.9066 (tp) cc_final: 0.8627 (tp) outliers start: 62 outliers final: 45 residues processed: 429 average time/residue: 0.2048 time to fit residues: 142.8899 Evaluate side-chains 425 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 373 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 3 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 348 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054876 restraints weight = 109370.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056514 restraints weight = 56140.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057581 restraints weight = 36886.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058247 restraints weight = 28288.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058662 restraints weight = 24103.057| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33705 Z= 0.122 Angle : 0.636 14.938 45898 Z= 0.317 Chirality : 0.043 0.238 5156 Planarity : 0.004 0.061 5607 Dihedral : 16.638 163.996 5259 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 1.52 % Allowed : 14.86 % Favored : 83.63 % 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: 0.49 (0.14), residues: 3837 helix: 1.63 (0.15), residues: 1346 sheet: -0.26 (0.20), residues: 634 loop : -0.38 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 192 TYR 0.029 0.001 TYR G 74 PHE 0.034 0.001 PHE G 121 TRP 0.008 0.001 TRP A 656 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33673) covalent geometry : angle 0.62583 / 0.32 (45853) hydrogen bonds : bond 0.03341 / 2.25 ( 1421) hydrogen bonds : angle 4.54453 / 3.23 ( 3925) metal coordination : bond 0.00595 / 0.39 ( 32) metal coordination : angle 3.74305 / 2.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 401 time to evaluate : 1.197 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: A 22 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: A 250 ILE cc_start: 0.8966 (mm) cc_final: 0.8508 (pt) REVERT: A 341 MET cc_start: 0.9526 (mmm) cc_final: 0.8846 (mmm) REVERT: A 345 VAL cc_start: 0.9521 (m) cc_final: 0.9264 (p) REVERT: A 605 MET cc_start: 0.9111 (tpt) cc_final: 0.8880 (tpp) REVERT: A 826 ASP cc_start: 0.8993 (t70) cc_final: 0.8782 (t0) REVERT: A 919 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9308 (mm) REVERT: A 939 ASP cc_start: 0.8858 (m-30) cc_final: 0.8529 (m-30) REVERT: A 1062 GLU cc_start: 0.8496 (tp30) cc_final: 0.8197 (mm-30) REVERT: A 1111 MET cc_start: 0.8197 (mtp) cc_final: 0.7984 (mtm) REVERT: A 1259 MET cc_start: 0.9098 (mmt) cc_final: 0.8204 (tmm) REVERT: A 1315 GLU cc_start: 0.8719 (tt0) cc_final: 0.8508 (tp30) REVERT: A 1336 MET cc_start: 0.9158 (tmm) cc_final: 0.8839 (tmm) REVERT: A 1444 MET cc_start: 0.7806 (tpp) cc_final: 0.7562 (tpp) REVERT: B 101 MET cc_start: 0.8701 (mmm) cc_final: 0.8422 (tpt) REVERT: B 173 MET cc_start: 0.9443 (tpp) cc_final: 0.9183 (tpp) REVERT: B 319 GLU cc_start: 0.9376 (tp30) cc_final: 0.9170 (tp30) REVERT: B 427 ASP cc_start: 0.8915 (m-30) cc_final: 0.8637 (m-30) REVERT: B 563 MET cc_start: 0.9268 (tmm) cc_final: 0.8821 (tmm) REVERT: B 778 MET cc_start: 0.9243 (ttm) cc_final: 0.8984 (ttm) REVERT: B 809 MET cc_start: 0.9116 (ptm) cc_final: 0.8645 (ptp) REVERT: B 1011 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8916 (mm) REVERT: B 1152 MET cc_start: 0.8809 (mmt) cc_final: 0.8292 (mmm) REVERT: C 75 MET cc_start: 0.8578 (mmm) cc_final: 0.8312 (tpp) REVERT: C 125 MET cc_start: 0.8636 (mpp) cc_final: 0.8222 (mpp) REVERT: D 1 MET cc_start: 0.3028 (ptm) cc_final: 0.2192 (mmt) REVERT: D 46 GLU cc_start: 0.7311 (tp30) cc_final: 0.6971 (tp30) REVERT: D 50 LEU cc_start: 0.7686 (mt) cc_final: 0.7335 (mp) REVERT: D 54 GLU cc_start: 0.8940 (tt0) cc_final: 0.8320 (tp30) REVERT: D 57 LEU cc_start: 0.8712 (mt) cc_final: 0.8257 (pp) REVERT: D 58 VAL cc_start: 0.8582 (t) cc_final: 0.8121 (p) REVERT: D 67 ARG cc_start: 0.7285 (ttt180) cc_final: 0.6954 (tpt170) REVERT: E 8 ASN cc_start: 0.9431 (m110) cc_final: 0.8979 (m110) REVERT: E 57 MET cc_start: 0.8916 (pmm) cc_final: 0.8543 (pmm) REVERT: E 58 MET cc_start: 0.8668 (mtp) cc_final: 0.8354 (mtp) REVERT: E 112 TYR cc_start: 0.9051 (p90) cc_final: 0.8451 (p90) REVERT: F 89 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: F 104 ASN cc_start: 0.8928 (m-40) cc_final: 0.8481 (t0) REVERT: F 108 PHE cc_start: 0.8762 (m-80) cc_final: 0.8409 (m-80) REVERT: F 110 ASP cc_start: 0.8988 (m-30) cc_final: 0.8525 (p0) REVERT: F 124 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8804 (mt-10) REVERT: F 144 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7790 (mt-10) REVERT: G 3 PHE cc_start: 0.8313 (m-10) cc_final: 0.8109 (m-10) REVERT: G 69 GLU cc_start: 0.8728 (tt0) cc_final: 0.8313 (tt0) REVERT: H 14 GLU cc_start: 0.8424 (tt0) cc_final: 0.7823 (tm-30) REVERT: H 27 GLU cc_start: 0.8413 (mp0) cc_final: 0.7605 (pm20) REVERT: H 37 LYS cc_start: 0.9403 (ptpp) cc_final: 0.9027 (pttp) REVERT: H 45 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7709 (mp0) REVERT: H 103 LYS cc_start: 0.9471 (tptt) cc_final: 0.9043 (tptp) REVERT: H 105 GLU cc_start: 0.8953 (tt0) cc_final: 0.8523 (tm-30) REVERT: H 123 MET cc_start: 0.8982 (ppp) cc_final: 0.8781 (ppp) REVERT: I 13 MET cc_start: 0.7560 (ptt) cc_final: 0.6822 (ppp) REVERT: I 15 TYR cc_start: 0.7325 (m-80) cc_final: 0.6790 (m-80) REVERT: I 44 TYR cc_start: 0.8269 (t80) cc_final: 0.7927 (t80) REVERT: I 80 SER cc_start: 0.7202 (t) cc_final: 0.6478 (p) REVERT: I 91 ARG cc_start: 0.8460 (mpt180) cc_final: 0.7989 (mmp80) REVERT: I 98 VAL cc_start: 0.7683 (m) cc_final: 0.7474 (m) REVERT: K 85 ASP cc_start: 0.8987 (m-30) cc_final: 0.8632 (m-30) REVERT: L 28 LYS cc_start: 0.8126 (mptt) cc_final: 0.7602 (mttt) REVERT: L 33 GLU cc_start: 0.8463 (tt0) cc_final: 0.7952 (tm-30) REVERT: L 56 LEU cc_start: 0.8950 (tp) cc_final: 0.8649 (tp) outliers start: 52 outliers final: 38 residues processed: 429 average time/residue: 0.1977 time to fit residues: 138.3093 Evaluate side-chains 419 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 4 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 271 optimal weight: 0.0050 chunk 370 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 381 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.054734 restraints weight = 112896.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.056364 restraints weight = 58970.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057425 restraints weight = 39014.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058083 restraints weight = 30107.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058466 restraints weight = 25749.439| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33705 Z= 0.126 Angle : 0.643 13.067 45898 Z= 0.318 Chirality : 0.044 0.282 5156 Planarity : 0.004 0.072 5607 Dihedral : 16.608 164.645 5259 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 1.37 % Allowed : 15.09 % Favored : 83.54 % 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: 0.49 (0.14), residues: 3837 helix: 1.63 (0.15), residues: 1343 sheet: -0.24 (0.20), residues: 634 loop : -0.39 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 192 TYR 0.027 0.001 TYR G 74 PHE 0.022 0.001 PHE A 219 TRP 0.008 0.001 TRP A 556 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (33673) covalent geometry : angle 0.63352 / 0.32 (45853) hydrogen bonds : bond 0.03303 / 2.21 ( 1421) hydrogen bonds : angle 4.51237 / 3.21 ( 3925) metal coordination : bond 0.00596 / 0.39 ( 32) metal coordination : angle 3.65435 / 2.41 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 389 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: A 250 ILE cc_start: 0.8968 (mm) cc_final: 0.8507 (pt) REVERT: A 345 VAL cc_start: 0.9521 (m) cc_final: 0.9275 (p) REVERT: A 521 MET cc_start: 0.8350 (mpp) cc_final: 0.7754 (mtm) REVERT: A 654 ASN cc_start: 0.9382 (m-40) cc_final: 0.8927 (m-40) REVERT: A 826 ASP cc_start: 0.8972 (t70) cc_final: 0.8765 (t0) REVERT: A 838 GLN cc_start: 0.9244 (tp40) cc_final: 0.8518 (tm-30) REVERT: A 849 MET cc_start: 0.8573 (ttm) cc_final: 0.8307 (ttp) REVERT: A 919 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9309 (mm) REVERT: A 939 ASP cc_start: 0.8847 (m-30) cc_final: 0.8577 (m-30) REVERT: A 1020 CYS cc_start: 0.9119 (m) cc_final: 0.8560 (t) REVERT: A 1062 GLU cc_start: 0.8528 (tp30) cc_final: 0.8233 (mm-30) REVERT: A 1111 MET cc_start: 0.8174 (mtp) cc_final: 0.7952 (mtm) REVERT: A 1259 MET cc_start: 0.9097 (mmt) cc_final: 0.8205 (tmm) REVERT: A 1315 GLU cc_start: 0.8723 (tt0) cc_final: 0.8509 (tp30) REVERT: A 1336 MET cc_start: 0.9173 (tmm) cc_final: 0.8846 (tmm) REVERT: A 1444 MET cc_start: 0.7770 (tpp) cc_final: 0.7540 (tpp) REVERT: B 101 MET cc_start: 0.8697 (mmm) cc_final: 0.8410 (tpt) REVERT: B 173 MET cc_start: 0.9429 (tpp) cc_final: 0.9156 (tpp) REVERT: B 313 MET cc_start: 0.9654 (mmm) cc_final: 0.9451 (mmm) REVERT: B 319 GLU cc_start: 0.9371 (tp30) cc_final: 0.9161 (tp30) REVERT: B 427 ASP cc_start: 0.9018 (m-30) cc_final: 0.8737 (m-30) REVERT: B 563 MET cc_start: 0.9263 (tmm) cc_final: 0.8819 (tmm) REVERT: B 778 MET cc_start: 0.9258 (ttm) cc_final: 0.9016 (ttm) REVERT: B 809 MET cc_start: 0.9066 (ptm) cc_final: 0.8739 (ptp) REVERT: B 1011 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8917 (mm) REVERT: B 1152 MET cc_start: 0.8725 (mmt) cc_final: 0.8318 (mmm) REVERT: C 75 MET cc_start: 0.8580 (mmm) cc_final: 0.8317 (tpp) REVERT: C 125 MET cc_start: 0.8646 (mpp) cc_final: 0.8243 (mpp) REVERT: D 1 MET cc_start: 0.3357 (ptm) cc_final: 0.2887 (mtt) REVERT: D 46 GLU cc_start: 0.7288 (tp30) cc_final: 0.6950 (tp30) REVERT: D 50 LEU cc_start: 0.7697 (mt) cc_final: 0.7356 (mp) REVERT: D 54 GLU cc_start: 0.8911 (tt0) cc_final: 0.8317 (tp30) REVERT: D 57 LEU cc_start: 0.8716 (mt) cc_final: 0.8261 (pp) REVERT: D 58 VAL cc_start: 0.8577 (t) cc_final: 0.8119 (p) REVERT: D 67 ARG cc_start: 0.7331 (ttt180) cc_final: 0.7023 (mtt-85) REVERT: E 8 ASN cc_start: 0.9438 (m110) cc_final: 0.8987 (m110) REVERT: E 57 MET cc_start: 0.8915 (pmm) cc_final: 0.8552 (pmm) REVERT: E 58 MET cc_start: 0.8670 (mtp) cc_final: 0.8358 (mtp) REVERT: E 112 TYR cc_start: 0.9059 (p90) cc_final: 0.8502 (p90) REVERT: F 89 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8806 (mp0) REVERT: F 104 ASN cc_start: 0.8924 (m-40) cc_final: 0.8660 (t0) REVERT: F 108 PHE cc_start: 0.8758 (m-80) cc_final: 0.8490 (m-80) REVERT: F 110 ASP cc_start: 0.8986 (m-30) cc_final: 0.8528 (p0) REVERT: F 144 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7759 (mt-10) REVERT: G 3 PHE cc_start: 0.8309 (m-10) cc_final: 0.8106 (m-10) REVERT: G 69 GLU cc_start: 0.8715 (tt0) cc_final: 0.8326 (tt0) REVERT: H 14 GLU cc_start: 0.8415 (tt0) cc_final: 0.7825 (tm-30) REVERT: H 27 GLU cc_start: 0.8438 (mp0) cc_final: 0.7637 (pm20) REVERT: H 37 LYS cc_start: 0.9418 (ptpp) cc_final: 0.9042 (pttp) REVERT: H 45 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7779 (mp0) REVERT: H 103 LYS cc_start: 0.9464 (tptt) cc_final: 0.9002 (tptp) REVERT: H 105 GLU cc_start: 0.8945 (tt0) cc_final: 0.8521 (tm-30) REVERT: H 123 MET cc_start: 0.8979 (ppp) cc_final: 0.8769 (ppp) REVERT: I 13 MET cc_start: 0.7554 (ptt) cc_final: 0.6818 (ppp) REVERT: I 15 TYR cc_start: 0.7333 (m-80) cc_final: 0.6804 (m-80) REVERT: I 44 TYR cc_start: 0.8280 (t80) cc_final: 0.7945 (t80) REVERT: I 80 SER cc_start: 0.7120 (t) cc_final: 0.6422 (p) REVERT: I 91 ARG cc_start: 0.8462 (mpt180) cc_final: 0.8002 (mmp80) REVERT: K 85 ASP cc_start: 0.8985 (m-30) cc_final: 0.8629 (m-30) REVERT: L 28 LYS cc_start: 0.8115 (mptt) cc_final: 0.7552 (mttt) REVERT: L 33 GLU cc_start: 0.8466 (tt0) cc_final: 0.7973 (tm-30) REVERT: L 56 LEU cc_start: 0.8934 (tp) cc_final: 0.8627 (tp) outliers start: 47 outliers final: 39 residues processed: 414 average time/residue: 0.2170 time to fit residues: 147.0147 Evaluate side-chains 421 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1354 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 130 TYR Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 38 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 chunk 385 optimal weight: 50.0000 chunk 208 optimal weight: 0.0270 chunk 230 optimal weight: 0.0270 chunk 134 optimal weight: 4.9990 overall best weight: 1.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055023 restraints weight = 110425.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056651 restraints weight = 57287.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057718 restraints weight = 37855.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058362 restraints weight = 29111.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058778 restraints weight = 24909.973| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33705 Z= 0.128 Angle : 0.637 14.785 45898 Z= 0.315 Chirality : 0.043 0.267 5156 Planarity : 0.004 0.057 5607 Dihedral : 16.583 165.011 5259 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 1.34 % Allowed : 15.18 % Favored : 83.48 % 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: 0.51 (0.14), residues: 3837 helix: 1.65 (0.15), residues: 1336 sheet: -0.21 (0.20), residues: 628 loop : -0.37 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 192 TYR 0.028 0.001 TYR G 74 PHE 0.022 0.001 PHE A 219 TRP 0.008 0.001 TRP A 556 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (33673) covalent geometry : angle 0.62720 / 0.31 (45853) hydrogen bonds : bond 0.03283 / 2.20 ( 1421) hydrogen bonds : angle 4.48763 / 3.19 ( 3925) metal coordination : bond 0.00588 / 0.39 ( 32) metal coordination : angle 3.60537 / 2.39 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5671.30 seconds wall clock time: 99 minutes 3.32 seconds (5943.32 seconds total)