Starting phenix.real_space_refine on Tue Aug 26 17:09:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqy_39510/08_2025/8yqy_39510_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqy_39510/08_2025/8yqy_39510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yqy_39510/08_2025/8yqy_39510_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqy_39510/08_2025/8yqy_39510_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yqy_39510/08_2025/8yqy_39510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqy_39510/08_2025/8yqy_39510.map" } resolution = 3.68 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 Mg 1 5.21 5 S 216 5.16 5 C 25130 2.51 5 N 6715 2.21 5 O 7303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39374 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11201 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1341} Chain breaks: 2 Chain: "B" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9553 Classifications: {'peptide': 1207} Link IDs: {'PTRANS': 53, 'TRANS': 1153} Chain breaks: 4 Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2897 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain: "D" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "F" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2694 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "J" Number of atoms: 9053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 9053 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1066} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 442 SG CYS A 59 108.063 76.249 68.216 1.00 63.57 S ATOM 463 SG CYS A 62 105.729 75.035 65.480 1.00 49.39 S ATOM 523 SG CYS A 69 104.824 78.095 67.528 1.00 54.37 S ATOM 767 SG CYS A 99 94.004 59.400 110.686 1.00 87.13 S ATOM 789 SG CYS A 102 94.412 56.103 108.998 1.00 86.15 S ATOM 1041 SG CYS A 134 91.816 56.190 111.173 1.00 98.16 S ATOM 1066 SG CYS A 137 95.482 56.496 112.664 1.00100.92 S ATOM 20274 SG CYS B1180 97.947 61.036 69.309 1.00 57.15 S ATOM 20299 SG CYS B1183 98.020 61.667 73.019 1.00 61.57 S ATOM 20415 SG CYS B1198 100.509 63.277 71.043 1.00 67.07 S ATOM 20437 SG CYS B1201 100.816 59.419 71.207 1.00 71.16 S ATOM 29433 SG CYS G 73 37.082 131.158 112.325 1.00 67.48 S ATOM 29454 SG CYS G 76 38.449 134.719 112.677 1.00 72.67 S ATOM 29611 SG CYS G 96 40.737 131.994 111.524 1.00 71.61 S ATOM 29628 SG CYS G 98 39.484 132.005 115.120 1.00 69.72 S ATOM 28897 SG CYS G 4 69.558 99.872 140.979 1.00 72.79 S ATOM 28917 SG CYS G 7 72.873 100.509 139.120 1.00 77.80 S ATOM 29051 SG CYS G 24 70.944 97.433 138.349 1.00 77.30 S ATOM 29063 SG CYS G 26 72.579 97.765 141.781 1.00 88.67 S ATOM 29732 SG CYS H 7 69.447 134.056 48.596 1.00 38.01 S ATOM 29756 SG CYS H 10 68.046 134.144 44.994 1.00 43.38 S ATOM 30175 SG CYS H 65 65.786 133.838 48.115 1.00 30.16 S ATOM 30181 SG CYS H 66 67.566 137.097 47.024 1.00 46.95 S ATOM 37075 SG CYS J 937 22.502 93.361 105.537 1.00 77.95 S ATOM 37177 SG CYS J 950 20.264 91.060 103.291 1.00 90.10 S ATOM 37199 SG CYS J 953 19.322 94.701 103.878 1.00 88.99 S ATOM 36759 SG CYS J 898 21.292 113.220 77.494 1.00 71.30 S ATOM 36778 SG CYS J 901 18.698 115.559 78.700 1.00 70.41 S ATOM 32937 SG CYS J 401 111.226 72.309 29.189 1.00 90.48 S ATOM 33276 SG CYS J 442 113.859 75.232 30.164 1.00102.27 S Time building chain proxies: 7.92, per 1000 atoms: 0.20 Number of scatterers: 39374 At special positions: 0 Unit cell: (159.984, 172.912, 176.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 216 16.00 Mg 1 11.99 O 7303 8.00 N 6715 7.00 C 25130 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 62 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 59 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 69 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 102 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 134 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 99 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 137 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 73 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 4 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb=" ZN J1301 " pdb="ZN ZN J1301 " - pdb=" ND1 HIS J 943 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 953 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 950 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 937 " pdb=" ZN J1302 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 901 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1302 " - pdb=" ND1 HIS J 857 " pdb=" ZN J1303 " pdb="ZN ZN J1303 " - pdb=" ND1 HIS J 403 " pdb="ZN ZN J1303 " - pdb=" SG CYS J 442 " pdb="ZN ZN J1303 " - pdb=" SG CYS J 401 " Number of angles added : 36 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9324 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 52 sheets defined 45.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.829A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.858A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.703A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.655A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.527A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix removed outlier: 3.577A pdb=" N GLY A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.318A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.797A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.528A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.766A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.518A pdb=" N MET A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.690A pdb=" N PHE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.036A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.752A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.875A pdb=" N GLU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.616A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1051 through 1059 removed outlier: 4.381A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1063 removed outlier: 3.689A pdb=" N ARG A1063 " --> pdb=" O SER A1060 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1060 through 1063' Processing helix chain 'A' and resid 1075 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1102 through 1105 Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 5.210A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.962A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1229 through 1234 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 4.027A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.877A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A1355 " --> pdb=" O ARG A1351 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A1356 " --> pdb=" O HIS A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.981A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 removed outlier: 3.747A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.630A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 removed outlier: 4.410A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.567A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.965A pdb=" N PHE B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.865A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.807A pdb=" N PHE B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 4.025A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.988A pdb=" N HIS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.566A pdb=" N VAL B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 382 through 402 removed outlier: 3.522A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.641A pdb=" N ALA B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.597A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 489 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 535 through 542 removed outlier: 3.501A pdb=" N ASP B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.925A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.554A pdb=" N VAL B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.517A pdb=" N ARG B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.549A pdb=" N GLU B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.564A pdb=" N ILE B 778 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.611A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 removed outlier: 3.565A pdb=" N HIS B 839 " --> pdb=" O THR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1032 through 1037 removed outlier: 4.156A pdb=" N ARG B1036 " --> pdb=" O SER B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.841A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 removed outlier: 3.711A pdb=" N ALA B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1160 through 1169 removed outlier: 3.678A pdb=" N ILE B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.661A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.560A pdb=" N ARG C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.647A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 358 removed outlier: 3.535A pdb=" N ILE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.552A pdb=" N THR D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.789A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.596A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.663A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.673A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.528A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 194 removed outlier: 3.843A pdb=" N LEU F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 removed outlier: 4.015A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 Processing helix chain 'F' and resid 288 through 314 removed outlier: 3.844A pdb=" N MET F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.653A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 332 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 17 through 33 removed outlier: 3.600A pdb=" N GLU H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 44 Proline residue: H 42 - end of helix Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'J' and resid 75 through 84 removed outlier: 3.834A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.705A pdb=" N PHE J 142 " --> pdb=" O SER J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 163 Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 194 through 212 Processing helix chain 'J' and resid 215 through 236 removed outlier: 3.501A pdb=" N ILE J 219 " --> pdb=" O HIS J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 267 removed outlier: 4.327A pdb=" N THR J 267 " --> pdb=" O LYS J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 289 Processing helix chain 'J' and resid 299 through 343 removed outlier: 3.975A pdb=" N PHE J 303 " --> pdb=" O VAL J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 356 Processing helix chain 'J' and resid 364 through 371 Processing helix chain 'J' and resid 375 through 398 removed outlier: 3.772A pdb=" N ALA J 379 " --> pdb=" O GLY J 375 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 382 " --> pdb=" O GLU J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 411 removed outlier: 4.376A pdb=" N LYS J 405 " --> pdb=" O CYS J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 428 removed outlier: 3.530A pdb=" N LEU J 419 " --> pdb=" O GLN J 415 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS J 421 " --> pdb=" O ALA J 417 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL J 428 " --> pdb=" O GLU J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 463 Processing helix chain 'J' and resid 466 through 474 removed outlier: 3.784A pdb=" N LYS J 473 " --> pdb=" O THR J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 537 Processing helix chain 'J' and resid 547 through 565 Proline residue: J 561 - end of helix Processing helix chain 'J' and resid 576 through 601 Processing helix chain 'J' and resid 617 through 633 Processing helix chain 'J' and resid 633 through 638 Processing helix chain 'J' and resid 644 through 664 Processing helix chain 'J' and resid 673 through 683 removed outlier: 3.536A pdb=" N LEU J 683 " --> pdb=" O THR J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 697 removed outlier: 3.738A pdb=" N ASP J 697 " --> pdb=" O VAL J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 720 Processing helix chain 'J' and resid 722 through 727 removed outlier: 3.582A pdb=" N LEU J 727 " --> pdb=" O PRO J 723 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 748 Processing helix chain 'J' and resid 769 through 791 Processing helix chain 'J' and resid 795 through 816 Processing helix chain 'J' and resid 845 through 849 Processing helix chain 'J' and resid 879 through 881 No H-bonds generated for 'chain 'J' and resid 879 through 881' Processing helix chain 'J' and resid 882 through 887 Processing helix chain 'J' and resid 907 through 911 removed outlier: 3.628A pdb=" N GLN J 910 " --> pdb=" O GLU J 907 " (cutoff:3.500A) Processing helix chain 'J' and resid 912 through 933 Processing helix chain 'J' and resid 956 through 960 removed outlier: 3.571A pdb=" N ILE J 960 " --> pdb=" O THR J 957 " (cutoff:3.500A) Processing helix chain 'J' and resid 966 through 977 removed outlier: 3.826A pdb=" N TYR J 973 " --> pdb=" O LEU J 969 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR J 974 " --> pdb=" O VAL J 970 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN J 975 " --> pdb=" O HIS J 971 " (cutoff:3.500A) Processing helix chain 'J' and resid 977 through 989 Processing helix chain 'J' and resid 1017 through 1028 Processing helix chain 'J' and resid 1030 through 1036 removed outlier: 3.903A pdb=" N ILE J1034 " --> pdb=" O SER J1030 " (cutoff:3.500A) Processing helix chain 'J' and resid 1044 through 1051 Processing helix chain 'J' and resid 1063 through 1085 removed outlier: 4.041A pdb=" N MET J1067 " --> pdb=" O ASP J1063 " (cutoff:3.500A) Processing helix chain 'J' and resid 1086 through 1089 Processing helix chain 'J' and resid 1093 through 1098 removed outlier: 3.993A pdb=" N ARG J1098 " --> pdb=" O ILE J1094 " (cutoff:3.500A) Processing helix chain 'J' and resid 1104 through 1109 Processing helix chain 'J' and resid 1121 through 1133 removed outlier: 3.694A pdb=" N THR J1125 " --> pdb=" O GLU J1121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL J1131 " --> pdb=" O LYS J1127 " (cutoff:3.500A) Processing helix chain 'J' and resid 1133 through 1154 removed outlier: 3.771A pdb=" N LEU J1139 " --> pdb=" O ALA J1135 " (cutoff:3.500A) Processing helix chain 'J' and resid 1161 through 1182 removed outlier: 4.033A pdb=" N GLU J1167 " --> pdb=" O ASN J1163 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE J1168 " --> pdb=" O ILE J1164 " (cutoff:3.500A) Processing helix chain 'J' and resid 1190 through 1195 removed outlier: 3.628A pdb=" N ILE J1193 " --> pdb=" O ASN J1190 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE J1194 " --> pdb=" O PHE J1191 " (cutoff:3.500A) Processing helix chain 'J' and resid 1209 through 1213 Processing helix chain 'J' and resid 1242 through 1247 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.250A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.895A pdb=" N LEU A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.300A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.553A pdb=" N SER A 325 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.979A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 569 removed outlier: 3.622A pdb=" N GLU A 600 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG A 594 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 837 through 838 removed outlier: 3.542A pdb=" N SER A 845 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 6.600A pdb=" N ASN A1267 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR A1295 " --> pdb=" O ASN A1267 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.662A pdb=" N ILE A1120 " --> pdb=" O ILE A1259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.507A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER G 40 " --> pdb=" O LEU A1131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 3.841A pdb=" N ASP A1428 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 161 removed outlier: 3.762A pdb=" N ALA B 132 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 130 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN B 156 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 128 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER B 158 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 126 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 84 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.198A pdb=" N LEU B 204 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 217 removed outlier: 6.852A pdb=" N TYR B 250 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG B 229 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 248 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 231 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 246 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 233 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER B 244 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.539A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 598 removed outlier: 5.568A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 removed outlier: 7.147A pdb=" N LEU B 981 " --> pdb=" O VAL B 968 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 968 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.099A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 894 through 896 removed outlier: 3.711A pdb=" N ASP B 952 " --> pdb=" O LYS B 905 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 932 through 934 Processing sheet with id=AD5, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD6, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.123A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 46 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 67 through 73 removed outlier: 5.094A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AE2, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.746A pdb=" N GLU C 318 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 20 through 21 removed outlier: 5.141A pdb=" N ILE D 52 " --> pdb=" O TYR D 85 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 87 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU D 86 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN D 119 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 88 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR D 121 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 90 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 138 through 142 removed outlier: 4.473A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 3 through 13 removed outlier: 6.241A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 3 through 13 Processing sheet with id=AE7, first strand: chain 'F' and resid 86 through 95 removed outlier: 6.582A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 100 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL F 110 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 237 through 238 removed outlier: 6.940A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AF1, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AF2, first strand: chain 'J' and resid 117 through 119 removed outlier: 5.662A pdb=" N ILE J 91 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL J 92 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY J 129 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 440 through 441 removed outlier: 6.780A pdb=" N ASN J 440 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 493 through 495 removed outlier: 3.810A pdb=" N ALA J 504 " --> pdb=" O TYR J 494 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 540 through 542 Processing sheet with id=AF6, first strand: chain 'J' and resid 875 through 878 removed outlier: 6.473A pdb=" N TRP J 859 " --> pdb=" O CYS J 898 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS J 898 " --> pdb=" O TRP J 859 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE J 861 " --> pdb=" O LEU J 896 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU J 896 " --> pdb=" O ILE J 861 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL J 863 " --> pdb=" O ALA J 894 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 945 through 946 1775 hydrogen bonds defined for protein. 4947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.62 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7106 1.32 - 1.45: 9857 1.45 - 1.57: 22845 1.57 - 1.70: 0 1.70 - 1.82: 350 Bond restraints: 40158 Sorted by residual: bond pdb=" C GLN J 729 " pdb=" N LYS J 730 " ideal model delta sigma weight residual 1.332 1.489 -0.156 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CA TYR J 733 " pdb=" C TYR J 733 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.31e-02 5.83e+03 2.84e+01 bond pdb=" N THR J 738 " pdb=" CA THR J 738 " ideal model delta sigma weight residual 1.459 1.415 0.044 1.22e-02 6.72e+03 1.29e+01 bond pdb=" CZ ARG J 526 " pdb=" NH2 ARG J 526 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.28e+01 bond pdb=" CA LYS J 740 " pdb=" C LYS J 740 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.25e-02 6.40e+03 1.24e+01 ... (remaining 40153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.40: 54318 7.40 - 14.81: 11 14.81 - 22.21: 1 22.21 - 29.62: 0 29.62 - 37.02: 1 Bond angle restraints: 54331 Sorted by residual: angle pdb=" O GLN J 729 " pdb=" C GLN J 729 " pdb=" N LYS J 730 " ideal model delta sigma weight residual 122.59 85.57 37.02 1.33e+00 5.65e-01 7.75e+02 angle pdb=" N GLN J 747 " pdb=" CA GLN J 747 " pdb=" C GLN J 747 " ideal model delta sigma weight residual 113.30 100.68 12.62 1.34e+00 5.57e-01 8.87e+01 angle pdb=" N LEU J 748 " pdb=" CA LEU J 748 " pdb=" C LEU J 748 " ideal model delta sigma weight residual 113.20 102.09 11.11 1.21e+00 6.83e-01 8.43e+01 angle pdb=" CA GLN J 729 " pdb=" C GLN J 729 " pdb=" N LYS J 730 " ideal model delta sigma weight residual 116.84 132.24 -15.40 1.71e+00 3.42e-01 8.11e+01 angle pdb=" C ARG J 750 " pdb=" CA ARG J 750 " pdb=" CB ARG J 750 " ideal model delta sigma weight residual 110.10 121.81 -11.71 1.90e+00 2.77e-01 3.80e+01 ... (remaining 54326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 22819 17.11 - 34.23: 1388 34.23 - 51.34: 199 51.34 - 68.45: 40 68.45 - 85.57: 27 Dihedral angle restraints: 24473 sinusoidal: 10051 harmonic: 14422 Sorted by residual: dihedral pdb=" CA GLY A1073 " pdb=" C GLY A1073 " pdb=" N ILE A1074 " pdb=" CA ILE A1074 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" CA ILE J 371 " pdb=" C ILE J 371 " pdb=" N LYS J 372 " pdb=" CA LYS J 372 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 24470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 5813 0.100 - 0.200: 315 0.200 - 0.300: 3 0.300 - 0.401: 0 0.401 - 0.501: 2 Chirality restraints: 6133 Sorted by residual: chirality pdb=" CA ASN J 522 " pdb=" N ASN J 522 " pdb=" C ASN J 522 " pdb=" CB ASN J 522 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA ARG J 750 " pdb=" N ARG J 750 " pdb=" C ARG J 750 " pdb=" CB ARG J 750 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA TYR J 741 " pdb=" N TYR J 741 " pdb=" C TYR J 741 " pdb=" CB TYR J 741 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 6130 not shown) Planarity restraints: 6972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN J 729 " -0.107 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C GLN J 729 " 0.275 2.00e-02 2.50e+03 pdb=" O GLN J 729 " -0.084 2.00e-02 2.50e+03 pdb=" N LYS J 730 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 586 " -0.012 2.00e-02 2.50e+03 3.99e-02 3.19e+01 pdb=" CG TYR J 586 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR J 586 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR J 586 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR J 586 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR J 586 " 0.054 2.00e-02 2.50e+03 pdb=" CZ TYR J 586 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 586 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 575 " 0.051 2.00e-02 2.50e+03 3.68e-02 2.71e+01 pdb=" CG TYR J 575 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR J 575 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR J 575 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR J 575 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR J 575 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR J 575 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR J 575 " 0.066 2.00e-02 2.50e+03 ... (remaining 6969 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 324 2.60 - 3.17: 32937 3.17 - 3.75: 60609 3.75 - 4.32: 88401 4.32 - 4.90: 146453 Nonbonded interactions: 328724 Sorted by model distance: nonbonded pdb=" OD2 ASP A 459 " pdb="MG MG A2001 " model vdw 2.020 2.170 nonbonded pdb=" OE1 GLN J 729 " pdb=" N LYS J 730 " model vdw 2.027 3.120 nonbonded pdb=" OG1 THR A1135 " pdb=" OD1 ASN A1173 " model vdw 2.118 3.040 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A2001 " model vdw 2.158 2.170 nonbonded pdb=" O ILE B 486 " pdb=" OG1 THR B 506 " model vdw 2.171 3.040 ... (remaining 328719 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 41.680 Find NCS groups from input model: 0.310 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.156 40192 Z= 0.190 Angle : 0.643 37.020 54367 Z= 0.373 Chirality : 0.046 0.501 6133 Planarity : 0.005 0.159 6972 Dihedral : 11.515 85.565 15149 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 0.25 % Allowed : 0.16 % Favored : 99.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.12), residues: 4872 helix: 0.05 (0.11), residues: 1974 sheet: 0.06 (0.21), residues: 621 loop : -0.47 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 526 TYR 0.066 0.002 TYR J 575 PHE 0.036 0.001 PHE A 417 TRP 0.031 0.002 TRP J 647 HIS 0.013 0.001 HIS J 541 Details of bonding type rmsd covalent geometry : bond 0.00347 (40158) covalent geometry : angle 0.63288 (54331) hydrogen bonds : bond 0.20848 ( 1751) hydrogen bonds : angle 7.23443 ( 4947) metal coordination : bond 0.00740 ( 34) metal coordination : angle 4.42949 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1482 time to evaluate : 1.417 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 27 MET cc_start: 0.8806 (ppp) cc_final: 0.8491 (ppp) REVERT: A 114 HIS cc_start: 0.7322 (p-80) cc_final: 0.6970 (p-80) REVERT: A 119 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7898 (mttm) REVERT: A 178 THR cc_start: 0.8134 (p) cc_final: 0.7914 (t) REVERT: A 254 LEU cc_start: 0.7036 (tp) cc_final: 0.6614 (tp) REVERT: A 266 LEU cc_start: 0.8686 (mt) cc_final: 0.8389 (mm) REVERT: A 273 ASP cc_start: 0.6291 (t0) cc_final: 0.5837 (t0) REVERT: A 300 MET cc_start: 0.9248 (mmp) cc_final: 0.9041 (mmm) REVERT: A 362 LEU cc_start: 0.9238 (mt) cc_final: 0.9035 (mt) REVERT: A 363 MET cc_start: 0.9297 (tpt) cc_final: 0.8835 (mmm) REVERT: A 376 CYS cc_start: 0.8901 (p) cc_final: 0.8665 (p) REVERT: A 384 THR cc_start: 0.8320 (p) cc_final: 0.8058 (p) REVERT: A 385 GLN cc_start: 0.8489 (mm110) cc_final: 0.8117 (mp10) REVERT: A 461 ASP cc_start: 0.8374 (m-30) cc_final: 0.7856 (m-30) REVERT: A 652 SER cc_start: 0.9011 (p) cc_final: 0.8103 (p) REVERT: A 674 LEU cc_start: 0.9404 (mt) cc_final: 0.9194 (mt) REVERT: A 676 GLU cc_start: 0.8528 (tp30) cc_final: 0.8144 (tp30) REVERT: A 733 MET cc_start: 0.9295 (mtm) cc_final: 0.9069 (mtm) REVERT: A 734 VAL cc_start: 0.9477 (t) cc_final: 0.9251 (m) REVERT: A 772 LEU cc_start: 0.9424 (mt) cc_final: 0.9202 (mt) REVERT: A 828 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8493 (mttp) REVERT: A 860 LEU cc_start: 0.9147 (mt) cc_final: 0.8915 (mp) REVERT: A 867 THR cc_start: 0.8545 (m) cc_final: 0.8248 (t) REVERT: A 1002 ILE cc_start: 0.8967 (mt) cc_final: 0.8631 (mt) REVERT: A 1051 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 1057 MET cc_start: 0.9154 (tpt) cc_final: 0.8731 (tpt) REVERT: A 1087 GLU cc_start: 0.7239 (mp0) cc_final: 0.6979 (mm-30) REVERT: A 1124 ARG cc_start: 0.8284 (ptm160) cc_final: 0.7554 (mtm110) REVERT: A 1126 ILE cc_start: 0.8568 (mm) cc_final: 0.7892 (mt) REVERT: A 1127 LEU cc_start: 0.7832 (mt) cc_final: 0.7535 (tp) REVERT: A 1145 TYR cc_start: 0.8033 (t80) cc_final: 0.7761 (t80) REVERT: A 1181 ASN cc_start: 0.7381 (t0) cc_final: 0.7138 (t0) REVERT: A 1209 MET cc_start: 0.8127 (mtp) cc_final: 0.7565 (mtp) REVERT: A 1240 MET cc_start: 0.1542 (mpp) cc_final: 0.1031 (ttm) REVERT: A 1355 MET cc_start: 0.9098 (mmm) cc_final: 0.8648 (tpp) REVERT: A 1358 ASP cc_start: 0.7571 (m-30) cc_final: 0.7348 (m-30) REVERT: A 1401 ASP cc_start: 0.8072 (m-30) cc_final: 0.7842 (m-30) REVERT: A 1402 SER cc_start: 0.8271 (m) cc_final: 0.8011 (p) REVERT: B 26 MET cc_start: 0.8523 (mmm) cc_final: 0.8322 (mmt) REVERT: B 72 GLN cc_start: 0.7783 (pt0) cc_final: 0.7473 (pt0) REVERT: B 216 HIS cc_start: 0.7947 (m-70) cc_final: 0.7411 (m90) REVERT: B 294 ASP cc_start: 0.7925 (t0) cc_final: 0.7302 (t0) REVERT: B 304 PHE cc_start: 0.8384 (t80) cc_final: 0.7895 (t80) REVERT: B 305 MET cc_start: 0.9057 (mmt) cc_final: 0.8789 (mmt) REVERT: B 324 GLN cc_start: 0.7811 (tt0) cc_final: 0.7435 (pt0) REVERT: B 457 LEU cc_start: 0.7016 (mt) cc_final: 0.6753 (mt) REVERT: B 482 MET cc_start: 0.8577 (mmm) cc_final: 0.7995 (tpp) REVERT: B 561 THR cc_start: 0.8969 (m) cc_final: 0.8495 (p) REVERT: B 629 PHE cc_start: 0.8689 (t80) cc_final: 0.8467 (t80) REVERT: B 633 GLN cc_start: 0.8001 (tp40) cc_final: 0.7720 (tp40) REVERT: B 701 TRP cc_start: 0.8105 (p-90) cc_final: 0.7886 (p-90) REVERT: B 788 TYR cc_start: 0.9202 (m-80) cc_final: 0.8827 (m-80) REVERT: B 800 GLU cc_start: 0.9357 (tp30) cc_final: 0.9145 (tp30) REVERT: B 831 MET cc_start: 0.8855 (tpp) cc_final: 0.8636 (mmm) REVERT: B 889 LEU cc_start: 0.8143 (mt) cc_final: 0.7819 (mt) REVERT: B 932 ILE cc_start: 0.9374 (mm) cc_final: 0.8638 (tp) REVERT: B 970 ARG cc_start: 0.8453 (mtt90) cc_final: 0.8131 (mtt-85) REVERT: B 981 LEU cc_start: 0.9335 (tp) cc_final: 0.9036 (tp) REVERT: B 982 MET cc_start: 0.9083 (ttm) cc_final: 0.8867 (ttp) REVERT: B 987 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 992 ILE cc_start: 0.8921 (mm) cc_final: 0.8211 (mt) REVERT: B 1005 ILE cc_start: 0.9332 (mm) cc_final: 0.9054 (mt) REVERT: B 1037 MET cc_start: 0.8982 (mtm) cc_final: 0.8635 (mtm) REVERT: B 1042 MET cc_start: 0.8614 (mmm) cc_final: 0.8258 (mmt) REVERT: B 1161 MET cc_start: 0.9511 (mmm) cc_final: 0.9254 (mmt) REVERT: B 1171 ASP cc_start: 0.9015 (m-30) cc_final: 0.8765 (m-30) REVERT: C 78 TYR cc_start: 0.8560 (t80) cc_final: 0.8334 (t80) REVERT: C 91 GLN cc_start: 0.8750 (tt0) cc_final: 0.8322 (tt0) REVERT: C 185 SER cc_start: 0.9335 (p) cc_final: 0.9056 (t) REVERT: C 197 LYS cc_start: 0.8348 (mttp) cc_final: 0.7881 (mppt) REVERT: C 339 SER cc_start: 0.8853 (m) cc_final: 0.8471 (p) REVERT: C 345 GLN cc_start: 0.8729 (pt0) cc_final: 0.8220 (mt0) REVERT: D 1 MET cc_start: 0.6797 (ttt) cc_final: 0.6573 (ttt) REVERT: D 25 LYS cc_start: 0.7333 (mttt) cc_final: 0.7027 (mtpt) REVERT: D 36 LEU cc_start: 0.8583 (tt) cc_final: 0.7965 (mt) REVERT: D 37 ASN cc_start: 0.8488 (t0) cc_final: 0.7993 (t0) REVERT: D 38 THR cc_start: 0.7293 (m) cc_final: 0.6952 (m) REVERT: D 148 GLN cc_start: 0.7680 (mm110) cc_final: 0.7434 (mm-40) REVERT: D 155 TYR cc_start: 0.9108 (m-80) cc_final: 0.8904 (m-80) REVERT: D 165 SER cc_start: 0.8756 (p) cc_final: 0.8213 (m) REVERT: E 60 ILE cc_start: 0.8830 (mt) cc_final: 0.8570 (tt) REVERT: E 83 ARG cc_start: 0.9231 (tpt170) cc_final: 0.8980 (mmm160) REVERT: E 90 ASN cc_start: 0.8810 (t0) cc_final: 0.8557 (t0) REVERT: E 109 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8271 (tt0) REVERT: E 120 MET cc_start: 0.9180 (ttp) cc_final: 0.8911 (ttp) REVERT: E 123 ILE cc_start: 0.8926 (mm) cc_final: 0.8672 (mm) REVERT: F 6 ILE cc_start: 0.8942 (mt) cc_final: 0.8692 (tt) REVERT: F 11 LEU cc_start: 0.8690 (mt) cc_final: 0.8373 (mt) REVERT: F 70 MET cc_start: 0.8248 (ttm) cc_final: 0.7539 (ttm) REVERT: F 320 ILE cc_start: 0.8141 (pt) cc_final: 0.7780 (mt) REVERT: F 333 ARG cc_start: 0.5684 (mpt-90) cc_final: 0.4572 (tpm170) REVERT: G 75 ASN cc_start: 0.8984 (m110) cc_final: 0.8751 (m-40) REVERT: G 83 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8618 (tm-30) REVERT: H 62 MET cc_start: 0.8715 (tpp) cc_final: 0.8120 (tpt) REVERT: J 83 LEU cc_start: 0.8506 (mt) cc_final: 0.8289 (tp) REVERT: J 158 TYR cc_start: 0.7103 (t80) cc_final: 0.6863 (t80) REVERT: J 217 TRP cc_start: 0.6702 (t60) cc_final: 0.6066 (t-100) REVERT: J 257 ARG cc_start: 0.7572 (ptm-80) cc_final: 0.6978 (tmm-80) REVERT: J 266 SER cc_start: 0.9143 (p) cc_final: 0.8902 (t) REVERT: J 312 LYS cc_start: 0.8265 (mttt) cc_final: 0.7713 (mtmm) REVERT: J 357 GLU cc_start: 0.7497 (tp30) cc_final: 0.7283 (tp30) REVERT: J 414 LEU cc_start: 0.8096 (mt) cc_final: 0.7860 (mt) REVERT: J 619 ASN cc_start: 0.6416 (m-40) cc_final: 0.5840 (m-40) REVERT: J 688 ASP cc_start: 0.8407 (m-30) cc_final: 0.8109 (t0) REVERT: J 750 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.4008 (mtp180) REVERT: J 777 ILE cc_start: 0.8833 (mm) cc_final: 0.8350 (mt) REVERT: J 780 ARG cc_start: 0.8122 (tpt170) cc_final: 0.7316 (tpp-160) REVERT: J 906 HIS cc_start: 0.6655 (m170) cc_final: 0.6160 (m90) REVERT: J 1023 THR cc_start: 0.8395 (m) cc_final: 0.8089 (t) REVERT: J 1189 PHE cc_start: 0.7901 (p90) cc_final: 0.7504 (p90) outliers start: 11 outliers final: 0 residues processed: 1489 average time/residue: 0.2454 time to fit residues: 578.1891 Evaluate side-chains 772 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 771 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 750 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN A 814 ASN A 834 GLN A1111 GLN A1115 ASN A1203 HIS A1267 ASN A1439 ASN B 115 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 516 ASN ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1086 GLN B1112 GLN B1162 GLN B1200 ASN B1240 GLN C 98 ASN C 264 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 251 ASN J 164 ASN J 201 HIS ** J 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 487 ASN J 834 GLN ** J 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 917 GLN J 927 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105678 restraints weight = 67822.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108645 restraints weight = 35511.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108854 restraints weight = 21686.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109560 restraints weight = 19793.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109662 restraints weight = 17517.942| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 40192 Z= 0.224 Angle : 0.679 16.831 54367 Z= 0.353 Chirality : 0.048 0.267 6133 Planarity : 0.005 0.065 6972 Dihedral : 4.735 57.319 5345 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 2.85 % Allowed : 11.12 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.12), residues: 4872 helix: 0.59 (0.11), residues: 1994 sheet: -0.09 (0.21), residues: 639 loop : -0.45 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 258 TYR 0.032 0.002 TYR J 689 PHE 0.026 0.002 PHE A 417 TRP 0.020 0.002 TRP A 466 HIS 0.023 0.002 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00523 (40158) covalent geometry : angle 0.67237 (54331) hydrogen bonds : bond 0.04763 ( 1751) hydrogen bonds : angle 5.26572 ( 4947) metal coordination : bond 0.00897 ( 34) metal coordination : angle 3.85349 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 768 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7774 (tt0) cc_final: 0.7327 (tt0) REVERT: A 114 HIS cc_start: 0.6995 (p-80) cc_final: 0.6734 (p90) REVERT: A 119 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7721 (mtpp) REVERT: A 266 LEU cc_start: 0.8760 (mt) cc_final: 0.8471 (mm) REVERT: A 363 MET cc_start: 0.9359 (tpt) cc_final: 0.9122 (mmm) REVERT: A 384 THR cc_start: 0.8693 (p) cc_final: 0.8457 (p) REVERT: A 461 ASP cc_start: 0.7999 (m-30) cc_final: 0.7666 (m-30) REVERT: A 463 MET cc_start: 0.8681 (mtp) cc_final: 0.8294 (mtp) REVERT: A 559 LEU cc_start: 0.9483 (tp) cc_final: 0.9267 (tt) REVERT: A 561 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7603 (mtp180) REVERT: A 722 SER cc_start: 0.9016 (m) cc_final: 0.8549 (p) REVERT: A 828 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8279 (mttp) REVERT: A 860 LEU cc_start: 0.9052 (mt) cc_final: 0.8769 (mp) REVERT: A 1002 ILE cc_start: 0.9091 (mt) cc_final: 0.8816 (mt) REVERT: A 1051 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 1057 MET cc_start: 0.8917 (tpt) cc_final: 0.8389 (tpt) REVERT: A 1087 GLU cc_start: 0.7044 (mp0) cc_final: 0.6811 (mm-30) REVERT: A 1089 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6796 (mm-30) REVERT: A 1126 ILE cc_start: 0.8760 (mm) cc_final: 0.8302 (mt) REVERT: A 1240 MET cc_start: 0.2191 (mpp) cc_final: 0.1361 (ttm) REVERT: A 1343 MET cc_start: 0.8272 (mmm) cc_final: 0.7871 (mmt) REVERT: A 1356 TYR cc_start: 0.8931 (m-80) cc_final: 0.7900 (m-80) REVERT: A 1402 SER cc_start: 0.8990 (m) cc_final: 0.8743 (p) REVERT: B 55 ILE cc_start: 0.8972 (mt) cc_final: 0.8692 (mt) REVERT: B 60 LYS cc_start: 0.8044 (mttt) cc_final: 0.7841 (mtpt) REVERT: B 72 GLN cc_start: 0.7917 (pt0) cc_final: 0.7699 (pt0) REVERT: B 124 TYR cc_start: 0.9065 (t80) cc_final: 0.8770 (t80) REVERT: B 294 ASP cc_start: 0.7693 (t0) cc_final: 0.7432 (t0) REVERT: B 324 GLN cc_start: 0.7883 (tt0) cc_final: 0.7627 (pt0) REVERT: B 354 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: B 414 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.8198 (ptm-80) REVERT: B 482 MET cc_start: 0.8316 (mmm) cc_final: 0.7897 (mmt) REVERT: B 701 TRP cc_start: 0.8315 (p-90) cc_final: 0.7806 (p-90) REVERT: B 831 MET cc_start: 0.8626 (tpp) cc_final: 0.8318 (mmm) REVERT: B 894 GLU cc_start: 0.8164 (mp0) cc_final: 0.7711 (mt-10) REVERT: B 932 ILE cc_start: 0.9390 (mm) cc_final: 0.8814 (tp) REVERT: B 966 ASP cc_start: 0.8172 (t0) cc_final: 0.7893 (m-30) REVERT: B 982 MET cc_start: 0.8892 (ttm) cc_final: 0.8660 (ttp) REVERT: B 992 ILE cc_start: 0.9006 (mm) cc_final: 0.8573 (mt) REVERT: B 1042 MET cc_start: 0.8113 (mmm) cc_final: 0.7675 (mmt) REVERT: B 1113 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8113 (mmtp) REVERT: B 1212 SER cc_start: 0.8918 (t) cc_final: 0.8536 (m) REVERT: B 1224 ARG cc_start: 0.8706 (mtt90) cc_final: 0.8294 (mtt-85) REVERT: C 91 GLN cc_start: 0.8888 (tt0) cc_final: 0.8488 (tt0) REVERT: C 95 ASN cc_start: 0.8348 (t0) cc_final: 0.8122 (t0) REVERT: C 197 LYS cc_start: 0.8465 (mttp) cc_final: 0.8124 (mppt) REVERT: C 272 MET cc_start: 0.7551 (mmm) cc_final: 0.7272 (mtt) REVERT: C 339 SER cc_start: 0.8717 (m) cc_final: 0.8453 (p) REVERT: D 38 THR cc_start: 0.7503 (m) cc_final: 0.7017 (p) REVERT: D 40 PHE cc_start: 0.7515 (p90) cc_final: 0.6756 (p90) REVERT: D 119 ASN cc_start: 0.7921 (m110) cc_final: 0.7511 (t0) REVERT: D 148 GLN cc_start: 0.7688 (mm110) cc_final: 0.7485 (mm-40) REVERT: D 155 TYR cc_start: 0.9116 (m-80) cc_final: 0.8864 (m-10) REVERT: D 165 SER cc_start: 0.8974 (p) cc_final: 0.8360 (m) REVERT: D 168 ASP cc_start: 0.9004 (t70) cc_final: 0.8521 (t0) REVERT: E 51 GLN cc_start: 0.7297 (tt0) cc_final: 0.6932 (tt0) REVERT: E 60 ILE cc_start: 0.8998 (mt) cc_final: 0.8706 (tt) REVERT: E 120 MET cc_start: 0.8531 (ttp) cc_final: 0.8304 (ttp) REVERT: F 1 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6751 (ttm) REVERT: F 6 ILE cc_start: 0.9014 (mt) cc_final: 0.8682 (tt) REVERT: F 70 MET cc_start: 0.8394 (ttm) cc_final: 0.7720 (ttm) REVERT: F 120 GLN cc_start: 0.5380 (OUTLIER) cc_final: 0.5119 (pt0) REVERT: F 333 ARG cc_start: 0.6032 (mpt-90) cc_final: 0.4374 (tpm170) REVERT: G 92 ILE cc_start: 0.9154 (mm) cc_final: 0.8859 (mm) REVERT: H 3 ILE cc_start: 0.9182 (mp) cc_final: 0.8791 (mt) REVERT: H 50 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6740 (mt-10) REVERT: J 221 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6937 (mmm-85) REVERT: J 228 HIS cc_start: 0.6065 (OUTLIER) cc_final: 0.5801 (t70) REVERT: J 308 GLU cc_start: 0.7436 (tp30) cc_final: 0.6963 (tp30) REVERT: J 312 LYS cc_start: 0.8211 (mttt) cc_final: 0.7854 (mtmm) REVERT: J 475 MET cc_start: 0.8202 (mmm) cc_final: 0.7998 (tpp) REVERT: J 544 LYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3862 (mmpt) REVERT: J 619 ASN cc_start: 0.7485 (m-40) cc_final: 0.7265 (m-40) REVERT: J 629 MET cc_start: 0.5078 (ttp) cc_final: 0.4191 (ttt) REVERT: J 750 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.4147 (mtp-110) REVERT: J 794 ASN cc_start: 0.7064 (t0) cc_final: 0.6861 (t0) REVERT: J 895 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6096 (m-30) REVERT: J 927 ASN cc_start: 0.8105 (m-40) cc_final: 0.7847 (m-40) REVERT: J 1189 PHE cc_start: 0.7911 (p90) cc_final: 0.7431 (p90) outliers start: 125 outliers final: 74 residues processed: 853 average time/residue: 0.2133 time to fit residues: 297.5412 Evaluate side-chains 701 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 620 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1380 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 355 THR Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 540 ILE Chi-restraints excluded: chain J residue 544 LYS Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 779 LEU Chi-restraints excluded: chain J residue 870 SER Chi-restraints excluded: chain J residue 895 ASP Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1082 CYS Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 196 optimal weight: 7.9990 chunk 433 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 382 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 419 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 33 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 388 HIS B 115 ASN B 570 GLN ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 HIS ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 341 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN F 159 HIS J 164 ASN J 202 GLN J 632 GLN J 834 GLN J 906 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099602 restraints weight = 68727.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102026 restraints weight = 35529.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103545 restraints weight = 23136.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104334 restraints weight = 17886.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104898 restraints weight = 15555.804| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 40192 Z= 0.275 Angle : 0.695 18.311 54367 Z= 0.359 Chirality : 0.049 0.186 6133 Planarity : 0.005 0.069 6972 Dihedral : 4.905 52.236 5345 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.65 % Allowed : 13.90 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.12), residues: 4872 helix: 0.59 (0.11), residues: 2000 sheet: -0.39 (0.21), residues: 592 loop : -0.58 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 17 TYR 0.033 0.002 TYR J 689 PHE 0.026 0.002 PHE A 417 TRP 0.033 0.002 TRP J 530 HIS 0.013 0.002 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00644 (40158) covalent geometry : angle 0.68831 (54331) hydrogen bonds : bond 0.04881 ( 1751) hydrogen bonds : angle 5.14619 ( 4947) metal coordination : bond 0.01130 ( 34) metal coordination : angle 3.66371 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 657 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8400 (ppp) cc_final: 0.8158 (ppp) REVERT: A 119 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7648 (mtpp) REVERT: A 266 LEU cc_start: 0.8892 (mt) cc_final: 0.8668 (mm) REVERT: A 363 MET cc_start: 0.9411 (tpt) cc_final: 0.9167 (mmm) REVERT: A 403 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7603 (t0) REVERT: A 425 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8267 (ptm160) REVERT: A 463 MET cc_start: 0.8542 (mtp) cc_final: 0.8203 (mtp) REVERT: A 497 ASN cc_start: 0.8737 (m110) cc_final: 0.8497 (m110) REVERT: A 558 MET cc_start: 0.8385 (mtp) cc_final: 0.8157 (mtm) REVERT: A 559 LEU cc_start: 0.9468 (tp) cc_final: 0.9239 (tt) REVERT: A 828 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8391 (mttp) REVERT: A 1057 MET cc_start: 0.9012 (tpt) cc_final: 0.8488 (tpt) REVERT: A 1089 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6849 (mm-30) REVERT: A 1111 GLN cc_start: 0.8384 (tp40) cc_final: 0.8165 (tp-100) REVERT: A 1126 ILE cc_start: 0.8860 (mm) cc_final: 0.8439 (mt) REVERT: A 1240 MET cc_start: 0.2380 (mpp) cc_final: 0.1782 (ttp) REVERT: A 1274 MET cc_start: 0.7578 (mtm) cc_final: 0.7354 (mtm) REVERT: A 1288 ASP cc_start: 0.7681 (m-30) cc_final: 0.7382 (m-30) REVERT: A 1329 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 1356 TYR cc_start: 0.9062 (m-80) cc_final: 0.8357 (m-80) REVERT: B 55 ILE cc_start: 0.9263 (mt) cc_final: 0.8935 (mt) REVERT: B 294 ASP cc_start: 0.7653 (t0) cc_final: 0.7323 (t0) REVERT: B 727 LEU cc_start: 0.8921 (tp) cc_final: 0.8710 (tp) REVERT: B 894 GLU cc_start: 0.8061 (mp0) cc_final: 0.7358 (mp0) REVERT: B 932 ILE cc_start: 0.9518 (mm) cc_final: 0.8904 (tp) REVERT: B 966 ASP cc_start: 0.8664 (t0) cc_final: 0.8324 (m-30) REVERT: B 982 MET cc_start: 0.8839 (ttm) cc_final: 0.8478 (ttp) REVERT: B 1042 MET cc_start: 0.8266 (mmm) cc_final: 0.7848 (mmt) REVERT: B 1182 ASN cc_start: 0.8917 (t0) cc_final: 0.8496 (t0) REVERT: B 1212 SER cc_start: 0.8833 (t) cc_final: 0.8501 (m) REVERT: B 1224 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8387 (mtt-85) REVERT: C 108 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8531 (m) REVERT: C 180 VAL cc_start: 0.9584 (m) cc_final: 0.9371 (p) REVERT: C 270 PHE cc_start: 0.8232 (m-80) cc_final: 0.7990 (m-80) REVERT: C 272 MET cc_start: 0.7490 (mmm) cc_final: 0.7222 (mtt) REVERT: C 339 SER cc_start: 0.8775 (m) cc_final: 0.8514 (p) REVERT: D 4 GLN cc_start: 0.6840 (tp-100) cc_final: 0.6446 (tp-100) REVERT: D 5 LYS cc_start: 0.8563 (mmtt) cc_final: 0.7973 (mmmt) REVERT: D 37 ASN cc_start: 0.8339 (t0) cc_final: 0.8032 (t0) REVERT: D 40 PHE cc_start: 0.7786 (p90) cc_final: 0.7104 (p90) REVERT: D 119 ASN cc_start: 0.8162 (m110) cc_final: 0.7791 (m-40) REVERT: D 148 GLN cc_start: 0.7745 (mm110) cc_final: 0.7518 (mm-40) REVERT: D 155 TYR cc_start: 0.9132 (m-80) cc_final: 0.8880 (m-10) REVERT: D 168 ASP cc_start: 0.9059 (t70) cc_final: 0.8729 (t0) REVERT: D 192 MET cc_start: 0.8726 (ttt) cc_final: 0.8448 (tmm) REVERT: E 60 ILE cc_start: 0.9120 (mt) cc_final: 0.8764 (tt) REVERT: E 109 GLU cc_start: 0.8210 (tt0) cc_final: 0.7986 (tt0) REVERT: E 111 PHE cc_start: 0.8750 (m-10) cc_final: 0.8463 (m-10) REVERT: F 6 ILE cc_start: 0.9069 (mt) cc_final: 0.8552 (tt) REVERT: F 70 MET cc_start: 0.8433 (ttm) cc_final: 0.7852 (ttm) REVERT: F 117 SER cc_start: 0.7064 (m) cc_final: 0.6817 (t) REVERT: F 328 MET cc_start: 0.7926 (tmm) cc_final: 0.7693 (ptm) REVERT: F 333 ARG cc_start: 0.5711 (mpt-90) cc_final: 0.4316 (tpm170) REVERT: G 91 ILE cc_start: 0.8992 (mt) cc_final: 0.8779 (mm) REVERT: J 221 ARG cc_start: 0.7203 (tpp80) cc_final: 0.6982 (mmm-85) REVERT: J 228 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6354 (t70) REVERT: J 299 VAL cc_start: 0.7809 (m) cc_final: 0.7580 (p) REVERT: J 308 GLU cc_start: 0.7474 (tp30) cc_final: 0.7227 (tp30) REVERT: J 509 GLU cc_start: 0.8213 (tt0) cc_final: 0.7609 (tp30) REVERT: J 556 VAL cc_start: 0.5091 (t) cc_final: 0.4773 (t) REVERT: J 619 ASN cc_start: 0.6862 (m-40) cc_final: 0.6619 (m-40) REVERT: J 621 TYR cc_start: 0.5051 (m-80) cc_final: 0.4226 (m-10) REVERT: J 750 ARG cc_start: 0.5510 (OUTLIER) cc_final: 0.4449 (mpp80) REVERT: J 784 LEU cc_start: 0.9099 (mt) cc_final: 0.8854 (mt) REVERT: J 1098 ARG cc_start: 0.6412 (mtm180) cc_final: 0.6039 (mtm180) REVERT: J 1189 PHE cc_start: 0.8086 (p90) cc_final: 0.7631 (p90) outliers start: 160 outliers final: 108 residues processed: 770 average time/residue: 0.1986 time to fit residues: 253.4077 Evaluate side-chains 685 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 572 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 625 CYS Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1002 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 355 THR Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 779 LEU Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 834 GLN Chi-restraints excluded: chain J residue 863 VAL Chi-restraints excluded: chain J residue 870 SER Chi-restraints excluded: chain J residue 884 ILE Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1082 CYS Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 141 optimal weight: 9.9990 chunk 461 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 285 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 128 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN B 115 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 GLN B1029 ASN ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 91 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 834 GLN J 927 ASN J1085 HIS ** J1095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1102 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103335 restraints weight = 67083.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105780 restraints weight = 34228.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107340 restraints weight = 22212.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108264 restraints weight = 17144.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108595 restraints weight = 14789.942| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40192 Z= 0.120 Angle : 0.571 17.494 54367 Z= 0.293 Chirality : 0.044 0.206 6133 Planarity : 0.004 0.069 6972 Dihedral : 4.574 52.809 5345 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.83 % Allowed : 16.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.12), residues: 4872 helix: 0.98 (0.12), residues: 1996 sheet: -0.32 (0.20), residues: 612 loop : -0.42 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 695 TYR 0.049 0.001 TYR J 430 PHE 0.021 0.001 PHE J 656 TRP 0.035 0.002 TRP J 217 HIS 0.009 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00265 (40158) covalent geometry : angle 0.56657 (54331) hydrogen bonds : bond 0.03837 ( 1751) hydrogen bonds : angle 4.78334 ( 4947) metal coordination : bond 0.00467 ( 34) metal coordination : angle 2.84757 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 689 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8591 (ppp) cc_final: 0.8122 (ppp) REVERT: A 119 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7259 (mmtm) REVERT: A 266 LEU cc_start: 0.8838 (mt) cc_final: 0.8595 (mm) REVERT: A 403 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7573 (t0) REVERT: A 463 MET cc_start: 0.8534 (mtp) cc_final: 0.8207 (mtp) REVERT: A 499 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8651 (mp10) REVERT: A 558 MET cc_start: 0.8225 (mtp) cc_final: 0.7990 (mtm) REVERT: A 559 LEU cc_start: 0.9450 (tp) cc_final: 0.9250 (tt) REVERT: A 722 SER cc_start: 0.9059 (m) cc_final: 0.8577 (p) REVERT: A 828 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8355 (mttp) REVERT: A 847 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7575 (t0) REVERT: A 1051 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 1057 MET cc_start: 0.8951 (tpt) cc_final: 0.8446 (tpt) REVERT: A 1089 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6757 (mm-30) REVERT: A 1111 GLN cc_start: 0.8287 (tp40) cc_final: 0.8013 (tp-100) REVERT: A 1126 ILE cc_start: 0.8828 (mm) cc_final: 0.8488 (mt) REVERT: A 1187 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 1240 MET cc_start: 0.2141 (mpp) cc_final: 0.1506 (ttm) REVERT: A 1274 MET cc_start: 0.7662 (mtm) cc_final: 0.7360 (mtm) REVERT: A 1288 ASP cc_start: 0.7690 (m-30) cc_final: 0.7061 (t0) REVERT: A 1304 MET cc_start: 0.8018 (ttm) cc_final: 0.7740 (mtm) REVERT: A 1329 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 1356 TYR cc_start: 0.8946 (m-80) cc_final: 0.8318 (m-80) REVERT: A 1386 MET cc_start: 0.9450 (ttm) cc_final: 0.8908 (ttm) REVERT: B 55 ILE cc_start: 0.9229 (mt) cc_final: 0.8932 (mt) REVERT: B 294 ASP cc_start: 0.7376 (t0) cc_final: 0.7071 (t0) REVERT: B 403 ASN cc_start: 0.8384 (t0) cc_final: 0.8051 (t0) REVERT: B 831 MET cc_start: 0.8605 (tpp) cc_final: 0.8309 (mmm) REVERT: B 894 GLU cc_start: 0.7928 (mp0) cc_final: 0.7415 (mp0) REVERT: B 932 ILE cc_start: 0.9427 (mm) cc_final: 0.8904 (tp) REVERT: B 966 ASP cc_start: 0.8382 (t0) cc_final: 0.8168 (m-30) REVERT: B 982 MET cc_start: 0.8765 (ttm) cc_final: 0.8427 (ttp) REVERT: B 992 ILE cc_start: 0.8874 (mm) cc_final: 0.8508 (mm) REVERT: B 1042 MET cc_start: 0.8174 (mmm) cc_final: 0.7748 (mmt) REVERT: B 1182 ASN cc_start: 0.8781 (t0) cc_final: 0.8406 (t0) REVERT: B 1212 SER cc_start: 0.8839 (t) cc_final: 0.8546 (m) REVERT: B 1224 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8305 (mtt-85) REVERT: C 270 PHE cc_start: 0.8212 (m-80) cc_final: 0.7914 (m-80) REVERT: C 272 MET cc_start: 0.7383 (mmm) cc_final: 0.6837 (mtt) REVERT: C 319 MET cc_start: 0.8357 (tmm) cc_final: 0.8116 (tmm) REVERT: C 339 SER cc_start: 0.8693 (m) cc_final: 0.8395 (p) REVERT: D 4 GLN cc_start: 0.6506 (tp-100) cc_final: 0.6266 (tp-100) REVERT: D 5 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7724 (mptt) REVERT: D 119 ASN cc_start: 0.8074 (m110) cc_final: 0.7633 (m-40) REVERT: D 148 GLN cc_start: 0.7803 (mm110) cc_final: 0.7597 (mm-40) REVERT: D 155 TYR cc_start: 0.9136 (m-80) cc_final: 0.8901 (m-10) REVERT: D 168 ASP cc_start: 0.8947 (t70) cc_final: 0.8737 (t0) REVERT: D 192 MET cc_start: 0.8671 (ttt) cc_final: 0.8446 (tmm) REVERT: E 109 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: F 6 ILE cc_start: 0.9053 (mt) cc_final: 0.8655 (tt) REVERT: F 70 MET cc_start: 0.8016 (ttm) cc_final: 0.7409 (ttm) REVERT: F 117 SER cc_start: 0.6896 (m) cc_final: 0.6620 (t) REVERT: F 196 ASP cc_start: 0.5489 (t70) cc_final: 0.5251 (p0) REVERT: F 333 ARG cc_start: 0.5757 (mpt-90) cc_final: 0.4356 (tpm170) REVERT: G 91 ILE cc_start: 0.9112 (mt) cc_final: 0.8829 (mm) REVERT: J 291 TYR cc_start: 0.7163 (t80) cc_final: 0.6872 (t80) REVERT: J 299 VAL cc_start: 0.8005 (m) cc_final: 0.7780 (m) REVERT: J 364 ASN cc_start: 0.7780 (p0) cc_final: 0.7532 (p0) REVERT: J 372 LYS cc_start: 0.8429 (tppp) cc_final: 0.7862 (tptt) REVERT: J 475 MET cc_start: 0.8228 (mmm) cc_final: 0.7820 (mmm) REVERT: J 503 LEU cc_start: 0.8523 (mt) cc_final: 0.8243 (mt) REVERT: J 515 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6849 (p) REVERT: J 619 ASN cc_start: 0.7648 (m-40) cc_final: 0.7428 (m-40) REVERT: J 621 TYR cc_start: 0.5571 (m-80) cc_final: 0.4071 (m-10) REVERT: J 629 MET cc_start: 0.5905 (ppp) cc_final: 0.5433 (ppp) REVERT: J 722 THR cc_start: 0.8653 (m) cc_final: 0.8407 (p) REVERT: J 750 ARG cc_start: 0.5716 (OUTLIER) cc_final: 0.4767 (mpp80) REVERT: J 784 LEU cc_start: 0.9185 (mt) cc_final: 0.8942 (mt) REVERT: J 927 ASN cc_start: 0.8053 (m-40) cc_final: 0.7816 (m-40) REVERT: J 1189 PHE cc_start: 0.7989 (p90) cc_final: 0.7594 (p90) outliers start: 124 outliers final: 77 residues processed: 766 average time/residue: 0.2000 time to fit residues: 255.8810 Evaluate side-chains 694 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 611 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 834 GLN Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 140 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 417 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 400 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 438 optimal weight: 2.9990 chunk 443 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN A 681 ASN B 115 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 ASN C 63 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN J 834 GLN ** J1095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1102 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104557 restraints weight = 66889.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107059 restraints weight = 34160.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108613 restraints weight = 22127.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109564 restraints weight = 17130.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110008 restraints weight = 14727.105| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40192 Z= 0.110 Angle : 0.558 17.462 54367 Z= 0.284 Chirality : 0.044 0.205 6133 Planarity : 0.004 0.066 6972 Dihedral : 4.413 53.754 5345 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.92 % Allowed : 16.94 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.12), residues: 4872 helix: 1.14 (0.12), residues: 2003 sheet: -0.24 (0.21), residues: 612 loop : -0.36 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 835 TYR 0.036 0.001 TYR J 430 PHE 0.021 0.001 PHE C 5 TRP 0.032 0.001 TRP J 217 HIS 0.010 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00244 (40158) covalent geometry : angle 0.55442 (54331) hydrogen bonds : bond 0.03535 ( 1751) hydrogen bonds : angle 4.64441 ( 4947) metal coordination : bond 0.00404 ( 34) metal coordination : angle 2.57740 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 660 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7232 (mmtm) REVERT: A 266 LEU cc_start: 0.8827 (mt) cc_final: 0.8618 (mm) REVERT: A 403 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7792 (t0) REVERT: A 425 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8270 (ptm160) REVERT: A 461 ASP cc_start: 0.7972 (m-30) cc_final: 0.7719 (m-30) REVERT: A 499 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8563 (mp10) REVERT: A 558 MET cc_start: 0.8191 (mtp) cc_final: 0.7963 (mtm) REVERT: A 561 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7698 (mtp180) REVERT: A 722 SER cc_start: 0.9194 (m) cc_final: 0.8613 (p) REVERT: A 828 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8517 (mttp) REVERT: A 847 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7478 (t0) REVERT: A 1051 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 1057 MET cc_start: 0.8952 (tpt) cc_final: 0.8434 (tpt) REVERT: A 1089 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6750 (mm-30) REVERT: A 1111 GLN cc_start: 0.8308 (tp40) cc_final: 0.8002 (tp-100) REVERT: A 1126 ILE cc_start: 0.8852 (mm) cc_final: 0.8499 (mt) REVERT: A 1155 MET cc_start: 0.7703 (mtt) cc_final: 0.6619 (mtp) REVERT: A 1179 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 1240 MET cc_start: 0.2075 (mpp) cc_final: 0.1622 (ttm) REVERT: A 1274 MET cc_start: 0.7421 (mtm) cc_final: 0.7110 (mtm) REVERT: A 1304 MET cc_start: 0.8091 (ttm) cc_final: 0.7812 (mtm) REVERT: A 1329 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7226 (mm-30) REVERT: A 1356 TYR cc_start: 0.8805 (m-80) cc_final: 0.8363 (m-80) REVERT: A 1431 MET cc_start: 0.7577 (mmm) cc_final: 0.6821 (mmp) REVERT: B 55 ILE cc_start: 0.9214 (mt) cc_final: 0.8881 (mt) REVERT: B 109 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8212 (mppt) REVERT: B 270 ILE cc_start: 0.8876 (mt) cc_final: 0.8418 (mt) REVERT: B 294 ASP cc_start: 0.7419 (t0) cc_final: 0.7071 (t0) REVERT: B 354 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: B 403 ASN cc_start: 0.8324 (t0) cc_final: 0.8092 (t0) REVERT: B 482 MET cc_start: 0.8993 (tpp) cc_final: 0.8749 (tpp) REVERT: B 677 ASP cc_start: 0.7782 (m-30) cc_final: 0.7171 (m-30) REVERT: B 831 MET cc_start: 0.8562 (tpp) cc_final: 0.8265 (mmm) REVERT: B 894 GLU cc_start: 0.7944 (mp0) cc_final: 0.7115 (mp0) REVERT: B 932 ILE cc_start: 0.9413 (mm) cc_final: 0.8884 (tp) REVERT: B 966 ASP cc_start: 0.8361 (t0) cc_final: 0.8120 (m-30) REVERT: B 982 MET cc_start: 0.8777 (ttm) cc_final: 0.8472 (ttp) REVERT: B 992 ILE cc_start: 0.8832 (mm) cc_final: 0.8419 (mm) REVERT: B 1042 MET cc_start: 0.8199 (mmm) cc_final: 0.7729 (mmt) REVERT: B 1182 ASN cc_start: 0.8766 (t0) cc_final: 0.8446 (t0) REVERT: B 1212 SER cc_start: 0.8870 (t) cc_final: 0.8584 (m) REVERT: B 1224 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8332 (mtt-85) REVERT: C 103 TYR cc_start: 0.8158 (t80) cc_final: 0.7913 (t80) REVERT: C 272 MET cc_start: 0.7442 (mmm) cc_final: 0.6825 (mtt) REVERT: C 319 MET cc_start: 0.8438 (tmm) cc_final: 0.8093 (tmm) REVERT: C 339 SER cc_start: 0.8681 (m) cc_final: 0.8379 (p) REVERT: D 4 GLN cc_start: 0.6432 (tp-100) cc_final: 0.6204 (tp-100) REVERT: D 119 ASN cc_start: 0.8043 (m110) cc_final: 0.7748 (t0) REVERT: D 125 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (tt) REVERT: D 148 GLN cc_start: 0.7769 (mm110) cc_final: 0.7555 (mm-40) REVERT: D 155 TYR cc_start: 0.9135 (m-80) cc_final: 0.8874 (m-80) REVERT: D 168 ASP cc_start: 0.8840 (t70) cc_final: 0.8457 (t0) REVERT: D 192 MET cc_start: 0.8712 (ttt) cc_final: 0.8475 (tmm) REVERT: E 87 LEU cc_start: 0.9220 (mt) cc_final: 0.8945 (mt) REVERT: E 109 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: F 6 ILE cc_start: 0.9028 (mt) cc_final: 0.8592 (tt) REVERT: F 70 MET cc_start: 0.8035 (ttm) cc_final: 0.7409 (ttm) REVERT: F 333 ARG cc_start: 0.6393 (mpt-90) cc_final: 0.4779 (tpm170) REVERT: G 91 ILE cc_start: 0.9182 (mt) cc_final: 0.8939 (mm) REVERT: J 193 LYS cc_start: 0.6441 (ptpt) cc_final: 0.6151 (mmmt) REVERT: J 372 LYS cc_start: 0.8335 (tppp) cc_final: 0.7847 (tptp) REVERT: J 396 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7871 (tm-30) REVERT: J 464 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: J 475 MET cc_start: 0.8039 (mmm) cc_final: 0.7682 (mmm) REVERT: J 515 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6845 (p) REVERT: J 619 ASN cc_start: 0.7648 (m-40) cc_final: 0.7433 (m-40) REVERT: J 621 TYR cc_start: 0.5770 (m-80) cc_final: 0.4230 (m-10) REVERT: J 629 MET cc_start: 0.5164 (ppp) cc_final: 0.4930 (ppp) REVERT: J 750 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.4954 (mpp80) REVERT: J 784 LEU cc_start: 0.9193 (mt) cc_final: 0.8949 (mt) REVERT: J 794 ASN cc_start: 0.6977 (t0) cc_final: 0.6750 (t0) REVERT: J 927 ASN cc_start: 0.8019 (m-40) cc_final: 0.7752 (m-40) REVERT: J 1189 PHE cc_start: 0.7959 (p90) cc_final: 0.7550 (p90) REVERT: J 1240 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8614 (mt) outliers start: 128 outliers final: 80 residues processed: 750 average time/residue: 0.2073 time to fit residues: 258.7451 Evaluate side-chains 683 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 592 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 319 GLN Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1048 ILE Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1238 ILE Chi-restraints excluded: chain J residue 1240 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 6 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 468 optimal weight: 20.0000 chunk 313 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 475 optimal weight: 20.0000 chunk 258 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 474 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS A 724 ASN A 744 ASN A1350 HIS B 242 ASN B 516 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 729 GLN ** J1095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1102 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.099234 restraints weight = 67980.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101670 restraints weight = 35398.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102412 restraints weight = 23518.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103037 restraints weight = 18663.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103273 restraints weight = 17050.040| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 40192 Z= 0.260 Angle : 0.668 15.415 54367 Z= 0.342 Chirality : 0.048 0.205 6133 Planarity : 0.005 0.062 6972 Dihedral : 4.733 50.183 5345 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.86 % Allowed : 16.98 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.12), residues: 4872 helix: 0.89 (0.11), residues: 1998 sheet: -0.49 (0.20), residues: 598 loop : -0.51 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 322 TYR 0.042 0.002 TYR J 430 PHE 0.039 0.002 PHE A 417 TRP 0.018 0.002 TRP A 466 HIS 0.009 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00614 (40158) covalent geometry : angle 0.66339 (54331) hydrogen bonds : bond 0.04323 ( 1751) hydrogen bonds : angle 4.89792 ( 4947) metal coordination : bond 0.01076 ( 34) metal coordination : angle 3.23700 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 600 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7305 (mmtm) REVERT: A 266 LEU cc_start: 0.8929 (mt) cc_final: 0.8630 (mm) REVERT: A 403 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7759 (t0) REVERT: A 425 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7897 (tmm-80) REVERT: A 461 ASP cc_start: 0.7688 (m-30) cc_final: 0.7474 (m-30) REVERT: A 558 MET cc_start: 0.8296 (mtp) cc_final: 0.8031 (mtm) REVERT: A 828 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8413 (mttp) REVERT: A 959 GLN cc_start: 0.8343 (mm110) cc_final: 0.8095 (mm-40) REVERT: A 1057 MET cc_start: 0.8963 (tpt) cc_final: 0.8432 (tpt) REVERT: A 1079 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: A 1089 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6721 (mm-30) REVERT: A 1126 ILE cc_start: 0.8960 (mm) cc_final: 0.8640 (mt) REVERT: A 1187 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 1240 MET cc_start: 0.2931 (mpp) cc_final: 0.1882 (ttm) REVERT: A 1355 MET cc_start: 0.8691 (tpp) cc_final: 0.8301 (tpp) REVERT: A 1356 TYR cc_start: 0.9126 (m-80) cc_final: 0.8513 (m-80) REVERT: A 1386 MET cc_start: 0.9444 (ttm) cc_final: 0.8967 (ttm) REVERT: A 1428 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7373 (p0) REVERT: B 55 ILE cc_start: 0.9208 (mt) cc_final: 0.8904 (mt) REVERT: B 109 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8232 (mppt) REVERT: B 181 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 251 MET cc_start: 0.8587 (mpp) cc_final: 0.8353 (mpp) REVERT: B 294 ASP cc_start: 0.7403 (t0) cc_final: 0.7051 (t0) REVERT: B 325 HIS cc_start: 0.8131 (m90) cc_final: 0.7778 (m170) REVERT: B 390 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9056 (tt) REVERT: B 403 ASN cc_start: 0.8407 (t0) cc_final: 0.8124 (t0) REVERT: B 413 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: B 460 ARG cc_start: 0.8208 (tmm-80) cc_final: 0.7596 (tmm-80) REVERT: B 894 GLU cc_start: 0.8179 (mp0) cc_final: 0.7621 (mp0) REVERT: B 932 ILE cc_start: 0.9467 (mm) cc_final: 0.8943 (tp) REVERT: B 982 MET cc_start: 0.8892 (ttm) cc_final: 0.8538 (ttp) REVERT: B 1042 MET cc_start: 0.8298 (mmm) cc_final: 0.7907 (mmt) REVERT: B 1170 ASP cc_start: 0.7876 (m-30) cc_final: 0.7316 (m-30) REVERT: B 1182 ASN cc_start: 0.8958 (t0) cc_final: 0.8676 (t0) REVERT: B 1212 SER cc_start: 0.8805 (t) cc_final: 0.8504 (m) REVERT: B 1224 ARG cc_start: 0.8808 (mtt90) cc_final: 0.8440 (mtt-85) REVERT: C 319 MET cc_start: 0.8526 (tmm) cc_final: 0.8173 (tmm) REVERT: C 339 SER cc_start: 0.8831 (m) cc_final: 0.8529 (p) REVERT: D 80 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7716 (t0) REVERT: D 119 ASN cc_start: 0.8152 (m110) cc_final: 0.7883 (m-40) REVERT: D 125 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7890 (tt) REVERT: D 148 GLN cc_start: 0.7903 (mm110) cc_final: 0.7682 (mm-40) REVERT: D 155 TYR cc_start: 0.9244 (m-80) cc_final: 0.9035 (m-10) REVERT: D 168 ASP cc_start: 0.8833 (t70) cc_final: 0.8591 (t0) REVERT: E 109 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: F 70 MET cc_start: 0.8039 (ttm) cc_final: 0.7500 (ttm) REVERT: F 333 ARG cc_start: 0.6105 (mpt-90) cc_final: 0.5041 (tpm170) REVERT: G 1 MET cc_start: 0.8252 (ppp) cc_final: 0.7952 (ppp) REVERT: H 3 ILE cc_start: 0.9040 (mp) cc_final: 0.8778 (mt) REVERT: J 80 ARG cc_start: 0.5170 (ptt180) cc_final: 0.4950 (ptt180) REVERT: J 143 MET cc_start: 0.7792 (tmm) cc_final: 0.7396 (tmm) REVERT: J 299 VAL cc_start: 0.7647 (m) cc_final: 0.7314 (p) REVERT: J 317 LEU cc_start: 0.8771 (mm) cc_final: 0.8389 (tp) REVERT: J 362 ASP cc_start: 0.7764 (t0) cc_final: 0.7511 (t0) REVERT: J 372 LYS cc_start: 0.8560 (tppp) cc_final: 0.8038 (tptt) REVERT: J 396 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7951 (tm-30) REVERT: J 405 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7356 (pttm) REVERT: J 464 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: J 470 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7651 (ttm) REVERT: J 475 MET cc_start: 0.8514 (mmm) cc_final: 0.8105 (tpp) REVERT: J 619 ASN cc_start: 0.6906 (m-40) cc_final: 0.6705 (m-40) REVERT: J 621 TYR cc_start: 0.6141 (m-80) cc_final: 0.5604 (m-10) REVERT: J 629 MET cc_start: 0.5406 (ppp) cc_final: 0.5083 (ppp) REVERT: J 741 TYR cc_start: 0.7192 (t80) cc_final: 0.6885 (t80) REVERT: J 750 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.4831 (mpp80) REVERT: J 784 LEU cc_start: 0.9250 (mt) cc_final: 0.8986 (mt) REVERT: J 927 ASN cc_start: 0.8152 (m-40) cc_final: 0.7818 (m-40) REVERT: J 1098 ARG cc_start: 0.6007 (mtm180) cc_final: 0.5339 (mtm180) REVERT: J 1173 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8080 (tp) REVERT: J 1189 PHE cc_start: 0.7975 (p90) cc_final: 0.7494 (p90) REVERT: J 1240 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8758 (mt) outliers start: 169 outliers final: 121 residues processed: 718 average time/residue: 0.1967 time to fit residues: 236.3402 Evaluate side-chains 694 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 558 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1171 ASP Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 279 TYR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 438 ASN Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 688 ASP Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 863 VAL Chi-restraints excluded: chain J residue 884 ILE Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1048 ILE Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1173 LEU Chi-restraints excluded: chain J residue 1238 ILE Chi-restraints excluded: chain J residue 1240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 56 optimal weight: 7.9990 chunk 379 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 359 optimal weight: 20.0000 chunk 465 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 432 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN J 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100903 restraints weight = 67253.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103316 restraints weight = 34575.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104821 restraints weight = 22569.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105589 restraints weight = 17513.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106130 restraints weight = 15278.587| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 40192 Z= 0.160 Angle : 0.598 16.895 54367 Z= 0.304 Chirality : 0.045 0.225 6133 Planarity : 0.004 0.065 6972 Dihedral : 4.576 51.239 5345 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.36 % Allowed : 18.17 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.12), residues: 4872 helix: 1.03 (0.12), residues: 2000 sheet: -0.46 (0.20), residues: 599 loop : -0.43 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 410 TYR 0.037 0.002 TYR J 430 PHE 0.026 0.002 PHE A 417 TRP 0.026 0.002 TRP A1129 HIS 0.006 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00375 (40158) covalent geometry : angle 0.59390 (54331) hydrogen bonds : bond 0.03836 ( 1751) hydrogen bonds : angle 4.74787 ( 4947) metal coordination : bond 0.00565 ( 34) metal coordination : angle 2.72820 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 602 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7223 (ptp-110) REVERT: A 119 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7217 (mmtm) REVERT: A 153 THR cc_start: 0.7772 (m) cc_final: 0.7500 (p) REVERT: A 266 LEU cc_start: 0.8877 (mt) cc_final: 0.8592 (mm) REVERT: A 403 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7769 (t0) REVERT: A 425 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8238 (ptm160) REVERT: A 461 ASP cc_start: 0.7623 (m-30) cc_final: 0.7412 (m-30) REVERT: A 499 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8712 (mp10) REVERT: A 558 MET cc_start: 0.8253 (mtp) cc_final: 0.7983 (mtm) REVERT: A 646 ASN cc_start: 0.9200 (p0) cc_final: 0.8938 (p0) REVERT: A 828 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8408 (mttp) REVERT: A 1057 MET cc_start: 0.8966 (tpt) cc_final: 0.8438 (tpt) REVERT: A 1079 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: A 1089 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6723 (mm-30) REVERT: A 1126 ILE cc_start: 0.8923 (mm) cc_final: 0.8587 (mt) REVERT: A 1155 MET cc_start: 0.7702 (mtt) cc_final: 0.6660 (mtp) REVERT: A 1240 MET cc_start: 0.2813 (mpp) cc_final: 0.1800 (ttm) REVERT: A 1329 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7241 (mm-30) REVERT: A 1355 MET cc_start: 0.8443 (tpp) cc_final: 0.8218 (tpp) REVERT: A 1356 TYR cc_start: 0.9027 (m-80) cc_final: 0.8492 (m-80) REVERT: B 51 MET cc_start: 0.8550 (mmm) cc_final: 0.8340 (mmm) REVERT: B 55 ILE cc_start: 0.9175 (mt) cc_final: 0.8880 (mt) REVERT: B 181 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 251 MET cc_start: 0.8506 (mpp) cc_final: 0.8234 (mpp) REVERT: B 270 ILE cc_start: 0.8933 (mt) cc_final: 0.8439 (mt) REVERT: B 294 ASP cc_start: 0.7326 (t0) cc_final: 0.6987 (t0) REVERT: B 325 HIS cc_start: 0.8035 (m90) cc_final: 0.7709 (m170) REVERT: B 354 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: B 390 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 413 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: B 482 MET cc_start: 0.8876 (tpp) cc_final: 0.8571 (tpp) REVERT: B 831 MET cc_start: 0.8672 (tpp) cc_final: 0.8345 (mmm) REVERT: B 894 GLU cc_start: 0.8216 (mp0) cc_final: 0.7492 (mp0) REVERT: B 932 ILE cc_start: 0.9448 (mm) cc_final: 0.8930 (tp) REVERT: B 982 MET cc_start: 0.8796 (ttm) cc_final: 0.8433 (ttp) REVERT: B 1042 MET cc_start: 0.8328 (mmm) cc_final: 0.7841 (mmt) REVERT: B 1083 ASN cc_start: 0.8958 (p0) cc_final: 0.8745 (p0) REVERT: B 1170 ASP cc_start: 0.7865 (m-30) cc_final: 0.7237 (m-30) REVERT: B 1182 ASN cc_start: 0.8841 (t0) cc_final: 0.8606 (t0) REVERT: B 1195 ILE cc_start: 0.8524 (mt) cc_final: 0.8217 (mm) REVERT: B 1212 SER cc_start: 0.8734 (t) cc_final: 0.8515 (m) REVERT: B 1224 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8358 (mtt-85) REVERT: C 103 TYR cc_start: 0.8199 (t80) cc_final: 0.7951 (t80) REVERT: C 270 PHE cc_start: 0.8284 (m-80) cc_final: 0.7992 (m-10) REVERT: C 319 MET cc_start: 0.8558 (tmm) cc_final: 0.8201 (tmm) REVERT: C 339 SER cc_start: 0.8814 (m) cc_final: 0.8491 (p) REVERT: D 80 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7533 (t0) REVERT: D 119 ASN cc_start: 0.8125 (m110) cc_final: 0.7859 (t0) REVERT: D 125 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7979 (tt) REVERT: D 155 TYR cc_start: 0.9183 (m-80) cc_final: 0.8953 (m-10) REVERT: D 168 ASP cc_start: 0.8831 (t70) cc_final: 0.8577 (t0) REVERT: E 49 PHE cc_start: 0.6843 (m-80) cc_final: 0.6282 (m-10) REVERT: E 109 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: F 70 MET cc_start: 0.8012 (ttm) cc_final: 0.7466 (ttm) REVERT: F 129 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7358 (tt) REVERT: F 322 ARG cc_start: 0.6952 (mmm160) cc_final: 0.6715 (mtm110) REVERT: F 333 ARG cc_start: 0.6411 (mpt-90) cc_final: 0.5385 (tpm170) REVERT: G 1 MET cc_start: 0.8296 (ppp) cc_final: 0.8034 (ppp) REVERT: H 33 MET cc_start: 0.8535 (ttp) cc_final: 0.8300 (ttp) REVERT: J 80 ARG cc_start: 0.5204 (ptt180) cc_final: 0.4991 (ptt180) REVERT: J 143 MET cc_start: 0.7816 (tmm) cc_final: 0.7392 (tmm) REVERT: J 299 VAL cc_start: 0.7537 (m) cc_final: 0.7125 (p) REVERT: J 372 LYS cc_start: 0.8442 (tppp) cc_final: 0.7915 (tptt) REVERT: J 396 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7996 (tm-30) REVERT: J 405 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7079 (pttm) REVERT: J 409 GLN cc_start: 0.7792 (mm110) cc_final: 0.7584 (mp10) REVERT: J 464 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: J 470 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7672 (ttm) REVERT: J 475 MET cc_start: 0.8205 (mmm) cc_final: 0.7972 (tpp) REVERT: J 621 TYR cc_start: 0.5758 (m-80) cc_final: 0.4242 (m-10) REVERT: J 629 MET cc_start: 0.5213 (ppp) cc_final: 0.4960 (ppp) REVERT: J 750 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.4794 (mpp80) REVERT: J 784 LEU cc_start: 0.9211 (mt) cc_final: 0.8937 (mt) REVERT: J 927 ASN cc_start: 0.8017 (m-40) cc_final: 0.7674 (m-40) REVERT: J 955 LEU cc_start: 0.8017 (tp) cc_final: 0.7563 (tp) REVERT: J 1098 ARG cc_start: 0.5933 (mtm180) cc_final: 0.5259 (mtm180) REVERT: J 1173 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8066 (tp) REVERT: J 1189 PHE cc_start: 0.7986 (p90) cc_final: 0.7583 (p90) REVERT: J 1240 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8790 (mt) outliers start: 147 outliers final: 106 residues processed: 705 average time/residue: 0.1903 time to fit residues: 223.6088 Evaluate side-chains 689 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 567 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 279 TYR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 688 ASP Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 863 VAL Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1048 ILE Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1173 LEU Chi-restraints excluded: chain J residue 1238 ILE Chi-restraints excluded: chain J residue 1240 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 219 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 473 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 439 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 662 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101509 restraints weight = 67162.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103902 restraints weight = 34591.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105407 restraints weight = 22634.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106235 restraints weight = 17513.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106802 restraints weight = 15189.079| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40192 Z= 0.144 Angle : 0.589 16.583 54367 Z= 0.298 Chirality : 0.045 0.240 6133 Planarity : 0.004 0.065 6972 Dihedral : 4.498 50.922 5345 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.24 % Allowed : 18.63 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 4872 helix: 1.08 (0.12), residues: 2004 sheet: -0.32 (0.21), residues: 586 loop : -0.40 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 258 TYR 0.035 0.001 TYR J 430 PHE 0.024 0.001 PHE A 417 TRP 0.022 0.001 TRP A1129 HIS 0.006 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00336 (40158) covalent geometry : angle 0.58588 (54331) hydrogen bonds : bond 0.03729 ( 1751) hydrogen bonds : angle 4.69948 ( 4947) metal coordination : bond 0.00517 ( 34) metal coordination : angle 2.57593 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 593 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7312 (ptp-110) REVERT: A 119 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7197 (mmtm) REVERT: A 153 THR cc_start: 0.7787 (m) cc_final: 0.7497 (p) REVERT: A 266 LEU cc_start: 0.8874 (mt) cc_final: 0.8590 (mm) REVERT: A 403 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7789 (t0) REVERT: A 425 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8234 (ptm160) REVERT: A 461 ASP cc_start: 0.7618 (m-30) cc_final: 0.7413 (m-30) REVERT: A 499 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8691 (mp10) REVERT: A 558 MET cc_start: 0.8225 (mtp) cc_final: 0.7976 (mtm) REVERT: A 646 ASN cc_start: 0.9118 (p0) cc_final: 0.8891 (p0) REVERT: A 828 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8416 (mttp) REVERT: A 1057 MET cc_start: 0.8956 (tpt) cc_final: 0.8422 (tpt) REVERT: A 1079 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: A 1089 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6738 (mm-30) REVERT: A 1126 ILE cc_start: 0.8922 (mm) cc_final: 0.8598 (mt) REVERT: A 1155 MET cc_start: 0.7690 (mtt) cc_final: 0.6658 (mtp) REVERT: A 1240 MET cc_start: 0.2603 (mpp) cc_final: 0.1597 (ttm) REVERT: A 1329 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 1349 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7921 (m-40) REVERT: A 1356 TYR cc_start: 0.9021 (m-80) cc_final: 0.8542 (m-80) REVERT: B 51 MET cc_start: 0.8513 (mmm) cc_final: 0.8213 (mmm) REVERT: B 55 ILE cc_start: 0.9155 (mt) cc_final: 0.8857 (mt) REVERT: B 181 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 251 MET cc_start: 0.8679 (mpp) cc_final: 0.8266 (mpp) REVERT: B 270 ILE cc_start: 0.8945 (mt) cc_final: 0.8429 (mt) REVERT: B 294 ASP cc_start: 0.7442 (t0) cc_final: 0.7080 (t0) REVERT: B 324 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: B 325 HIS cc_start: 0.8053 (m90) cc_final: 0.7703 (m170) REVERT: B 354 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: B 390 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8938 (tt) REVERT: B 413 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.7284 (m-80) REVERT: B 482 MET cc_start: 0.8891 (tpp) cc_final: 0.8595 (tpp) REVERT: B 831 MET cc_start: 0.8643 (tpp) cc_final: 0.8303 (mmm) REVERT: B 894 GLU cc_start: 0.8197 (mp0) cc_final: 0.7587 (mp0) REVERT: B 932 ILE cc_start: 0.9441 (mm) cc_final: 0.8933 (tp) REVERT: B 982 MET cc_start: 0.8793 (ttm) cc_final: 0.8449 (ttp) REVERT: B 1042 MET cc_start: 0.8336 (mmm) cc_final: 0.7802 (mmt) REVERT: B 1083 ASN cc_start: 0.8912 (p0) cc_final: 0.8696 (p0) REVERT: B 1170 ASP cc_start: 0.7758 (m-30) cc_final: 0.7199 (m-30) REVERT: B 1182 ASN cc_start: 0.8837 (t0) cc_final: 0.8612 (t0) REVERT: B 1195 ILE cc_start: 0.8562 (mt) cc_final: 0.8318 (mm) REVERT: B 1212 SER cc_start: 0.8736 (t) cc_final: 0.8525 (m) REVERT: B 1224 ARG cc_start: 0.8771 (mtt90) cc_final: 0.8358 (mtt-85) REVERT: C 103 TYR cc_start: 0.8163 (t80) cc_final: 0.7910 (t80) REVERT: C 270 PHE cc_start: 0.8275 (m-80) cc_final: 0.7965 (m-10) REVERT: C 319 MET cc_start: 0.8588 (tmm) cc_final: 0.8241 (tmm) REVERT: C 339 SER cc_start: 0.8785 (m) cc_final: 0.8467 (p) REVERT: D 80 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7357 (t0) REVERT: D 119 ASN cc_start: 0.8142 (m110) cc_final: 0.7842 (t0) REVERT: D 125 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7987 (tt) REVERT: D 155 TYR cc_start: 0.9188 (m-80) cc_final: 0.8930 (m-80) REVERT: D 168 ASP cc_start: 0.8830 (t70) cc_final: 0.8608 (t0) REVERT: E 109 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: F 70 MET cc_start: 0.8018 (ttm) cc_final: 0.7470 (ttm) REVERT: F 231 MET cc_start: 0.5518 (tpp) cc_final: 0.5294 (tpt) REVERT: F 333 ARG cc_start: 0.6406 (mpt-90) cc_final: 0.5409 (tpm170) REVERT: G 83 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8791 (pp30) REVERT: H 33 MET cc_start: 0.8466 (ttp) cc_final: 0.8252 (ttp) REVERT: J 80 ARG cc_start: 0.5161 (ptt180) cc_final: 0.4952 (ptt180) REVERT: J 143 MET cc_start: 0.7817 (tmm) cc_final: 0.7386 (tmm) REVERT: J 299 VAL cc_start: 0.7509 (m) cc_final: 0.7120 (p) REVERT: J 372 LYS cc_start: 0.8360 (tppp) cc_final: 0.7837 (tptt) REVERT: J 396 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8074 (tm-30) REVERT: J 405 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7275 (pttm) REVERT: J 464 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: J 470 MET cc_start: 0.7993 (ttm) cc_final: 0.7663 (ttm) REVERT: J 475 MET cc_start: 0.8146 (mmm) cc_final: 0.7940 (tpp) REVERT: J 621 TYR cc_start: 0.5878 (m-80) cc_final: 0.4293 (m-10) REVERT: J 629 MET cc_start: 0.5299 (ppp) cc_final: 0.5004 (ppp) REVERT: J 750 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.4815 (mpp80) REVERT: J 784 LEU cc_start: 0.9135 (mt) cc_final: 0.8895 (mt) REVERT: J 927 ASN cc_start: 0.7830 (m-40) cc_final: 0.7493 (m-40) REVERT: J 955 LEU cc_start: 0.7951 (tp) cc_final: 0.7659 (tp) REVERT: J 1098 ARG cc_start: 0.6036 (mtm180) cc_final: 0.5197 (mtm180) REVERT: J 1173 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8062 (tp) REVERT: J 1189 PHE cc_start: 0.7971 (p90) cc_final: 0.7535 (p90) outliers start: 142 outliers final: 113 residues processed: 693 average time/residue: 0.2109 time to fit residues: 243.5495 Evaluate side-chains 697 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 569 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain J residue 276 THR Chi-restraints excluded: chain J residue 279 TYR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 688 ASP Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 863 VAL Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1048 ILE Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1173 LEU Chi-restraints excluded: chain J residue 1238 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 95 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 357 optimal weight: 20.0000 chunk 389 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN B 403 ASN B 604 ASN B 975 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100926 restraints weight = 67889.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103339 restraints weight = 34977.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104838 restraints weight = 22791.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105674 restraints weight = 17689.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106251 restraints weight = 15310.938| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40192 Z= 0.164 Angle : 0.602 16.413 54367 Z= 0.306 Chirality : 0.045 0.242 6133 Planarity : 0.004 0.067 6972 Dihedral : 4.515 50.350 5345 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.22 % Allowed : 18.74 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.12), residues: 4872 helix: 1.08 (0.12), residues: 1993 sheet: -0.32 (0.21), residues: 586 loop : -0.40 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 322 TYR 0.033 0.002 TYR J 430 PHE 0.024 0.002 PHE C 5 TRP 0.027 0.002 TRP A1129 HIS 0.005 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00387 (40158) covalent geometry : angle 0.59875 (54331) hydrogen bonds : bond 0.03790 ( 1751) hydrogen bonds : angle 4.72187 ( 4947) metal coordination : bond 0.00594 ( 34) metal coordination : angle 2.62358 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 575 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7310 (ptp-110) REVERT: A 119 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7194 (mmtm) REVERT: A 153 THR cc_start: 0.7770 (m) cc_final: 0.7493 (p) REVERT: A 266 LEU cc_start: 0.8879 (mt) cc_final: 0.8594 (mm) REVERT: A 403 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7775 (t0) REVERT: A 425 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8231 (ptm160) REVERT: A 499 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8718 (mp10) REVERT: A 558 MET cc_start: 0.8210 (mtp) cc_final: 0.7957 (mtm) REVERT: A 646 ASN cc_start: 0.9061 (p0) cc_final: 0.8845 (p0) REVERT: A 828 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8409 (mttp) REVERT: A 1057 MET cc_start: 0.8944 (tpt) cc_final: 0.8403 (tpt) REVERT: A 1079 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 1089 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6705 (mm-30) REVERT: A 1126 ILE cc_start: 0.8949 (mm) cc_final: 0.8658 (mt) REVERT: A 1240 MET cc_start: 0.2818 (mpp) cc_final: 0.1937 (ttm) REVERT: A 1329 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 1349 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: A 1356 TYR cc_start: 0.9007 (m-80) cc_final: 0.8501 (m-80) REVERT: B 51 MET cc_start: 0.8361 (mmm) cc_final: 0.8034 (mmm) REVERT: B 55 ILE cc_start: 0.9156 (mt) cc_final: 0.8857 (mt) REVERT: B 251 MET cc_start: 0.8711 (mpp) cc_final: 0.8432 (mpp) REVERT: B 270 ILE cc_start: 0.8975 (mt) cc_final: 0.8468 (mt) REVERT: B 294 ASP cc_start: 0.7414 (t0) cc_final: 0.7074 (t0) REVERT: B 324 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: B 325 HIS cc_start: 0.8071 (m90) cc_final: 0.7720 (m170) REVERT: B 354 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: B 390 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 413 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: B 482 MET cc_start: 0.8878 (tpp) cc_final: 0.8622 (tpp) REVERT: B 894 GLU cc_start: 0.8286 (mp0) cc_final: 0.7557 (mp0) REVERT: B 932 ILE cc_start: 0.9445 (mm) cc_final: 0.8944 (tp) REVERT: B 982 MET cc_start: 0.8785 (ttm) cc_final: 0.8452 (ttp) REVERT: B 1042 MET cc_start: 0.8336 (mmm) cc_final: 0.7794 (mmt) REVERT: B 1170 ASP cc_start: 0.7612 (m-30) cc_final: 0.7017 (m-30) REVERT: B 1182 ASN cc_start: 0.8832 (t0) cc_final: 0.8603 (t0) REVERT: B 1195 ILE cc_start: 0.8582 (mt) cc_final: 0.8341 (mm) REVERT: B 1212 SER cc_start: 0.8757 (t) cc_final: 0.8551 (m) REVERT: B 1224 ARG cc_start: 0.8757 (mtt90) cc_final: 0.8311 (mtt-85) REVERT: C 103 TYR cc_start: 0.8170 (t80) cc_final: 0.7901 (t80) REVERT: C 270 PHE cc_start: 0.8294 (m-80) cc_final: 0.7975 (m-10) REVERT: C 319 MET cc_start: 0.8592 (tmm) cc_final: 0.8244 (tmm) REVERT: C 339 SER cc_start: 0.9006 (m) cc_final: 0.8645 (p) REVERT: D 80 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7382 (t0) REVERT: D 119 ASN cc_start: 0.8134 (m110) cc_final: 0.7843 (t0) REVERT: D 123 TYR cc_start: 0.8766 (m-10) cc_final: 0.8090 (m-10) REVERT: D 125 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7997 (tt) REVERT: D 155 TYR cc_start: 0.9176 (m-80) cc_final: 0.8925 (m-80) REVERT: D 168 ASP cc_start: 0.8829 (t70) cc_final: 0.8621 (t0) REVERT: E 109 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: F 70 MET cc_start: 0.8033 (ttm) cc_final: 0.7490 (ttm) REVERT: F 231 MET cc_start: 0.5517 (tpp) cc_final: 0.5308 (tpt) REVERT: F 333 ARG cc_start: 0.6399 (mpt-90) cc_final: 0.5504 (tpm170) REVERT: G 83 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8786 (pp30) REVERT: J 143 MET cc_start: 0.7821 (tmm) cc_final: 0.7407 (tmm) REVERT: J 299 VAL cc_start: 0.7889 (m) cc_final: 0.7477 (p) REVERT: J 372 LYS cc_start: 0.8340 (tppp) cc_final: 0.7827 (tptt) REVERT: J 396 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7981 (tm-30) REVERT: J 405 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7286 (pttm) REVERT: J 464 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: J 470 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7654 (ttm) REVERT: J 621 TYR cc_start: 0.5605 (m-80) cc_final: 0.4153 (m-10) REVERT: J 629 MET cc_start: 0.5198 (ppp) cc_final: 0.4953 (ppp) REVERT: J 750 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.4783 (mpp80) REVERT: J 784 LEU cc_start: 0.9145 (mt) cc_final: 0.8908 (mt) REVERT: J 927 ASN cc_start: 0.7799 (m-40) cc_final: 0.7448 (m-40) REVERT: J 955 LEU cc_start: 0.7953 (tp) cc_final: 0.7573 (tp) REVERT: J 1173 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8081 (tp) REVERT: J 1189 PHE cc_start: 0.7992 (p90) cc_final: 0.7565 (p90) outliers start: 141 outliers final: 120 residues processed: 674 average time/residue: 0.2003 time to fit residues: 224.1151 Evaluate side-chains 693 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 557 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain J residue 279 TYR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 688 ASP Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 863 VAL Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1048 ILE Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1173 LEU Chi-restraints excluded: chain J residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 296 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 481 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 239 optimal weight: 0.0270 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1240 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100578 restraints weight = 67778.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102784 restraints weight = 35141.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103201 restraints weight = 22540.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103897 restraints weight = 20830.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103926 restraints weight = 18087.254| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 40192 Z= 0.207 Angle : 0.641 17.171 54367 Z= 0.325 Chirality : 0.046 0.250 6133 Planarity : 0.004 0.065 6972 Dihedral : 4.614 49.489 5345 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.26 % Allowed : 18.90 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.12), residues: 4872 helix: 0.97 (0.12), residues: 1998 sheet: -0.35 (0.21), residues: 587 loop : -0.45 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 322 TYR 0.029 0.002 TYR B 104 PHE 0.028 0.002 PHE A 417 TRP 0.025 0.002 TRP A1129 HIS 0.005 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00490 (40158) covalent geometry : angle 0.63677 (54331) hydrogen bonds : bond 0.03985 ( 1751) hydrogen bonds : angle 4.79805 ( 4947) metal coordination : bond 0.00785 ( 34) metal coordination : angle 2.86730 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 563 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7330 (ptp-110) REVERT: A 119 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7228 (mmtm) REVERT: A 153 THR cc_start: 0.7781 (m) cc_final: 0.7489 (p) REVERT: A 266 LEU cc_start: 0.8873 (mt) cc_final: 0.8620 (mm) REVERT: A 363 MET cc_start: 0.9202 (mmm) cc_final: 0.8490 (mmm) REVERT: A 403 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7773 (t0) REVERT: A 416 PHE cc_start: 0.9048 (m-80) cc_final: 0.8563 (m-80) REVERT: A 425 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: A 499 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8802 (mp10) REVERT: A 558 MET cc_start: 0.8230 (mtp) cc_final: 0.8017 (mtm) REVERT: A 646 ASN cc_start: 0.9015 (p0) cc_final: 0.8801 (p0) REVERT: A 828 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8425 (mttp) REVERT: A 1057 MET cc_start: 0.8944 (tpt) cc_final: 0.8410 (tpt) REVERT: A 1079 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: A 1089 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6669 (mm-30) REVERT: A 1126 ILE cc_start: 0.8974 (mm) cc_final: 0.8684 (mt) REVERT: A 1240 MET cc_start: 0.3232 (mpp) cc_final: 0.2063 (ttm) REVERT: A 1329 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 1349 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7984 (m110) REVERT: A 1356 TYR cc_start: 0.9022 (m-80) cc_final: 0.8569 (m-80) REVERT: B 51 MET cc_start: 0.8358 (mmm) cc_final: 0.8043 (mmm) REVERT: B 55 ILE cc_start: 0.9177 (mt) cc_final: 0.8876 (mt) REVERT: B 251 MET cc_start: 0.8694 (mpp) cc_final: 0.8469 (mpp) REVERT: B 270 ILE cc_start: 0.9011 (mt) cc_final: 0.8512 (mt) REVERT: B 294 ASP cc_start: 0.7352 (t0) cc_final: 0.7004 (t0) REVERT: B 324 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: B 325 HIS cc_start: 0.8129 (m90) cc_final: 0.7778 (m170) REVERT: B 354 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: B 390 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8993 (tt) REVERT: B 413 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: B 482 MET cc_start: 0.9088 (tpp) cc_final: 0.8884 (tpp) REVERT: B 890 GLU cc_start: 0.5818 (mp0) cc_final: 0.5418 (mp0) REVERT: B 894 GLU cc_start: 0.8287 (mp0) cc_final: 0.7530 (mp0) REVERT: B 932 ILE cc_start: 0.9450 (mm) cc_final: 0.8948 (tp) REVERT: B 982 MET cc_start: 0.8775 (ttm) cc_final: 0.8414 (ttp) REVERT: B 1042 MET cc_start: 0.8328 (mmm) cc_final: 0.7870 (mmt) REVERT: B 1170 ASP cc_start: 0.7783 (m-30) cc_final: 0.7219 (m-30) REVERT: B 1195 ILE cc_start: 0.8660 (mt) cc_final: 0.8417 (mm) REVERT: B 1212 SER cc_start: 0.8797 (t) cc_final: 0.8569 (m) REVERT: B 1224 ARG cc_start: 0.8765 (mtt90) cc_final: 0.8332 (mtt-85) REVERT: C 30 PHE cc_start: 0.8397 (m-80) cc_final: 0.8079 (m-10) REVERT: C 270 PHE cc_start: 0.8367 (m-80) cc_final: 0.8070 (m-10) REVERT: C 319 MET cc_start: 0.8610 (tmm) cc_final: 0.8250 (tmm) REVERT: C 339 SER cc_start: 0.9055 (m) cc_final: 0.8697 (p) REVERT: D 1 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4268 (tmm) REVERT: D 31 PHE cc_start: 0.8330 (t80) cc_final: 0.8118 (t80) REVERT: D 33 GLN cc_start: 0.8092 (tp40) cc_final: 0.7863 (pt0) REVERT: D 80 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7705 (t0) REVERT: D 119 ASN cc_start: 0.8169 (m110) cc_final: 0.7890 (t0) REVERT: D 125 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7965 (tt) REVERT: D 155 TYR cc_start: 0.9195 (m-80) cc_final: 0.8948 (m-80) REVERT: F 70 MET cc_start: 0.8005 (ttm) cc_final: 0.7474 (ttm) REVERT: F 333 ARG cc_start: 0.6428 (mpt-90) cc_final: 0.5463 (tpm170) REVERT: J 80 ARG cc_start: 0.4593 (ptt180) cc_final: 0.4015 (ptt180) REVERT: J 143 MET cc_start: 0.7855 (tmm) cc_final: 0.7468 (tmm) REVERT: J 299 VAL cc_start: 0.8135 (m) cc_final: 0.7624 (p) REVERT: J 372 LYS cc_start: 0.8494 (tppp) cc_final: 0.7944 (tptt) REVERT: J 396 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8142 (tm-30) REVERT: J 464 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: J 470 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7810 (ttm) REVERT: J 621 TYR cc_start: 0.5887 (m-80) cc_final: 0.4282 (m-10) REVERT: J 629 MET cc_start: 0.5361 (ppp) cc_final: 0.5037 (ppp) REVERT: J 750 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.4806 (mpp80) REVERT: J 784 LEU cc_start: 0.9223 (mt) cc_final: 0.8944 (mt) REVERT: J 927 ASN cc_start: 0.7842 (m-40) cc_final: 0.7511 (m-40) REVERT: J 955 LEU cc_start: 0.8146 (tp) cc_final: 0.7745 (tp) REVERT: J 1098 ARG cc_start: 0.6214 (mtm180) cc_final: 0.5387 (mtm110) REVERT: J 1189 PHE cc_start: 0.7885 (p90) cc_final: 0.7419 (p90) outliers start: 143 outliers final: 115 residues processed: 660 average time/residue: 0.1984 time to fit residues: 217.8526 Evaluate side-chains 674 residues out of total 4382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 544 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1269 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1217 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 209 PHE Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain J residue 279 TYR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 688 ASP Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 816 LEU Chi-restraints excluded: chain J residue 863 VAL Chi-restraints excluded: chain J residue 924 LEU Chi-restraints excluded: chain J residue 984 GLU Chi-restraints excluded: chain J residue 1048 ILE Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1129 LEU Chi-restraints excluded: chain J residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 278 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 319 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 408 optimal weight: 7.9990 chunk 444 optimal weight: 0.0570 chunk 98 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 469 optimal weight: 7.9990 chunk 383 optimal weight: 8.9990 overall best weight: 2.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101600 restraints weight = 67730.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104037 restraints weight = 34946.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105547 restraints weight = 22755.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106378 restraints weight = 17556.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106897 restraints weight = 15214.306| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40192 Z= 0.135 Angle : 0.596 16.871 54367 Z= 0.302 Chirality : 0.045 0.251 6133 Planarity : 0.004 0.066 6972 Dihedral : 4.499 50.059 5345 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.90 % Allowed : 19.36 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.12), residues: 4872 helix: 1.10 (0.12), residues: 2000 sheet: -0.32 (0.21), residues: 591 loop : -0.39 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 410 TYR 0.026 0.001 TYR B 104 PHE 0.023 0.001 PHE C 5 TRP 0.030 0.002 TRP A1129 HIS 0.005 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00317 (40158) covalent geometry : angle 0.59298 (54331) hydrogen bonds : bond 0.03661 ( 1751) hydrogen bonds : angle 4.69471 ( 4947) metal coordination : bond 0.00440 ( 34) metal coordination : angle 2.48818 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.31 seconds wall clock time: 115 minutes 52.11 seconds (6952.11 seconds total)