Starting phenix.real_space_refine on Sun Feb 8 08:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7amv_11824/02_2026/7amv_11824_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7amv_11824/02_2026/7amv_11824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7amv_11824/02_2026/7amv_11824_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7amv_11824/02_2026/7amv_11824_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7amv_11824/02_2026/7amv_11824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7amv_11824/02_2026/7amv_11824.map" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.010 sd= 1.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 84 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 28784 2.51 5 N 7488 2.21 5 O 8608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45172 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1248, 10017 Classifications: {'peptide': 1248} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1204} Chain breaks: 2 Chain: "B" Number of atoms: 9060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 9060 Classifications: {'peptide': 1126} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1073} Chain breaks: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1233 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "I" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5807 Classifications: {'peptide': 694} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 670} Chain breaks: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "K" Number of atoms: 5776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5776 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 25, 'TRANS': 682} Chain: "N" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 861 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "S" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1036 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "T" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 861 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "W" Number of atoms: 5207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5207 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 21, 'TRANS': 615} 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 120.050 103.506 55.877 1.00103.12 S ATOM 382 SG CYS A 52 123.783 104.045 55.236 1.00 95.09 S ATOM 434 SG CYS A 59 122.608 100.850 56.928 1.00 90.50 S ATOM 694 SG CYS A 90 105.183 106.351 102.294 1.00106.28 S ATOM 718 SG CYS A 93 107.041 109.707 102.916 1.00107.20 S ATOM 1016 SG CYS A 130 106.990 108.284 105.806 1.00112.09 S ATOM 18486 SG CYS B1087 130.498 107.091 69.954 1.00 74.97 S ATOM 18509 SG CYS B1090 127.171 105.596 71.069 1.00 76.21 S ATOM 18598 SG CYS B1103 127.338 107.713 67.896 1.00 79.87 S ATOM 18623 SG CYS B1106 127.828 109.323 71.333 1.00 79.17 S ATOM 30984 SG CYS J 7 129.368 32.024 39.885 1.00 54.34 S ATOM 31003 SG CYS J 10 132.724 30.497 38.713 1.00 56.50 S ATOM 31240 SG CYS J 39 131.301 29.549 42.102 1.00 57.88 S ATOM 31246 SG CYS J 40 129.752 28.394 38.732 1.00 58.10 S Time building chain proxies: 10.36, per 1000 atoms: 0.23 Number of scatterers: 45172 At special positions: 0 Unit cell: (193.241, 159.487, 175.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 203 16.00 P 84 15.00 Mg 1 11.99 O 8608 8.00 N 7488 7.00 C 28784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 444 " distance=2.03 Simple disulfide: pdb=" SG CYS K 418 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 441 " - pdb=" SG CYS K 459 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 15 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10254 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 64 sheets defined 43.6% alpha, 17.7% beta 19 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.577A pdb=" N GLY A 42 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.632A pdb=" N LYS A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.616A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 219 through 231 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.738A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.975A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 489 removed outlier: 4.049A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 489 " --> pdb=" O TYR A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.885A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 586 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.747A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.669A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.576A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.273A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.567A pdb=" N ASN A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.523A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 4.070A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1171 removed outlier: 3.925A pdb=" N TYR A1171 " --> pdb=" O MET A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 3.952A pdb=" N ASP A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.751A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.800A pdb=" N MET A1264 " --> pdb=" O LEU A1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.532A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.557A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.590A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 361 through 393 removed outlier: 3.576A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.676A pdb=" N LEU B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 465 through 470 removed outlier: 4.769A pdb=" N TYR B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 removed outlier: 3.829A pdb=" N TYR B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.924A pdb=" N GLU B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 643 through 650 Processing helix chain 'B' and resid 651 through 656 removed outlier: 4.131A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.813A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.522A pdb=" N SER B 675 " --> pdb=" O TYR B 671 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.892A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 783 through 789 Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 916 through 923 removed outlier: 4.097A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.126A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.612A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 991 Processing helix chain 'B' and resid 1021 through 1026 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.984A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.857A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.903A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.655A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.908A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 Processing helix chain 'E' and resid 98 through 101 removed outlier: 3.558A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.733A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.516A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 3 through 10 removed outlier: 4.207A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.547A pdb=" N LEU I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.849A pdb=" N SER I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG I 35 " --> pdb=" O ASP I 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN I 36 " --> pdb=" O PHE I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 40 removed outlier: 3.987A pdb=" N PHE I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 37 through 40' Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.987A pdb=" N TYR I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 65 Processing helix chain 'I' and resid 69 through 78 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.962A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 192 Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.744A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 270 through 272 No H-bonds generated for 'chain 'I' and resid 270 through 272' Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 327 through 336 removed outlier: 3.684A pdb=" N ARG I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 406 through 421 Processing helix chain 'I' and resid 428 through 454 removed outlier: 5.761A pdb=" N GLN I 448 " --> pdb=" O ASN I 444 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU I 449 " --> pdb=" O SER I 445 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 502 Processing helix chain 'I' and resid 503 through 514 removed outlier: 3.629A pdb=" N ILE I 507 " --> pdb=" O SER I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 538 Processing helix chain 'I' and resid 545 through 558 Processing helix chain 'I' and resid 561 through 581 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 689 through 694 removed outlier: 4.121A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 Processing helix chain 'I' and resid 773 through 794 removed outlier: 5.854A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 62 through 75 Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 140 through 144 Processing helix chain 'K' and resid 150 through 164 removed outlier: 3.706A pdb=" N ILE K 154 " --> pdb=" O ASP K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 200 Processing helix chain 'K' and resid 254 through 262 Processing helix chain 'K' and resid 293 through 298 removed outlier: 4.404A pdb=" N PHE K 298 " --> pdb=" O GLU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 315 No H-bonds generated for 'chain 'K' and resid 313 through 315' Processing helix chain 'K' and resid 335 through 352 removed outlier: 3.580A pdb=" N TYR K 339 " --> pdb=" O ASN K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 372 Processing helix chain 'K' and resid 411 through 413 No H-bonds generated for 'chain 'K' and resid 411 through 413' Processing helix chain 'K' and resid 431 through 439 removed outlier: 3.768A pdb=" N HIS K 435 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 461 Processing helix chain 'K' and resid 490 through 498 Processing helix chain 'K' and resid 534 through 546 Processing helix chain 'K' and resid 560 through 564 removed outlier: 3.560A pdb=" N ILE K 564 " --> pdb=" O ALA K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 598 through 603 Processing helix chain 'K' and resid 652 through 664 Proline residue: K 661 - end of helix Processing helix chain 'K' and resid 670 through 686 removed outlier: 3.569A pdb=" N PHE K 674 " --> pdb=" O ALA K 670 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS K 685 " --> pdb=" O ASN K 681 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET K 686 " --> pdb=" O ILE K 682 " (cutoff:3.500A) Processing helix chain 'K' and resid 692 through 701 removed outlier: 3.598A pdb=" N THR K 696 " --> pdb=" O ASN K 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 706 Processing helix chain 'S' and resid 24 through 32 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 69 through 79 removed outlier: 4.393A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 85 removed outlier: 3.648A pdb=" N ASN S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 109 removed outlier: 3.962A pdb=" N LYS S 108 " --> pdb=" O CYS S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.540A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 139 Processing helix chain 'S' and resid 144 through 149 removed outlier: 3.646A pdb=" N PHE S 148 " --> pdb=" O TYR S 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 9 removed outlier: 3.771A pdb=" N ILE W 6 " --> pdb=" O ASN W 2 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE W 9 " --> pdb=" O ILE W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 38 removed outlier: 3.572A pdb=" N ILE W 35 " --> pdb=" O VAL W 31 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 49 No H-bonds generated for 'chain 'W' and resid 47 through 49' Processing helix chain 'W' and resid 50 through 63 removed outlier: 3.510A pdb=" N ILE W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 74 through 92 Processing helix chain 'W' and resid 97 through 99 No H-bonds generated for 'chain 'W' and resid 97 through 99' Processing helix chain 'W' and resid 106 through 115 removed outlier: 3.948A pdb=" N ASN W 115 " --> pdb=" O SER W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 127 Processing helix chain 'W' and resid 136 through 140 Processing helix chain 'W' and resid 143 through 157 Processing helix chain 'W' and resid 172 through 183 removed outlier: 3.803A pdb=" N GLY W 176 " --> pdb=" O PRO W 172 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 202 Processing helix chain 'W' and resid 205 through 216 Processing helix chain 'W' and resid 251 through 264 Processing helix chain 'W' and resid 273 through 281 removed outlier: 3.673A pdb=" N ASN W 277 " --> pdb=" O LYS W 273 " (cutoff:3.500A) Processing helix chain 'W' and resid 284 through 289 removed outlier: 3.704A pdb=" N LEU W 288 " --> pdb=" O GLY W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 297 removed outlier: 4.317A pdb=" N PHE W 296 " --> pdb=" O LEU W 292 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 322 Processing helix chain 'W' and resid 325 through 336 removed outlier: 3.834A pdb=" N GLN W 336 " --> pdb=" O ILE W 332 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 363 removed outlier: 4.217A pdb=" N LYS W 357 " --> pdb=" O GLY W 353 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR W 358 " --> pdb=" O LEU W 354 " (cutoff:3.500A) Processing helix chain 'W' and resid 390 through 394 removed outlier: 3.506A pdb=" N LYS W 394 " --> pdb=" O SER W 391 " (cutoff:3.500A) Processing helix chain 'W' and resid 396 through 405 removed outlier: 3.650A pdb=" N LEU W 400 " --> pdb=" O SER W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 444 through 454 Processing helix chain 'W' and resid 479 through 483 removed outlier: 3.975A pdb=" N ASP W 482 " --> pdb=" O ASP W 479 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 498 removed outlier: 3.514A pdb=" N ILE W 496 " --> pdb=" O GLN W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 500 through 526 Processing helix chain 'W' and resid 538 through 554 removed outlier: 3.962A pdb=" N ASN W 553 " --> pdb=" O GLN W 549 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN W 554 " --> pdb=" O PHE W 550 " (cutoff:3.500A) Processing helix chain 'W' and resid 561 through 570 Processing helix chain 'W' and resid 574 through 589 Processing helix chain 'W' and resid 627 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.236A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 282 removed outlier: 4.038A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.570A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.245A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 removed outlier: 3.673A pdb=" N GLY A 684 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.555A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB3, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB4, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB6, first strand: chain 'A' and resid 1006 through 1012 Processing sheet with id=AB7, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.878A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.878A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.887A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.887A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.714A pdb=" N LEU B 170 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.950A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.453A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.761A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.761A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP J 61 " --> pdb=" O VAL B 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD2, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.870A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1084 through 1087 removed outlier: 4.528A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD5, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'C' and resid 37 through 43 removed outlier: 4.942A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.680A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.679A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AE2, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.453A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 90 removed outlier: 7.477A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 114 through 118 Processing sheet with id=AE5, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.183A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 161 through 166 Processing sheet with id=AE7, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AE8, first strand: chain 'I' and resid 354 through 357 Processing sheet with id=AE9, first strand: chain 'I' and resid 656 through 659 Processing sheet with id=AF1, first strand: chain 'I' and resid 668 through 671 Processing sheet with id=AF2, first strand: chain 'K' and resid 51 through 53 removed outlier: 3.653A pdb=" N VAL K 53 " --> pdb=" O TYR K 24 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU K 9 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL K 132 " --> pdb=" O LEU K 9 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU K 11 " --> pdb=" O VAL K 132 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG K 134 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N VAL K 13 " --> pdb=" O ARG K 134 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 91 through 92 Processing sheet with id=AF4, first strand: chain 'K' and resid 171 through 176 removed outlier: 3.725A pdb=" N THR K 277 " --> pdb=" O LYS K 176 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 269 through 271 Processing sheet with id=AF6, first strand: chain 'K' and resid 362 through 363 Processing sheet with id=AF7, first strand: chain 'K' and resid 399 through 401 Processing sheet with id=AF8, first strand: chain 'K' and resid 427 through 430 Processing sheet with id=AF9, first strand: chain 'K' and resid 474 through 475 Processing sheet with id=AG1, first strand: chain 'K' and resid 504 through 505 removed outlier: 6.793A pdb=" N ASN K 504 " --> pdb=" O LYS K 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY K 517 " --> pdb=" O VAL K 582 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL K 582 " --> pdb=" O GLY K 517 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS K 519 " --> pdb=" O MET K 580 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET K 580 " --> pdb=" O HIS K 519 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL K 521 " --> pdb=" O GLU K 578 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU K 578 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS K 523 " --> pdb=" O VAL K 576 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N VAL K 576 " --> pdb=" O CYS K 523 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 504 through 505 removed outlier: 6.793A pdb=" N ASN K 504 " --> pdb=" O LYS K 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY K 517 " --> pdb=" O VAL K 582 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL K 582 " --> pdb=" O GLY K 517 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS K 519 " --> pdb=" O MET K 580 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET K 580 " --> pdb=" O HIS K 519 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL K 521 " --> pdb=" O GLU K 578 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU K 578 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS K 523 " --> pdb=" O VAL K 576 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N VAL K 576 " --> pdb=" O CYS K 523 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE K 568 " --> pdb=" O VAL K 579 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE K 548 " --> pdb=" O HIS K 569 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU K 571 " --> pdb=" O ILE K 548 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE K 550 " --> pdb=" O LEU K 571 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP W 623 " --> pdb=" O PHE K 557 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 613 through 617 Processing sheet with id=AG4, first strand: chain 'W' and resid 101 through 105 removed outlier: 6.499A pdb=" N LYS W 67 " --> pdb=" O ILE W 131 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE W 133 " --> pdb=" O LYS W 67 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR W 69 " --> pdb=" O ILE W 133 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N LEU W 161 " --> pdb=" O SER W 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE W 132 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU W 163 " --> pdb=" O PHE W 132 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL W 134 " --> pdb=" O LEU W 163 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL W 41 " --> pdb=" O LEU W 162 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU W 42 " --> pdb=" O SER W 221 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR W 223 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE W 44 " --> pdb=" O TYR W 223 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 193 through 194 removed outlier: 3.954A pdb=" N LEU W 203 " --> pdb=" O SER W 194 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 233 through 236 removed outlier: 4.796A pdb=" N LEU W 472 " --> pdb=" O HIS W 236 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG W 244 " --> pdb=" O VAL W 470 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU W 472 " --> pdb=" O ARG W 244 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 233 through 236 removed outlier: 4.796A pdb=" N LEU W 472 " --> pdb=" O HIS W 236 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR W 385 " --> pdb=" O PHE W 417 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE W 419 " --> pdb=" O THR W 385 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA W 387 " --> pdb=" O PHE W 419 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER W 366 " --> pdb=" O PHE W 386 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ILE W 388 " --> pdb=" O SER W 366 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 302 through 304 removed outlier: 5.187A pdb=" N GLU W 302 " --> pdb=" O ILE W 309 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE W 309 " --> pdb=" O GLU W 302 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 378 through 379 removed outlier: 3.677A pdb=" N LYS W 382 " --> pdb=" O ILE W 379 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 557 through 558 1958 hydrogen bonds defined for protein. 5403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 13.68 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13869 1.34 - 1.46: 8271 1.46 - 1.58: 23625 1.58 - 1.70: 164 1.70 - 1.82: 332 Bond restraints: 46261 Sorted by residual: bond pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.67e+00 bond pdb=" C3' DG N 59 " pdb=" O3' DG N 59 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.48e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" C3' DA N 10 " pdb=" O3' DA N 10 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.77e+00 ... (remaining 46256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 61681 1.52 - 3.03: 980 3.03 - 4.55: 206 4.55 - 6.06: 38 6.06 - 7.58: 2 Bond angle restraints: 62907 Sorted by residual: angle pdb=" CA VAL B 475 " pdb=" C VAL B 475 " pdb=" N PRO B 476 " ideal model delta sigma weight residual 116.57 119.68 -3.11 9.80e-01 1.04e+00 1.01e+01 angle pdb=" O3' DC N 54 " pdb=" C3' DC N 54 " pdb=" C2' DC N 54 " ideal model delta sigma weight residual 111.50 116.24 -4.74 1.50e+00 4.44e-01 9.97e+00 angle pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " pdb=" P DT T 13 " ideal model delta sigma weight residual 120.20 124.54 -4.34 1.50e+00 4.44e-01 8.39e+00 angle pdb=" N GLY K 14 " pdb=" CA GLY K 14 " pdb=" C GLY K 14 " ideal model delta sigma weight residual 112.13 115.99 -3.86 1.34e+00 5.57e-01 8.29e+00 angle pdb=" N LYS B1098 " pdb=" CA LYS B1098 " pdb=" C LYS B1098 " ideal model delta sigma weight residual 110.88 107.25 3.63 1.28e+00 6.10e-01 8.04e+00 ... (remaining 62902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 27423 35.10 - 70.21: 403 70.21 - 105.31: 22 105.31 - 140.42: 1 140.42 - 175.52: 5 Dihedral angle restraints: 27854 sinusoidal: 11988 harmonic: 15866 Sorted by residual: dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT T 12 " pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " pdb=" P DT T 13 " ideal model delta sinusoidal sigma weight residual 220.00 44.48 175.52 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU B 220 " pdb=" C LEU B 220 " pdb=" N ASN B 221 " pdb=" CA ASN B 221 " ideal model delta harmonic sigma weight residual 180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 27851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4772 0.034 - 0.067: 1559 0.067 - 0.101: 457 0.101 - 0.134: 317 0.134 - 0.168: 35 Chirality restraints: 7140 Sorted by residual: chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ILE K 442 " pdb=" N ILE K 442 " pdb=" C ILE K 442 " pdb=" CB ILE K 442 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE B 759 " pdb=" N ILE B 759 " pdb=" C ILE B 759 " pdb=" CB ILE B 759 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 7137 not shown) Planarity restraints: 7663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 41 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C PHE B 41 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE B 41 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.018 2.00e-02 2.50e+03 1.55e-02 4.18e+00 pdb=" CG PHE A 938 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 548 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C PHE B 548 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE B 548 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 549 " -0.011 2.00e-02 2.50e+03 ... (remaining 7660 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 522 2.64 - 3.20: 41885 3.20 - 3.77: 69287 3.77 - 4.33: 100817 4.33 - 4.90: 163861 Nonbonded interactions: 376372 Sorted by model distance: nonbonded pdb=" O ILE A 408 " pdb=" OG SER A 411 " model vdw 2.075 3.040 nonbonded pdb=" OH TYR B 798 " pdb=" OD1 ASP B 841 " model vdw 2.098 3.040 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.105 2.170 nonbonded pdb=" O PRO K 101 " pdb=" OG SER K 139 " model vdw 2.111 3.040 nonbonded pdb=" OG SER K 84 " pdb=" O ASN K 87 " model vdw 2.115 3.040 ... (remaining 376367 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.060 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 58.820 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 0.057 46279 Z= 0.145 Angle : 0.537 7.579 62928 Z= 0.299 Chirality : 0.043 0.168 7140 Planarity : 0.003 0.042 7663 Dihedral : 11.790 175.523 17591 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.41 % Allowed : 2.65 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.12), residues: 5306 helix: 1.72 (0.12), residues: 1941 sheet: -0.33 (0.18), residues: 757 loop : -0.34 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 673 TYR 0.013 0.001 TYR B 377 PHE 0.035 0.001 PHE A 938 TRP 0.011 0.001 TRP A 365 HIS 0.004 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00304 (46261) covalent geometry : angle 0.53602 (62907) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.54432 ( 6) hydrogen bonds : bond 0.14634 ( 1954) hydrogen bonds : angle 6.18056 ( 5493) metal coordination : bond 0.00427 ( 15) metal coordination : angle 2.24342 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1071 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 THR cc_start: 0.8581 (m) cc_final: 0.8197 (t) REVERT: A 104 ASP cc_start: 0.7311 (t0) cc_final: 0.7104 (t0) REVERT: A 137 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7668 (mp10) REVERT: A 141 LYS cc_start: 0.7186 (mppt) cc_final: 0.6846 (tptt) REVERT: A 226 MET cc_start: 0.7023 (mmm) cc_final: 0.6792 (mmm) REVERT: A 249 ASP cc_start: 0.7463 (t0) cc_final: 0.6327 (p0) REVERT: A 287 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7656 (ttp-110) REVERT: A 520 ASP cc_start: 0.7474 (m-30) cc_final: 0.7235 (m-30) REVERT: A 522 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7437 (mp0) REVERT: A 604 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 617 LYS cc_start: 0.8100 (mttt) cc_final: 0.7818 (mttt) REVERT: A 858 LYS cc_start: 0.8416 (tptt) cc_final: 0.8210 (tptm) REVERT: A 1010 ARG cc_start: 0.7970 (ptt-90) cc_final: 0.7669 (ptt-90) REVERT: A 1057 GLU cc_start: 0.7661 (tt0) cc_final: 0.7411 (tt0) REVERT: A 1131 LYS cc_start: 0.8620 (tttp) cc_final: 0.8306 (ttmm) REVERT: A 1196 GLU cc_start: 0.7555 (tt0) cc_final: 0.7247 (tp30) REVERT: A 1264 MET cc_start: 0.4736 (tpt) cc_final: 0.2782 (pmt) REVERT: B 72 ASN cc_start: 0.6802 (t0) cc_final: 0.6279 (t0) REVERT: B 74 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7048 (mmtp) REVERT: B 81 SER cc_start: 0.7838 (m) cc_final: 0.7602 (p) REVERT: B 205 TYR cc_start: 0.6571 (m-80) cc_final: 0.6166 (m-80) REVERT: B 657 GLN cc_start: 0.7590 (mm110) cc_final: 0.7325 (mm110) REVERT: B 860 GLU cc_start: 0.6379 (mm-30) cc_final: 0.5851 (mp0) REVERT: B 967 GLN cc_start: 0.6724 (tp40) cc_final: 0.6429 (tp40) REVERT: B 1055 GLU cc_start: 0.7122 (tt0) cc_final: 0.6818 (tt0) REVERT: B 1151 LYS cc_start: 0.8396 (pttp) cc_final: 0.7671 (mmtp) REVERT: C 8 ASN cc_start: 0.8281 (m-40) cc_final: 0.7840 (m-40) REVERT: C 28 ASN cc_start: 0.8401 (t0) cc_final: 0.8146 (t0) REVERT: C 297 LYS cc_start: 0.8231 (tttt) cc_final: 0.8002 (ttpt) REVERT: F 135 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7680 (mt-10) REVERT: I 56 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7503 (tpp80) REVERT: I 126 LYS cc_start: 0.5867 (mmtt) cc_final: 0.5498 (tppt) REVERT: I 166 PHE cc_start: 0.8307 (t80) cc_final: 0.8013 (t80) REVERT: I 177 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7473 (ptmt) REVERT: I 245 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6778 (tmtt) REVERT: I 428 MET cc_start: 0.5957 (mmm) cc_final: 0.5706 (mmm) REVERT: I 636 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6181 (tp30) REVERT: I 643 LYS cc_start: 0.7396 (tppp) cc_final: 0.7097 (tmtt) REVERT: I 713 ASP cc_start: 0.6926 (p0) cc_final: 0.6665 (p0) REVERT: I 715 MET cc_start: 0.7929 (mmp) cc_final: 0.7682 (mmm) REVERT: J 51 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7257 (mt0) REVERT: K 163 VAL cc_start: 0.8080 (m) cc_final: 0.7468 (p) REVERT: K 315 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7619 (mmtm) REVERT: S 135 ASN cc_start: 0.8146 (t0) cc_final: 0.7712 (t0) REVERT: W 410 ASP cc_start: 0.7008 (m-30) cc_final: 0.6801 (m-30) REVERT: W 577 ASP cc_start: 0.6869 (m-30) cc_final: 0.6361 (m-30) outliers start: 20 outliers final: 8 residues processed: 1083 average time/residue: 0.7265 time to fit residues: 977.7194 Evaluate side-chains 685 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 677 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 356 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 394 optimal weight: 0.0870 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 9.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 459 GLN A1006 ASN A1140 ASN A1199 ASN A1226 HIS B 295 HIS B 371 HIS B 376 ASN B 736 ASN B 971 GLN C 24 GLN E 62 GLN F 94 GLN F 111 GLN F 112 ASN I 64 GLN I 374 ASN I 448 GLN K 49 GLN K 203 ASN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 ASN K 547 ASN K 615 GLN K 692 ASN S 58 ASN W 113 ASN W 285 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133217 restraints weight = 66923.641| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.04 r_work: 0.3390 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 46279 Z= 0.209 Angle : 0.613 11.889 62928 Z= 0.330 Chirality : 0.047 0.177 7140 Planarity : 0.004 0.044 7663 Dihedral : 13.408 177.029 6787 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.90 % Allowed : 10.27 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.12), residues: 5306 helix: 1.51 (0.12), residues: 1965 sheet: -0.29 (0.18), residues: 777 loop : -0.37 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 586 TYR 0.027 0.002 TYR W 605 PHE 0.039 0.002 PHE A 938 TRP 0.016 0.002 TRP K 235 HIS 0.012 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00493 (46261) covalent geometry : angle 0.61019 (62907) SS BOND : bond 0.00462 ( 3) SS BOND : angle 1.43393 ( 6) hydrogen bonds : bond 0.04475 ( 1954) hydrogen bonds : angle 4.88683 ( 5493) metal coordination : bond 0.00870 ( 15) metal coordination : angle 3.78572 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 710 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7657 (p0) REVERT: A 56 GLU cc_start: 0.8482 (pt0) cc_final: 0.7876 (tt0) REVERT: A 71 THR cc_start: 0.8934 (m) cc_final: 0.8523 (t) REVERT: A 137 GLN cc_start: 0.8747 (mm-40) cc_final: 0.7765 (mp10) REVERT: A 296 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 327 GLN cc_start: 0.8206 (tm130) cc_final: 0.7948 (tm-30) REVERT: A 477 ASP cc_start: 0.8539 (m-30) cc_final: 0.8297 (m-30) REVERT: A 520 ASP cc_start: 0.8332 (m-30) cc_final: 0.8085 (m-30) REVERT: A 592 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6428 (mm-30) REVERT: A 604 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 608 LYS cc_start: 0.6982 (mptt) cc_final: 0.6517 (tttt) REVERT: A 617 LYS cc_start: 0.8299 (mttt) cc_final: 0.7789 (tttt) REVERT: A 650 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6835 (mtm110) REVERT: A 675 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8475 (mm-30) REVERT: A 694 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: A 858 LYS cc_start: 0.8695 (tptt) cc_final: 0.8417 (tttt) REVERT: A 1042 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8278 (mt-10) REVERT: A 1126 GLU cc_start: 0.8563 (tt0) cc_final: 0.8188 (tm-30) REVERT: A 1131 LYS cc_start: 0.8884 (tttp) cc_final: 0.8636 (ttmm) REVERT: A 1196 GLU cc_start: 0.8340 (tt0) cc_final: 0.7839 (tm-30) REVERT: A 1260 LEU cc_start: 0.8305 (tt) cc_final: 0.8086 (tp) REVERT: A 1264 MET cc_start: 0.4994 (tpt) cc_final: 0.3153 (pmt) REVERT: B 64 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: B 72 ASN cc_start: 0.6924 (t0) cc_final: 0.6304 (t0) REVERT: B 74 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7397 (mmtm) REVERT: B 255 ASP cc_start: 0.7748 (t0) cc_final: 0.7483 (t0) REVERT: B 282 ASN cc_start: 0.5371 (t0) cc_final: 0.5035 (t0) REVERT: B 386 MET cc_start: 0.6705 (mmm) cc_final: 0.5989 (mmm) REVERT: B 413 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7554 (t) REVERT: B 654 GLU cc_start: 0.7647 (pt0) cc_final: 0.6859 (tp30) REVERT: B 657 GLN cc_start: 0.8086 (mm110) cc_final: 0.7822 (mm110) REVERT: B 662 ASP cc_start: 0.8348 (t0) cc_final: 0.8066 (t70) REVERT: B 823 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6515 (tp) REVERT: B 860 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6197 (mp0) REVERT: B 887 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 890 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8613 (ptpp) REVERT: B 1151 LYS cc_start: 0.8598 (pttp) cc_final: 0.7687 (mmtp) REVERT: C 89 GLU cc_start: 0.7803 (mp0) cc_final: 0.7570 (mp0) REVERT: C 90 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7492 (mtm110) REVERT: E 62 GLN cc_start: 0.8496 (mt0) cc_final: 0.8273 (mt0) REVERT: E 77 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8072 (t0) REVERT: E 132 ASP cc_start: 0.8095 (t70) cc_final: 0.7642 (p0) REVERT: E 135 LYS cc_start: 0.8280 (mttt) cc_final: 0.8041 (mttt) REVERT: F 112 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7940 (p0) REVERT: F 135 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8337 (mt-10) REVERT: G 22 ASP cc_start: 0.8784 (m-30) cc_final: 0.8571 (m-30) REVERT: G 49 GLU cc_start: 0.7486 (tp30) cc_final: 0.7264 (tp30) REVERT: G 92 GLU cc_start: 0.6281 (pm20) cc_final: 0.5738 (pm20) REVERT: I 56 ARG cc_start: 0.8631 (ttm170) cc_final: 0.7648 (tpp80) REVERT: I 107 MET cc_start: 0.8103 (tpt) cc_final: 0.7841 (tpp) REVERT: I 176 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7247 (tm-30) REVERT: I 177 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7537 (ptmt) REVERT: I 180 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: I 194 LEU cc_start: 0.7834 (mt) cc_final: 0.7549 (mm) REVERT: I 245 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7131 (tmtt) REVERT: I 425 THR cc_start: 0.8355 (p) cc_final: 0.8118 (p) REVERT: I 636 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6118 (tp30) REVERT: I 715 MET cc_start: 0.8170 (mmp) cc_final: 0.7827 (mmm) REVERT: I 761 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: J 25 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8631 (mptt) REVERT: J 52 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8388 (mpt-90) REVERT: K 315 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8618 (mmtt) REVERT: K 392 MET cc_start: 0.7891 (tpp) cc_final: 0.7260 (tmm) REVERT: K 573 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: S 90 ASN cc_start: 0.8383 (t0) cc_final: 0.8077 (t0) REVERT: W 198 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: W 313 VAL cc_start: 0.7240 (OUTLIER) cc_final: 0.6787 (p) REVERT: W 315 TYR cc_start: 0.7212 (m-80) cc_final: 0.6885 (m-80) REVERT: W 399 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6781 (p0) REVERT: W 576 GLU cc_start: 0.7335 (pp20) cc_final: 0.7131 (pp20) REVERT: W 577 ASP cc_start: 0.8031 (m-30) cc_final: 0.7185 (m-30) outliers start: 143 outliers final: 47 residues processed: 795 average time/residue: 0.7327 time to fit residues: 722.2950 Evaluate side-chains 707 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 642 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 677 ILE Chi-restraints excluded: chain I residue 761 GLU Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 435 HIS Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 562 THR Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 243 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 341 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 318 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 496 optimal weight: 3.9990 chunk 533 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN A1226 HIS B 295 HIS B 371 HIS B 967 GLN C 8 ASN E 52 HIS E 98 ASN F 111 GLN F 112 ASN G 37 HIS I 254 ASN J 57 GLN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 ASN S 55 ASN S 58 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 372 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131655 restraints weight = 66497.519| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.26 r_work: 0.3367 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 46279 Z= 0.172 Angle : 0.549 10.587 62928 Z= 0.296 Chirality : 0.044 0.173 7140 Planarity : 0.004 0.041 7663 Dihedral : 13.579 179.407 6777 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.81 % Allowed : 11.93 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.12), residues: 5306 helix: 1.40 (0.12), residues: 1978 sheet: -0.28 (0.18), residues: 778 loop : -0.43 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 687 TYR 0.025 0.002 TYR I 699 PHE 0.034 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.010 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00400 (46261) covalent geometry : angle 0.54639 (62907) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.32766 ( 6) hydrogen bonds : bond 0.04098 ( 1954) hydrogen bonds : angle 4.78849 ( 5493) metal coordination : bond 0.00613 ( 15) metal coordination : angle 3.40006 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 667 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7868 (p0) REVERT: A 56 GLU cc_start: 0.8485 (pt0) cc_final: 0.7832 (tt0) REVERT: A 114 HIS cc_start: 0.7069 (m-70) cc_final: 0.6647 (p-80) REVERT: A 136 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7769 (mpp) REVERT: A 137 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8499 (mp10) REVERT: A 327 GLN cc_start: 0.8235 (tm130) cc_final: 0.7963 (tm-30) REVERT: A 520 ASP cc_start: 0.8365 (m-30) cc_final: 0.8110 (m-30) REVERT: A 592 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6483 (mm-30) REVERT: A 604 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 608 LYS cc_start: 0.7020 (mptt) cc_final: 0.6489 (tttt) REVERT: A 617 LYS cc_start: 0.8247 (mttt) cc_final: 0.7979 (mttp) REVERT: A 650 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6905 (mtm110) REVERT: A 675 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8522 (mm-30) REVERT: A 694 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: A 858 LYS cc_start: 0.8691 (tptt) cc_final: 0.8419 (tttt) REVERT: A 940 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: A 963 GLU cc_start: 0.8223 (tp30) cc_final: 0.7958 (tp30) REVERT: A 1042 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8259 (mt-10) REVERT: A 1126 GLU cc_start: 0.8562 (tt0) cc_final: 0.8133 (tm-30) REVERT: A 1196 GLU cc_start: 0.8319 (tt0) cc_final: 0.7829 (tm-30) REVERT: A 1260 LEU cc_start: 0.8381 (tt) cc_final: 0.8176 (tp) REVERT: A 1264 MET cc_start: 0.5088 (tpt) cc_final: 0.3053 (pmt) REVERT: B 74 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7443 (mmtm) REVERT: B 255 ASP cc_start: 0.7775 (t0) cc_final: 0.7471 (t0) REVERT: B 386 MET cc_start: 0.6721 (mmm) cc_final: 0.6141 (mmm) REVERT: B 413 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.7205 (t) REVERT: B 654 GLU cc_start: 0.7705 (pt0) cc_final: 0.6941 (tp30) REVERT: B 662 ASP cc_start: 0.8328 (t0) cc_final: 0.8092 (t70) REVERT: B 860 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6194 (mp0) REVERT: B 890 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8649 (ptpp) REVERT: B 1036 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6728 (tmtm) REVERT: B 1151 LYS cc_start: 0.8581 (pttp) cc_final: 0.7681 (mmtp) REVERT: C 90 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7559 (mtm110) REVERT: C 115 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: C 184 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8038 (tmt-80) REVERT: C 185 SER cc_start: 0.8720 (t) cc_final: 0.8113 (t) REVERT: E 3 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: E 62 GLN cc_start: 0.8485 (mt0) cc_final: 0.8260 (mt0) REVERT: E 77 ASP cc_start: 0.8438 (t70) cc_final: 0.8184 (t0) REVERT: F 135 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8434 (mt-10) REVERT: G 15 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7890 (mm-30) REVERT: G 22 ASP cc_start: 0.8890 (m-30) cc_final: 0.8612 (m-30) REVERT: G 92 GLU cc_start: 0.6198 (pm20) cc_final: 0.5652 (pm20) REVERT: I 56 ARG cc_start: 0.8688 (ttm170) cc_final: 0.7713 (tpp80) REVERT: I 107 MET cc_start: 0.8086 (tpt) cc_final: 0.7774 (tpp) REVERT: I 121 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8240 (tpp) REVERT: I 176 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7423 (tm-30) REVERT: I 177 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7512 (ptmt) REVERT: I 180 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: I 194 LEU cc_start: 0.7867 (mt) cc_final: 0.7579 (mm) REVERT: I 245 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7069 (tmtt) REVERT: I 425 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8160 (p) REVERT: I 636 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6087 (tp30) REVERT: I 715 MET cc_start: 0.8106 (mmp) cc_final: 0.7830 (mmm) REVERT: J 25 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8756 (mptt) REVERT: K 313 ASP cc_start: 0.6511 (t0) cc_final: 0.6269 (t70) REVERT: K 392 MET cc_start: 0.7816 (tpp) cc_final: 0.7396 (mmm) REVERT: K 573 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: S 60 LYS cc_start: 0.7749 (mtpt) cc_final: 0.6982 (mtmt) REVERT: W 110 TYR cc_start: 0.7915 (t80) cc_final: 0.7611 (t80) REVERT: W 198 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8124 (mtmm) REVERT: W 313 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.6744 (p) REVERT: W 315 TYR cc_start: 0.7279 (m-80) cc_final: 0.6973 (m-80) REVERT: W 393 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6640 (pp-130) REVERT: W 399 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6859 (p0) REVERT: W 463 ASP cc_start: 0.7098 (t0) cc_final: 0.6792 (t0) REVERT: W 577 ASP cc_start: 0.8060 (m-30) cc_final: 0.7511 (m-30) outliers start: 139 outliers final: 59 residues processed: 745 average time/residue: 0.7690 time to fit residues: 706.1947 Evaluate side-chains 712 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 634 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 425 THR Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 678 GLU Chi-restraints excluded: chain I residue 791 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 388 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain W residue 254 GLN Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 308 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 516 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 474 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 325 GLN B 371 HIS B 967 GLN B 971 GLN F 111 GLN F 112 ASN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129989 restraints weight = 66371.862| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.33 r_work: 0.3346 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 46279 Z= 0.192 Angle : 0.565 11.126 62928 Z= 0.303 Chirality : 0.045 0.178 7140 Planarity : 0.004 0.042 7663 Dihedral : 13.761 179.884 6777 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.38 % Allowed : 12.33 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 5306 helix: 1.30 (0.12), residues: 1973 sheet: -0.35 (0.18), residues: 789 loop : -0.47 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1010 TYR 0.028 0.002 TYR I 699 PHE 0.034 0.002 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.011 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00450 (46261) covalent geometry : angle 0.56269 (62907) SS BOND : bond 0.00449 ( 3) SS BOND : angle 1.41789 ( 6) hydrogen bonds : bond 0.04121 ( 1954) hydrogen bonds : angle 4.78659 ( 5493) metal coordination : bond 0.00730 ( 15) metal coordination : angle 3.55991 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 658 time to evaluate : 1.778 Fit side-chains REVERT: A 13 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 50 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8631 (mttt) REVERT: A 56 GLU cc_start: 0.8523 (pt0) cc_final: 0.7841 (tt0) REVERT: A 77 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 114 HIS cc_start: 0.7065 (m-70) cc_final: 0.6644 (p-80) REVERT: A 136 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7729 (mpp) REVERT: A 137 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8470 (mp10) REVERT: A 327 GLN cc_start: 0.8234 (tm130) cc_final: 0.7951 (tm-30) REVERT: A 592 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6522 (mm-30) REVERT: A 604 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 608 LYS cc_start: 0.7080 (mptt) cc_final: 0.6493 (tttt) REVERT: A 617 LYS cc_start: 0.8273 (mttt) cc_final: 0.7928 (mttt) REVERT: A 650 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6342 (ttp80) REVERT: A 675 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8532 (mm-30) REVERT: A 694 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7072 (pp20) REVERT: A 858 LYS cc_start: 0.8725 (tptt) cc_final: 0.8416 (tttt) REVERT: A 940 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: A 963 GLU cc_start: 0.8265 (tp30) cc_final: 0.7975 (tp30) REVERT: A 1042 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8237 (mt-10) REVERT: A 1126 GLU cc_start: 0.8561 (tt0) cc_final: 0.8127 (tm-30) REVERT: A 1196 GLU cc_start: 0.8336 (tt0) cc_final: 0.7813 (tm-30) REVERT: A 1200 LYS cc_start: 0.8247 (mppt) cc_final: 0.7791 (mptt) REVERT: A 1264 MET cc_start: 0.5291 (tpt) cc_final: 0.3133 (pmt) REVERT: B 74 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7455 (mmtm) REVERT: B 255 ASP cc_start: 0.7778 (t0) cc_final: 0.7539 (t70) REVERT: B 325 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: B 386 MET cc_start: 0.6556 (mmm) cc_final: 0.6061 (mmm) REVERT: B 413 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7211 (t) REVERT: B 511 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: B 662 ASP cc_start: 0.8334 (t0) cc_final: 0.8080 (t0) REVERT: B 860 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6224 (mp0) REVERT: B 890 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8632 (ptpp) REVERT: B 1036 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6796 (tmtm) REVERT: B 1151 LYS cc_start: 0.8591 (pttp) cc_final: 0.7776 (mmtp) REVERT: C 115 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: C 184 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7966 (tmt-80) REVERT: E 3 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: E 47 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8098 (mt) REVERT: E 132 ASP cc_start: 0.8127 (t70) cc_final: 0.7754 (p0) REVERT: F 135 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8390 (mt-10) REVERT: G 15 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7821 (mm-30) REVERT: G 18 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: G 92 GLU cc_start: 0.6089 (pm20) cc_final: 0.5581 (pm20) REVERT: I 107 MET cc_start: 0.8110 (tpt) cc_final: 0.7780 (tpp) REVERT: I 121 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: I 176 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7337 (tm-30) REVERT: I 180 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: I 194 LEU cc_start: 0.7833 (mt) cc_final: 0.7552 (mm) REVERT: I 245 LYS cc_start: 0.7583 (ttpt) cc_final: 0.6997 (tmtt) REVERT: I 327 GLU cc_start: 0.6140 (pm20) cc_final: 0.5844 (pm20) REVERT: I 636 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6107 (tp30) REVERT: I 715 MET cc_start: 0.8119 (mmp) cc_final: 0.7774 (mmm) REVERT: I 790 MET cc_start: 0.7636 (tpp) cc_final: 0.7419 (mpp) REVERT: J 25 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8818 (mptt) REVERT: J 51 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: K 95 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7755 (p0) REVERT: K 161 MET cc_start: 0.8341 (mmp) cc_final: 0.8091 (mmm) REVERT: K 315 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8356 (mmtm) REVERT: K 392 MET cc_start: 0.7730 (tpp) cc_final: 0.7467 (mmm) REVERT: K 540 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8010 (tm-30) REVERT: K 573 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8595 (mt0) REVERT: S 60 LYS cc_start: 0.7763 (mtpt) cc_final: 0.6989 (mtmt) REVERT: W 110 TYR cc_start: 0.7972 (t80) cc_final: 0.7636 (t80) REVERT: W 198 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: W 313 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.6803 (p) REVERT: W 315 TYR cc_start: 0.7285 (m-80) cc_final: 0.7046 (m-80) REVERT: W 393 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6598 (pp-130) REVERT: W 399 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6913 (p0) REVERT: W 463 ASP cc_start: 0.7180 (t0) cc_final: 0.6822 (t0) outliers start: 167 outliers final: 72 residues processed: 757 average time/residue: 0.7373 time to fit residues: 688.9482 Evaluate side-chains 727 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 630 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 678 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 388 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 278 VAL Chi-restraints excluded: chain W residue 295 LEU Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 311 optimal weight: 20.0000 chunk 357 optimal weight: 3.9990 chunk 457 optimal weight: 10.0000 chunk 348 optimal weight: 7.9990 chunk 532 optimal weight: 4.9990 chunk 467 optimal weight: 5.9990 chunk 442 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 512 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 325 GLN B 371 HIS B 967 GLN B 971 GLN E 62 GLN F 111 GLN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 615 GLN S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128529 restraints weight = 66147.084| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.28 r_work: 0.3326 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 46279 Z= 0.214 Angle : 0.585 11.229 62928 Z= 0.314 Chirality : 0.045 0.181 7140 Planarity : 0.004 0.044 7663 Dihedral : 13.829 179.771 6775 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.38 % Allowed : 12.88 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.11), residues: 5306 helix: 1.19 (0.12), residues: 1980 sheet: -0.46 (0.18), residues: 786 loop : -0.52 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1010 TYR 0.022 0.002 TYR I 699 PHE 0.034 0.002 PHE A 938 TRP 0.013 0.002 TRP A 365 HIS 0.011 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00506 (46261) covalent geometry : angle 0.58281 (62907) SS BOND : bond 0.00478 ( 3) SS BOND : angle 1.44328 ( 6) hydrogen bonds : bond 0.04259 ( 1954) hydrogen bonds : angle 4.83103 ( 5493) metal coordination : bond 0.00804 ( 15) metal coordination : angle 3.56948 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 652 time to evaluate : 1.731 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7898 (p0) REVERT: A 50 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8664 (mttt) REVERT: A 56 GLU cc_start: 0.8534 (pt0) cc_final: 0.7852 (tt0) REVERT: A 136 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7775 (mpp) REVERT: A 137 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8467 (mp10) REVERT: A 327 GLN cc_start: 0.8208 (tm130) cc_final: 0.7918 (tm-30) REVERT: A 592 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6493 (mm-30) REVERT: A 604 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7379 (mm-30) REVERT: A 608 LYS cc_start: 0.7039 (mptt) cc_final: 0.6478 (tttt) REVERT: A 617 LYS cc_start: 0.8289 (mttt) cc_final: 0.7937 (mttt) REVERT: A 650 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6330 (ttp80) REVERT: A 675 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 694 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7121 (pp20) REVERT: A 858 LYS cc_start: 0.8717 (tptt) cc_final: 0.8415 (tttt) REVERT: A 936 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 940 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: A 963 GLU cc_start: 0.8263 (tp30) cc_final: 0.8027 (tp30) REVERT: A 1010 ARG cc_start: 0.8539 (ptt90) cc_final: 0.8258 (ptt-90) REVERT: A 1126 GLU cc_start: 0.8573 (tt0) cc_final: 0.8175 (tm-30) REVERT: A 1131 LYS cc_start: 0.8765 (tttp) cc_final: 0.8495 (ttmm) REVERT: A 1196 GLU cc_start: 0.8338 (tt0) cc_final: 0.7774 (tm-30) REVERT: A 1200 LYS cc_start: 0.8242 (mppt) cc_final: 0.7849 (mptt) REVERT: A 1218 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8022 (mmtt) REVERT: A 1264 MET cc_start: 0.5238 (tpt) cc_final: 0.3212 (pmt) REVERT: B 74 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7535 (mmtm) REVERT: B 190 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.7527 (t80) REVERT: B 255 ASP cc_start: 0.7796 (t0) cc_final: 0.7558 (t70) REVERT: B 386 MET cc_start: 0.6650 (mmm) cc_final: 0.6151 (mmm) REVERT: B 413 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7203 (t) REVERT: B 720 ARG cc_start: 0.8621 (ptm-80) cc_final: 0.8273 (ptm-80) REVERT: B 860 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6329 (mp0) REVERT: B 890 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8617 (ptpp) REVERT: B 1036 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6746 (tmtm) REVERT: B 1151 LYS cc_start: 0.8590 (pttp) cc_final: 0.7767 (mmtp) REVERT: C 90 ARG cc_start: 0.8296 (mtm110) cc_final: 0.7953 (mtm110) REVERT: C 115 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: C 184 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7963 (tmt-80) REVERT: E 3 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: E 47 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8127 (mt) REVERT: E 132 ASP cc_start: 0.7896 (t70) cc_final: 0.7601 (p0) REVERT: E 135 LYS cc_start: 0.8387 (mttt) cc_final: 0.8112 (mttt) REVERT: E 144 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: F 135 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8412 (mt-10) REVERT: G 15 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7817 (mm-30) REVERT: G 18 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: G 55 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: G 92 GLU cc_start: 0.6143 (pm20) cc_final: 0.5560 (pm20) REVERT: G 149 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: I 107 MET cc_start: 0.8120 (tpt) cc_final: 0.7772 (tpp) REVERT: I 121 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (tpp) REVERT: I 126 LYS cc_start: 0.5419 (tppt) cc_final: 0.5101 (tppt) REVERT: I 176 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7362 (tm-30) REVERT: I 180 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: I 194 LEU cc_start: 0.7904 (mt) cc_final: 0.7610 (mm) REVERT: I 205 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8395 (ptpp) REVERT: I 245 LYS cc_start: 0.7530 (ttpt) cc_final: 0.6970 (tmtt) REVERT: I 304 LEU cc_start: 0.6982 (mt) cc_final: 0.6687 (mm) REVERT: I 327 GLU cc_start: 0.6257 (pm20) cc_final: 0.4996 (tm-30) REVERT: I 338 VAL cc_start: 0.5195 (OUTLIER) cc_final: 0.4950 (t) REVERT: I 487 MET cc_start: 0.4770 (mmm) cc_final: 0.4207 (pmt) REVERT: I 576 ARG cc_start: 0.7009 (ptm160) cc_final: 0.6707 (ptm-80) REVERT: I 636 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6118 (tp30) REVERT: I 715 MET cc_start: 0.8141 (mmp) cc_final: 0.7819 (mmm) REVERT: J 24 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8362 (mtm180) REVERT: J 25 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8949 (mptt) REVERT: J 51 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: K 161 MET cc_start: 0.8382 (mmp) cc_final: 0.8118 (mmm) REVERT: K 559 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8423 (ttp) REVERT: K 573 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8620 (mt0) REVERT: S 60 LYS cc_start: 0.7744 (mtpt) cc_final: 0.6943 (mtmt) REVERT: W 110 TYR cc_start: 0.8003 (t80) cc_final: 0.7668 (t80) REVERT: W 198 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8278 (mtmm) REVERT: W 313 VAL cc_start: 0.7441 (OUTLIER) cc_final: 0.6770 (p) REVERT: W 315 TYR cc_start: 0.7253 (m-80) cc_final: 0.7013 (m-80) REVERT: W 393 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6543 (pp-130) REVERT: W 399 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6901 (p0) REVERT: W 463 ASP cc_start: 0.7180 (t0) cc_final: 0.6807 (t0) REVERT: W 577 ASP cc_start: 0.8201 (m-30) cc_final: 0.7815 (m-30) outliers start: 167 outliers final: 68 residues processed: 755 average time/residue: 0.7721 time to fit residues: 716.9955 Evaluate side-chains 723 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 625 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 678 GLU Chi-restraints excluded: chain I residue 749 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 559 MET Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 562 THR Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 83 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 521 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 441 optimal weight: 1.9990 chunk 251 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 513 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 967 GLN B 971 GLN I 703 ASN ** K 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 632 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128636 restraints weight = 66457.584| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.23 r_work: 0.3328 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 46279 Z= 0.198 Angle : 0.585 12.383 62928 Z= 0.312 Chirality : 0.045 0.178 7140 Planarity : 0.004 0.043 7663 Dihedral : 13.875 179.860 6775 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.98 % Allowed : 13.67 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.11), residues: 5306 helix: 1.16 (0.12), residues: 1980 sheet: -0.48 (0.18), residues: 786 loop : -0.54 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1010 TYR 0.017 0.002 TYR A 732 PHE 0.033 0.002 PHE A 938 TRP 0.014 0.001 TRP A 365 HIS 0.011 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00467 (46261) covalent geometry : angle 0.58248 (62907) SS BOND : bond 0.00475 ( 3) SS BOND : angle 1.45644 ( 6) hydrogen bonds : bond 0.04132 ( 1954) hydrogen bonds : angle 4.82804 ( 5493) metal coordination : bond 0.00733 ( 15) metal coordination : angle 3.57137 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 644 time to evaluate : 1.784 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7935 (p0) REVERT: A 50 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8668 (mttt) REVERT: A 56 GLU cc_start: 0.8516 (pt0) cc_final: 0.7829 (tt0) REVERT: A 136 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7782 (mpp) REVERT: A 327 GLN cc_start: 0.8218 (tm130) cc_final: 0.7927 (tm-30) REVERT: A 592 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6465 (mm-30) REVERT: A 604 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 608 LYS cc_start: 0.7063 (mptt) cc_final: 0.6459 (tttt) REVERT: A 617 LYS cc_start: 0.8237 (mttt) cc_final: 0.7749 (tttt) REVERT: A 650 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6448 (ttp80) REVERT: A 675 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8582 (mm-30) REVERT: A 694 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7111 (pp20) REVERT: A 858 LYS cc_start: 0.8721 (tptt) cc_final: 0.8422 (tttt) REVERT: A 936 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 940 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: A 963 GLU cc_start: 0.8259 (tp30) cc_final: 0.8016 (tp30) REVERT: A 1126 GLU cc_start: 0.8584 (tt0) cc_final: 0.8173 (tm-30) REVERT: A 1131 LYS cc_start: 0.8804 (tttp) cc_final: 0.8528 (ttmm) REVERT: A 1218 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7914 (tptt) REVERT: A 1264 MET cc_start: 0.5467 (tpt) cc_final: 0.3234 (pmt) REVERT: B 74 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7541 (mmtm) REVERT: B 190 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7439 (t80) REVERT: B 255 ASP cc_start: 0.7846 (t0) cc_final: 0.7593 (t70) REVERT: B 386 MET cc_start: 0.6677 (mmm) cc_final: 0.6179 (mmm) REVERT: B 413 SER cc_start: 0.7603 (OUTLIER) cc_final: 0.7190 (t) REVERT: B 608 GLU cc_start: 0.6546 (tp30) cc_final: 0.6233 (tm-30) REVERT: B 720 ARG cc_start: 0.8621 (ptm-80) cc_final: 0.8295 (ptm-80) REVERT: B 860 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6394 (mp0) REVERT: B 890 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8635 (ptpp) REVERT: B 1036 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6800 (tmtm) REVERT: B 1151 LYS cc_start: 0.8588 (pttp) cc_final: 0.7738 (mmtp) REVERT: C 90 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8087 (mtm110) REVERT: C 115 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: C 184 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7932 (tmt-80) REVERT: E 47 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8120 (mt) REVERT: E 132 ASP cc_start: 0.7945 (t70) cc_final: 0.7556 (p0) REVERT: E 135 LYS cc_start: 0.8386 (mttt) cc_final: 0.8064 (mttt) REVERT: F 135 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8443 (mt-10) REVERT: G 15 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7769 (mm-30) REVERT: G 55 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: G 92 GLU cc_start: 0.6149 (pm20) cc_final: 0.5535 (pm20) REVERT: G 149 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6028 (mp0) REVERT: I 107 MET cc_start: 0.8118 (tpt) cc_final: 0.7828 (tpp) REVERT: I 126 LYS cc_start: 0.5500 (tppt) cc_final: 0.5175 (tppt) REVERT: I 177 LYS cc_start: 0.7971 (mttt) cc_final: 0.7504 (tttt) REVERT: I 180 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: I 194 LEU cc_start: 0.7916 (mt) cc_final: 0.7647 (mm) REVERT: I 205 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8372 (ptpp) REVERT: I 245 LYS cc_start: 0.7572 (ttpt) cc_final: 0.7032 (tmtt) REVERT: I 304 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6793 (mm) REVERT: I 327 GLU cc_start: 0.6156 (pm20) cc_final: 0.5026 (tm-30) REVERT: I 338 VAL cc_start: 0.5216 (OUTLIER) cc_final: 0.4983 (t) REVERT: I 487 MET cc_start: 0.4832 (mmm) cc_final: 0.4263 (pmt) REVERT: I 539 ARG cc_start: 0.5206 (mmp-170) cc_final: 0.4309 (ttm170) REVERT: I 546 LEU cc_start: 0.4907 (OUTLIER) cc_final: 0.4663 (tt) REVERT: I 576 ARG cc_start: 0.7054 (ptm160) cc_final: 0.6656 (ptm-80) REVERT: I 627 LYS cc_start: 0.5666 (tppp) cc_final: 0.5382 (ptmm) REVERT: I 636 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6207 (tp30) REVERT: I 790 MET cc_start: 0.7688 (tpp) cc_final: 0.7473 (mpp) REVERT: J 24 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8343 (mtm180) REVERT: J 25 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8988 (mptt) REVERT: J 51 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: K 540 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8078 (tm-30) REVERT: K 544 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7312 (mt-10) REVERT: K 573 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8619 (mt0) REVERT: S 60 LYS cc_start: 0.7708 (mtpt) cc_final: 0.6927 (mtmt) REVERT: W 85 MET cc_start: 0.8401 (tpp) cc_final: 0.8087 (tpp) REVERT: W 110 TYR cc_start: 0.7978 (t80) cc_final: 0.7758 (t80) REVERT: W 198 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8316 (mtmm) REVERT: W 313 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.6614 (p) REVERT: W 393 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6559 (pp-130) REVERT: W 399 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6821 (p0) REVERT: W 454 ARG cc_start: 0.7288 (mmt90) cc_final: 0.7085 (mmt90) REVERT: W 463 ASP cc_start: 0.7200 (t0) cc_final: 0.6815 (t0) REVERT: W 577 ASP cc_start: 0.8257 (m-30) cc_final: 0.7905 (m-30) outliers start: 147 outliers final: 73 residues processed: 740 average time/residue: 0.7878 time to fit residues: 718.2920 Evaluate side-chains 721 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 621 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 546 LEU Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 678 GLU Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 217 ASN Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 573 GLN Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 278 VAL Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 322 LEU Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 523 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 562 THR Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 493 optimal weight: 0.5980 chunk 387 optimal weight: 5.9990 chunk 488 optimal weight: 10.0000 chunk 413 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 451 optimal weight: 0.7980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 371 HIS B 391 ASN B 967 GLN B 971 GLN G 17 HIS S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130566 restraints weight = 65811.985| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.25 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46279 Z= 0.140 Angle : 0.551 13.781 62928 Z= 0.293 Chirality : 0.043 0.205 7140 Planarity : 0.004 0.042 7663 Dihedral : 13.826 179.597 6775 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.49 % Allowed : 14.78 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.12), residues: 5306 helix: 1.31 (0.12), residues: 1974 sheet: -0.42 (0.18), residues: 786 loop : -0.48 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1010 TYR 0.020 0.001 TYR S 78 PHE 0.030 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.011 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00323 (46261) covalent geometry : angle 0.54849 (62907) SS BOND : bond 0.00375 ( 3) SS BOND : angle 1.26689 ( 6) hydrogen bonds : bond 0.03746 ( 1954) hydrogen bonds : angle 4.73331 ( 5493) metal coordination : bond 0.00520 ( 15) metal coordination : angle 3.25792 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 644 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7737 (p0) REVERT: A 50 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8687 (mttt) REVERT: A 56 GLU cc_start: 0.8531 (pt0) cc_final: 0.7869 (tt0) REVERT: A 136 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (mpp) REVERT: A 327 GLN cc_start: 0.8264 (tm130) cc_final: 0.7961 (tm-30) REVERT: A 592 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6458 (mm-30) REVERT: A 604 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 608 LYS cc_start: 0.7071 (mptt) cc_final: 0.6483 (tttt) REVERT: A 617 LYS cc_start: 0.8217 (mttt) cc_final: 0.7732 (tttt) REVERT: A 650 ARG cc_start: 0.7358 (mtt180) cc_final: 0.6453 (ttp80) REVERT: A 675 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8569 (mm-30) REVERT: A 694 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: A 858 LYS cc_start: 0.8722 (tptt) cc_final: 0.8429 (tttt) REVERT: A 936 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8662 (tm-30) REVERT: A 940 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: A 1010 ARG cc_start: 0.8539 (ptt90) cc_final: 0.8223 (ptt-90) REVERT: A 1126 GLU cc_start: 0.8565 (tt0) cc_final: 0.8117 (tm-30) REVERT: A 1218 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7923 (tptt) REVERT: A 1264 MET cc_start: 0.5441 (tpt) cc_final: 0.3199 (pmt) REVERT: B 9 MET cc_start: 0.8557 (tpp) cc_final: 0.8296 (mmm) REVERT: B 59 PHE cc_start: 0.8132 (m-80) cc_final: 0.7884 (m-80) REVERT: B 74 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7547 (mmtm) REVERT: B 190 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 255 ASP cc_start: 0.7790 (t0) cc_final: 0.7533 (t70) REVERT: B 386 MET cc_start: 0.6644 (mmm) cc_final: 0.6209 (mmm) REVERT: B 413 SER cc_start: 0.7651 (OUTLIER) cc_final: 0.7217 (t) REVERT: B 425 SER cc_start: 0.7463 (t) cc_final: 0.6994 (t) REVERT: B 608 GLU cc_start: 0.6546 (tp30) cc_final: 0.6169 (tm-30) REVERT: B 720 ARG cc_start: 0.8621 (ptm-80) cc_final: 0.8315 (ptm-80) REVERT: B 823 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6361 (tp) REVERT: B 860 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6345 (mp0) REVERT: B 890 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8614 (ptpp) REVERT: B 1036 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6788 (tmtm) REVERT: B 1151 LYS cc_start: 0.8612 (pttp) cc_final: 0.7793 (mmtp) REVERT: C 115 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: C 184 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7940 (tmt-80) REVERT: E 47 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8159 (mt) REVERT: E 132 ASP cc_start: 0.7926 (t70) cc_final: 0.7591 (p0) REVERT: E 135 LYS cc_start: 0.8385 (mttt) cc_final: 0.8080 (mttt) REVERT: G 15 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7776 (mm-30) REVERT: G 55 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: G 92 GLU cc_start: 0.6106 (pm20) cc_final: 0.5483 (pm20) REVERT: I 107 MET cc_start: 0.8056 (tpt) cc_final: 0.7747 (tpp) REVERT: I 126 LYS cc_start: 0.5436 (tppt) cc_final: 0.5102 (tppt) REVERT: I 177 LYS cc_start: 0.7872 (mttt) cc_final: 0.7391 (tttt) REVERT: I 180 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: I 194 LEU cc_start: 0.7920 (mt) cc_final: 0.7685 (mm) REVERT: I 205 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8335 (ptpp) REVERT: I 245 LYS cc_start: 0.7564 (ttpt) cc_final: 0.7038 (tmtt) REVERT: I 304 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6812 (mm) REVERT: I 327 GLU cc_start: 0.6265 (pm20) cc_final: 0.5052 (tm-30) REVERT: I 338 VAL cc_start: 0.5194 (OUTLIER) cc_final: 0.4957 (t) REVERT: I 487 MET cc_start: 0.4741 (mmm) cc_final: 0.4169 (pmt) REVERT: I 539 ARG cc_start: 0.5125 (mmp-170) cc_final: 0.4274 (ttm170) REVERT: I 546 LEU cc_start: 0.4811 (OUTLIER) cc_final: 0.4580 (tt) REVERT: I 576 ARG cc_start: 0.7032 (ptm160) cc_final: 0.6828 (ptm-80) REVERT: I 627 LYS cc_start: 0.5673 (tppp) cc_final: 0.5379 (ptmm) REVERT: I 636 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6101 (tp30) REVERT: I 713 ASP cc_start: 0.8262 (p0) cc_final: 0.8028 (p0) REVERT: J 24 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8274 (mtm180) REVERT: J 25 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8994 (mptt) REVERT: J 51 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: K 540 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7972 (tm-30) REVERT: S 60 LYS cc_start: 0.7696 (mtpt) cc_final: 0.6915 (mtmt) REVERT: S 81 ASP cc_start: 0.8274 (p0) cc_final: 0.8027 (p0) REVERT: W 47 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8226 (ttt) REVERT: W 110 TYR cc_start: 0.7791 (t80) cc_final: 0.7514 (t80) REVERT: W 198 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8244 (mtmm) REVERT: W 250 MET cc_start: 0.7201 (mtp) cc_final: 0.6943 (mtm) REVERT: W 393 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6497 (pp-130) REVERT: W 409 ASN cc_start: 0.7045 (t0) cc_final: 0.6815 (t0) REVERT: W 463 ASP cc_start: 0.7240 (t0) cc_final: 0.6850 (t0) REVERT: W 577 ASP cc_start: 0.8271 (m-30) cc_final: 0.7939 (m-30) outliers start: 123 outliers final: 60 residues processed: 726 average time/residue: 0.7036 time to fit residues: 632.7108 Evaluate side-chains 705 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 621 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 546 LEU Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain W residue 47 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 295 LEU Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain W residue 326 SER Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 482 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 162 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 chunk 289 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 406 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 chunk 508 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 371 HIS B 967 GLN B 971 GLN S 55 ASN ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130231 restraints weight = 66228.256| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.27 r_work: 0.3345 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 46279 Z= 0.167 Angle : 0.574 12.297 62928 Z= 0.304 Chirality : 0.044 0.176 7140 Planarity : 0.004 0.042 7663 Dihedral : 13.862 179.786 6775 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.43 % Allowed : 15.39 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 5306 helix: 1.26 (0.12), residues: 1975 sheet: -0.44 (0.18), residues: 787 loop : -0.49 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1010 TYR 0.022 0.001 TYR S 78 PHE 0.031 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.011 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00392 (46261) covalent geometry : angle 0.57119 (62907) SS BOND : bond 0.00405 ( 3) SS BOND : angle 1.32557 ( 6) hydrogen bonds : bond 0.03915 ( 1954) hydrogen bonds : angle 4.75271 ( 5493) metal coordination : bond 0.00631 ( 15) metal coordination : angle 3.31475 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 631 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7879 (p0) REVERT: A 50 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8678 (mttt) REVERT: A 56 GLU cc_start: 0.8531 (pt0) cc_final: 0.7855 (tt0) REVERT: A 136 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7794 (mpp) REVERT: A 327 GLN cc_start: 0.8230 (tm130) cc_final: 0.7922 (tm-30) REVERT: A 592 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6466 (mm-30) REVERT: A 604 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 608 LYS cc_start: 0.7096 (mptt) cc_final: 0.6504 (tttt) REVERT: A 617 LYS cc_start: 0.8226 (mttt) cc_final: 0.7742 (tttt) REVERT: A 650 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6453 (ttp80) REVERT: A 675 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8536 (mm-30) REVERT: A 694 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7127 (pp20) REVERT: A 858 LYS cc_start: 0.8707 (tptt) cc_final: 0.8411 (tttt) REVERT: A 936 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 940 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: A 1010 ARG cc_start: 0.8525 (ptt90) cc_final: 0.8196 (ptt-90) REVERT: A 1126 GLU cc_start: 0.8563 (tt0) cc_final: 0.8100 (tm-30) REVERT: A 1131 LYS cc_start: 0.8807 (tttp) cc_final: 0.8517 (ttmm) REVERT: A 1264 MET cc_start: 0.5455 (tpt) cc_final: 0.3193 (pmt) REVERT: B 59 PHE cc_start: 0.8134 (m-80) cc_final: 0.7919 (m-80) REVERT: B 74 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7530 (mmtm) REVERT: B 190 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7443 (t80) REVERT: B 386 MET cc_start: 0.6650 (mmm) cc_final: 0.6169 (mmm) REVERT: B 413 SER cc_start: 0.7628 (OUTLIER) cc_final: 0.7200 (t) REVERT: B 608 GLU cc_start: 0.6469 (tp30) cc_final: 0.6209 (tm-30) REVERT: B 720 ARG cc_start: 0.8612 (ptm-80) cc_final: 0.8298 (ptm-80) REVERT: B 860 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6360 (mp0) REVERT: B 890 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8599 (ptpp) REVERT: B 1036 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6786 (tmtm) REVERT: B 1151 LYS cc_start: 0.8608 (pttp) cc_final: 0.7776 (mmtp) REVERT: C 89 GLU cc_start: 0.7863 (mp0) cc_final: 0.7620 (mp0) REVERT: C 115 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: C 184 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7940 (tmt-80) REVERT: E 47 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (mt) REVERT: E 132 ASP cc_start: 0.7936 (t70) cc_final: 0.7627 (p0) REVERT: E 135 LYS cc_start: 0.8490 (mttt) cc_final: 0.8235 (mttt) REVERT: G 15 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7729 (mm-30) REVERT: G 92 GLU cc_start: 0.6126 (pm20) cc_final: 0.5487 (pm20) REVERT: G 149 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: I 107 MET cc_start: 0.8105 (tpt) cc_final: 0.7801 (tpp) REVERT: I 126 LYS cc_start: 0.5464 (tppt) cc_final: 0.5126 (tppt) REVERT: I 177 LYS cc_start: 0.7908 (mttt) cc_final: 0.7458 (tttt) REVERT: I 180 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: I 194 LEU cc_start: 0.7898 (mt) cc_final: 0.7662 (mm) REVERT: I 205 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8338 (ptpp) REVERT: I 245 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7030 (tmtt) REVERT: I 304 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6816 (mm) REVERT: I 327 GLU cc_start: 0.6269 (pm20) cc_final: 0.5112 (tm-30) REVERT: I 338 VAL cc_start: 0.5232 (OUTLIER) cc_final: 0.4997 (t) REVERT: I 539 ARG cc_start: 0.5263 (mmp-170) cc_final: 0.4375 (ttm170) REVERT: I 546 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4648 (tt) REVERT: I 576 ARG cc_start: 0.7060 (ptm160) cc_final: 0.6846 (ptm-80) REVERT: I 627 LYS cc_start: 0.5679 (tppp) cc_final: 0.5381 (ptmm) REVERT: I 636 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6117 (tp30) REVERT: I 713 ASP cc_start: 0.8226 (p0) cc_final: 0.7974 (p0) REVERT: J 24 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8272 (mtm180) REVERT: J 25 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8977 (mptt) REVERT: J 51 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: K 161 MET cc_start: 0.8123 (mmp) cc_final: 0.7917 (mmm) REVERT: S 45 MET cc_start: 0.7632 (tpp) cc_final: 0.7332 (tpp) REVERT: S 60 LYS cc_start: 0.7680 (mtpt) cc_final: 0.6915 (mtmt) REVERT: S 81 ASP cc_start: 0.8270 (p0) cc_final: 0.8033 (p0) REVERT: W 47 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8235 (ttt) REVERT: W 110 TYR cc_start: 0.7930 (t80) cc_final: 0.7625 (t80) REVERT: W 198 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8276 (mtmm) REVERT: W 393 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6482 (pp-130) REVERT: W 409 ASN cc_start: 0.7037 (t0) cc_final: 0.6834 (t0) REVERT: W 463 ASP cc_start: 0.7289 (t0) cc_final: 0.6951 (t0) outliers start: 120 outliers final: 63 residues processed: 705 average time/residue: 0.7395 time to fit residues: 646.3510 Evaluate side-chains 706 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 619 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 546 LEU Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 47 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 89 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 chunk 512 optimal weight: 10.0000 chunk 422 optimal weight: 5.9990 chunk 67 optimal weight: 0.0470 chunk 519 optimal weight: 10.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 371 HIS B 391 ASN B 967 GLN B 971 GLN E 89 GLN F 111 GLN I 433 ASN S 30 GLN S 55 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 254 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128717 restraints weight = 66189.584| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.32 r_work: 0.3320 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 46279 Z= 0.207 Angle : 0.607 12.643 62928 Z= 0.321 Chirality : 0.045 0.194 7140 Planarity : 0.004 0.043 7663 Dihedral : 13.937 179.286 6775 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.43 % Allowed : 15.80 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.11), residues: 5306 helix: 1.15 (0.12), residues: 1975 sheet: -0.50 (0.18), residues: 788 loop : -0.52 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1010 TYR 0.024 0.002 TYR S 78 PHE 0.033 0.002 PHE A 938 TRP 0.013 0.002 TRP A 365 HIS 0.012 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00489 (46261) covalent geometry : angle 0.60419 (62907) SS BOND : bond 0.00453 ( 3) SS BOND : angle 1.45001 ( 6) hydrogen bonds : bond 0.04189 ( 1954) hydrogen bonds : angle 4.82035 ( 5493) metal coordination : bond 0.00768 ( 15) metal coordination : angle 3.51975 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 614 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 50 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8696 (mttt) REVERT: A 56 GLU cc_start: 0.8552 (pt0) cc_final: 0.7877 (tt0) REVERT: A 136 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7844 (mpp) REVERT: A 327 GLN cc_start: 0.8235 (tm130) cc_final: 0.7942 (tm-30) REVERT: A 349 ARG cc_start: 0.7018 (mmt180) cc_final: 0.6685 (mtm180) REVERT: A 592 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6527 (mm-30) REVERT: A 604 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 608 LYS cc_start: 0.7047 (mptt) cc_final: 0.6513 (tttt) REVERT: A 617 LYS cc_start: 0.8256 (mttt) cc_final: 0.7810 (tttt) REVERT: A 650 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6484 (ttp80) REVERT: A 675 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8602 (mm-30) REVERT: A 694 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: A 858 LYS cc_start: 0.8735 (tptt) cc_final: 0.8428 (tttt) REVERT: A 940 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: A 963 GLU cc_start: 0.8284 (tp30) cc_final: 0.8037 (tp30) REVERT: A 1010 ARG cc_start: 0.8526 (ptt90) cc_final: 0.8292 (ptt-90) REVERT: A 1126 GLU cc_start: 0.8639 (tt0) cc_final: 0.8215 (tm-30) REVERT: A 1131 LYS cc_start: 0.8834 (tttp) cc_final: 0.8535 (ttmm) REVERT: A 1218 LYS cc_start: 0.8127 (tptt) cc_final: 0.7908 (tptt) REVERT: A 1264 MET cc_start: 0.5505 (tpt) cc_final: 0.3199 (pmt) REVERT: B 59 PHE cc_start: 0.8144 (m-80) cc_final: 0.7899 (m-80) REVERT: B 74 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7494 (mmtm) REVERT: B 190 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 206 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7621 (mmm-85) REVERT: B 337 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7930 (mttp) REVERT: B 386 MET cc_start: 0.6620 (mmm) cc_final: 0.6185 (mmm) REVERT: B 413 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.7167 (t) REVERT: B 608 GLU cc_start: 0.6597 (tp30) cc_final: 0.6388 (tm-30) REVERT: B 720 ARG cc_start: 0.8629 (ptm-80) cc_final: 0.8313 (ptm-80) REVERT: B 890 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8608 (ptpp) REVERT: B 946 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8429 (mtmt) REVERT: B 1036 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6779 (tmtm) REVERT: B 1151 LYS cc_start: 0.8579 (pttp) cc_final: 0.7674 (mptt) REVERT: C 89 GLU cc_start: 0.7887 (mp0) cc_final: 0.7631 (mp0) REVERT: C 115 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: C 184 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7993 (tmt-80) REVERT: E 47 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8176 (mt) REVERT: E 132 ASP cc_start: 0.8006 (t70) cc_final: 0.7618 (p0) REVERT: E 135 LYS cc_start: 0.8498 (mttt) cc_final: 0.8207 (mttt) REVERT: F 135 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8447 (mt-10) REVERT: G 15 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7725 (mm-30) REVERT: G 55 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: G 92 GLU cc_start: 0.6113 (pm20) cc_final: 0.5389 (pm20) REVERT: G 149 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: I 107 MET cc_start: 0.8111 (tpt) cc_final: 0.7872 (tpp) REVERT: I 126 LYS cc_start: 0.5482 (tppt) cc_final: 0.5153 (tppt) REVERT: I 177 LYS cc_start: 0.7872 (mttt) cc_final: 0.7471 (tttt) REVERT: I 180 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: I 194 LEU cc_start: 0.7834 (mt) cc_final: 0.7582 (mm) REVERT: I 205 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8332 (ptpp) REVERT: I 289 ASP cc_start: 0.8441 (t0) cc_final: 0.7825 (m-30) REVERT: I 304 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6862 (mm) REVERT: I 327 GLU cc_start: 0.6206 (pm20) cc_final: 0.5622 (mp0) REVERT: I 338 VAL cc_start: 0.5216 (OUTLIER) cc_final: 0.4971 (t) REVERT: I 539 ARG cc_start: 0.5255 (mmp-170) cc_final: 0.4348 (ttm170) REVERT: I 546 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4644 (tt) REVERT: I 576 ARG cc_start: 0.7048 (ptm160) cc_final: 0.6817 (ptm-80) REVERT: I 627 LYS cc_start: 0.5584 (tppp) cc_final: 0.5317 (ptmm) REVERT: I 636 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6196 (tp30) REVERT: I 790 MET cc_start: 0.7656 (tpp) cc_final: 0.7411 (mpp) REVERT: J 24 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8320 (mtm180) REVERT: J 25 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8981 (mptt) REVERT: J 51 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: S 60 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7445 (mtpp) REVERT: W 110 TYR cc_start: 0.7955 (t80) cc_final: 0.7514 (t80) REVERT: W 114 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.5935 (t80) REVERT: W 198 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8304 (mtmm) REVERT: W 285 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: W 393 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6599 (pp-130) REVERT: W 409 ASN cc_start: 0.7113 (t0) cc_final: 0.6900 (t0) REVERT: W 463 ASP cc_start: 0.7336 (t0) cc_final: 0.6943 (t0) REVERT: W 567 MET cc_start: 0.8359 (tmm) cc_final: 0.8125 (tmm) REVERT: W 577 ASP cc_start: 0.8299 (m-30) cc_final: 0.7984 (m-30) outliers start: 120 outliers final: 68 residues processed: 690 average time/residue: 0.5423 time to fit residues: 464.2240 Evaluate side-chains 697 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 602 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 546 LEU Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 678 GLU Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 114 TYR Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 285 GLN Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 257 optimal weight: 10.0000 chunk 495 optimal weight: 0.7980 chunk 410 optimal weight: 20.0000 chunk 287 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 503 optimal weight: 0.2980 chunk 114 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 371 HIS B 376 ASN B 967 GLN B 971 GLN F 111 GLN S 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130342 restraints weight = 66535.332| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.29 r_work: 0.3345 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 46279 Z= 0.158 Angle : 0.579 12.643 62928 Z= 0.306 Chirality : 0.044 0.220 7140 Planarity : 0.004 0.042 7663 Dihedral : 13.900 179.953 6775 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.11 % Allowed : 16.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 5306 helix: 1.23 (0.12), residues: 1969 sheet: -0.46 (0.18), residues: 784 loop : -0.49 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1010 TYR 0.031 0.001 TYR W 315 PHE 0.031 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.012 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00369 (46261) covalent geometry : angle 0.57708 (62907) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.27943 ( 6) hydrogen bonds : bond 0.03868 ( 1954) hydrogen bonds : angle 4.76983 ( 5493) metal coordination : bond 0.00587 ( 15) metal coordination : angle 3.35247 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10612 Ramachandran restraints generated. 5306 Oldfield, 0 Emsley, 5306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 620 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7812 (p0) REVERT: A 50 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8703 (mttt) REVERT: A 56 GLU cc_start: 0.8547 (pt0) cc_final: 0.7891 (tt0) REVERT: A 136 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7861 (mpp) REVERT: A 327 GLN cc_start: 0.8218 (tm130) cc_final: 0.7902 (tm-30) REVERT: A 349 ARG cc_start: 0.6976 (mmt180) cc_final: 0.6547 (mtm180) REVERT: A 592 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6455 (mm-30) REVERT: A 604 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 608 LYS cc_start: 0.7039 (mptt) cc_final: 0.6511 (tttt) REVERT: A 617 LYS cc_start: 0.8241 (mttt) cc_final: 0.7822 (tttt) REVERT: A 650 ARG cc_start: 0.7412 (mtt180) cc_final: 0.6500 (ttp80) REVERT: A 675 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8574 (mm-30) REVERT: A 694 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: A 858 LYS cc_start: 0.8722 (tptt) cc_final: 0.8416 (tttt) REVERT: A 940 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: A 963 GLU cc_start: 0.8218 (tp30) cc_final: 0.7977 (tp30) REVERT: A 1010 ARG cc_start: 0.8531 (ptt90) cc_final: 0.8295 (ptt-90) REVERT: A 1126 GLU cc_start: 0.8644 (tt0) cc_final: 0.8222 (tm-30) REVERT: A 1131 LYS cc_start: 0.8800 (tttp) cc_final: 0.8511 (ttmm) REVERT: A 1264 MET cc_start: 0.5494 (tpt) cc_final: 0.3188 (pmt) REVERT: B 59 PHE cc_start: 0.8154 (m-80) cc_final: 0.7898 (m-80) REVERT: B 74 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7458 (mmtm) REVERT: B 190 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7455 (t80) REVERT: B 206 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7606 (mmm-85) REVERT: B 292 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6341 (mt-10) REVERT: B 386 MET cc_start: 0.6603 (mmm) cc_final: 0.6189 (mmm) REVERT: B 413 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7203 (t) REVERT: B 608 GLU cc_start: 0.6602 (tp30) cc_final: 0.6402 (tm-30) REVERT: B 720 ARG cc_start: 0.8603 (ptm-80) cc_final: 0.8292 (ptm-80) REVERT: B 890 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8607 (ptpp) REVERT: B 946 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8425 (mtmt) REVERT: B 1036 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6773 (tmtm) REVERT: B 1151 LYS cc_start: 0.8588 (pttp) cc_final: 0.7676 (mptt) REVERT: C 89 GLU cc_start: 0.7839 (mp0) cc_final: 0.7589 (mp0) REVERT: C 115 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: C 184 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7960 (tmt-80) REVERT: C 286 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8193 (tt) REVERT: E 47 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8180 (mt) REVERT: E 132 ASP cc_start: 0.7977 (t70) cc_final: 0.7627 (p0) REVERT: E 135 LYS cc_start: 0.8474 (mttt) cc_final: 0.8207 (mttt) REVERT: G 15 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7698 (mm-30) REVERT: G 55 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: G 92 GLU cc_start: 0.6110 (pm20) cc_final: 0.5369 (pm20) REVERT: G 149 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: I 107 MET cc_start: 0.8083 (tpt) cc_final: 0.7782 (tpp) REVERT: I 126 LYS cc_start: 0.5505 (tppt) cc_final: 0.5177 (tppt) REVERT: I 177 LYS cc_start: 0.7848 (mttt) cc_final: 0.7440 (tttt) REVERT: I 180 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: I 194 LEU cc_start: 0.7854 (mt) cc_final: 0.7610 (mm) REVERT: I 205 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (ptpp) REVERT: I 304 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6975 (mm) REVERT: I 327 GLU cc_start: 0.6208 (pm20) cc_final: 0.5619 (mp0) REVERT: I 338 VAL cc_start: 0.5286 (OUTLIER) cc_final: 0.5043 (t) REVERT: I 539 ARG cc_start: 0.5210 (mmp-170) cc_final: 0.4308 (ttm170) REVERT: I 546 LEU cc_start: 0.4818 (OUTLIER) cc_final: 0.4608 (tt) REVERT: I 576 ARG cc_start: 0.7015 (ptm160) cc_final: 0.6758 (ptm-80) REVERT: I 627 LYS cc_start: 0.5529 (tppp) cc_final: 0.5299 (ptmm) REVERT: I 636 GLU cc_start: 0.6402 (mm-30) cc_final: 0.6181 (tp30) REVERT: I 713 ASP cc_start: 0.8179 (p0) cc_final: 0.7964 (p0) REVERT: J 24 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8299 (mtm180) REVERT: J 51 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: K 289 ARG cc_start: 0.7984 (tpm-80) cc_final: 0.7603 (tpm-80) REVERT: K 540 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8113 (tm-30) REVERT: S 60 LYS cc_start: 0.7639 (mtpt) cc_final: 0.7415 (mtpp) REVERT: W 110 TYR cc_start: 0.7944 (t80) cc_final: 0.7741 (t80) REVERT: W 198 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8241 (mtmm) REVERT: W 285 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: W 393 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6550 (pp-130) REVERT: W 408 GLU cc_start: 0.7898 (pm20) cc_final: 0.7698 (pm20) REVERT: W 409 ASN cc_start: 0.7003 (t0) cc_final: 0.6761 (t0) REVERT: W 463 ASP cc_start: 0.7346 (t0) cc_final: 0.6998 (t0) REVERT: W 577 ASP cc_start: 0.8274 (m-30) cc_final: 0.7961 (m-30) outliers start: 104 outliers final: 68 residues processed: 683 average time/residue: 0.4808 time to fit residues: 410.0654 Evaluate side-chains 701 residues out of total 4938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 607 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 890 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1036 LYS Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 546 LEU Chi-restraints excluded: chain I residue 629 VAL Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 51 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 353 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 481 VAL Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 285 GLN Chi-restraints excluded: chain W residue 303 LEU Chi-restraints excluded: chain W residue 393 MET Chi-restraints excluded: chain W residue 399 ASP Chi-restraints excluded: chain W residue 484 VAL Chi-restraints excluded: chain W residue 491 THR Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 556 ARG Chi-restraints excluded: chain W residue 557 ILE Chi-restraints excluded: chain W residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 341 optimal weight: 5.9990 chunk 441 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 451 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 273 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1222 ASN B 295 HIS B 371 HIS B 376 ASN B 391 ASN B 967 GLN B 971 GLN F 111 GLN S 55 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130362 restraints weight = 66348.742| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.22 r_work: 0.3342 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 46279 Z= 0.167 Angle : 0.587 13.507 62928 Z= 0.310 Chirality : 0.044 0.184 7140 Planarity : 0.004 0.047 7663 Dihedral : 13.906 179.675 6775 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.27 % Allowed : 16.36 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 5306 helix: 1.21 (0.12), residues: 1971 sheet: -0.46 (0.18), residues: 784 loop : -0.50 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 90 TYR 0.031 0.002 TYR W 315 PHE 0.031 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.012 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00393 (46261) covalent geometry : angle 0.58497 (62907) SS BOND : bond 0.00394 ( 3) SS BOND : angle 1.30508 ( 6) hydrogen bonds : bond 0.03914 ( 1954) hydrogen bonds : angle 4.77374 ( 5493) metal coordination : bond 0.00625 ( 15) metal coordination : angle 3.33602 ( 15) =============================================================================== Job complete usr+sys time: 18494.28 seconds wall clock time: 314 minutes 40.85 seconds (18880.85 seconds total)