Starting phenix.real_space_refine on Sun Aug 9 20:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s55_19726/08_2026/8s55_19726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s55_19726/08_2026/8s55_19726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s55_19726/08_2026/8s55_19726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s55_19726/08_2026/8s55_19726.map" model { file = "/net/cci-nas-00/data/ceres_data/8s55_19726/08_2026/8s55_19726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s55_19726/08_2026/8s55_19726.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 9 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 217 5.16 5 C 23769 2.51 5 N 6713 2.21 5 O 7345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 302 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38148 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1417, 11234 Classifications: {'peptide': 1417} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1346} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1130, 9030 Classifications: {'peptide': 1130} Link IDs: {'PTRANS': 53, 'TRANS': 1076} Chain breaks: 3 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 712 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "P" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1070 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 1 Chain: "T" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 949 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" 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 464 SG CYS A 71 70.102 106.167 83.193 1.00171.09 S ATOM 486 SG CYS A 74 66.552 104.671 83.199 1.00166.47 S ATOM 533 SG CYS A 81 69.640 102.536 84.071 1.00161.10 S ATOM 768 SG CYS A 111 72.125 72.447 46.680 1.00212.97 S ATOM 796 SG CYS A 114 68.989 74.694 45.205 1.00212.90 S ATOM 1142 SG CYS A 184 71.841 74.110 42.932 1.00226.08 S ATOM 19834 SG CYS B1119 56.207 94.271 75.162 1.00170.32 S ATOM 19856 SG CYS B1122 59.476 92.946 73.679 1.00167.90 S ATOM 19971 SG CYS B1137 59.095 96.660 74.509 1.00174.40 S ATOM 19992 SG CYS B1140 57.498 94.996 71.498 1.00181.94 S ATOM 20958 SG CYS C 88 84.561 106.637 149.164 1.00156.67 S ATOM 20971 SG CYS C 90 86.413 108.809 145.860 1.00164.62 S ATOM 21006 SG CYS C 94 87.799 108.700 149.163 1.00150.56 S ATOM 21028 SG CYS C 97 87.613 105.606 147.306 1.00145.79 S ATOM 28358 SG CYS I 20 130.138 42.771 51.036 1.00232.73 S ATOM 28519 SG CYS I 39 126.472 41.659 50.644 1.00239.07 S ATOM 28544 SG CYS I 42 128.612 44.677 48.298 1.00246.74 S ATOM 28896 SG CYS I 86 134.376 27.519 94.027 1.00181.13 S ATOM 28920 SG CYS I 89 137.691 28.760 95.432 1.00182.74 S ATOM 29124 SG CYS I 114 134.636 31.088 95.669 1.00175.58 S ATOM 29159 SG CYS I 119 136.171 30.316 92.369 1.00183.75 S ATOM 29269 SG CYS J 7 103.012 78.476 140.057 1.00126.06 S ATOM 29293 SG CYS J 10 101.418 78.229 143.540 1.00125.94 S ATOM 29557 SG CYS J 44 102.673 75.140 141.579 1.00128.49 S ATOM 29563 SG CYS J 45 105.041 77.589 143.242 1.00130.35 S ATOM 30705 SG CYS L 19 117.932 111.305 115.321 1.00174.67 S ATOM 30724 SG CYS L 22 121.130 112.530 116.343 1.00181.77 S ATOM 30841 SG CYS L 36 119.483 114.277 113.389 1.00179.48 S ATOM 30867 SG CYS L 39 120.933 110.981 112.789 1.00182.92 S ATOM 36198 SG CYS W 129 56.942 129.035 73.122 1.00352.30 S ATOM 36390 SG CYS W 154 57.981 126.902 76.889 1.00352.13 S ATOM 36414 SG CYS W 157 59.392 129.600 76.289 1.00346.47 S Time building chain proxies: 7.26, per 1000 atoms: 0.19 Number of scatterers: 38148 At special positions: 0 Unit cell: (178.5, 152.25, 181.65, 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 9 29.99 S 217 16.00 P 94 15.00 Mg 1 11.99 O 7345 8.00 N 6713 7.00 C 23769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " Number of angles added : 33 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8512 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 52 sheets defined 40.3% alpha, 17.9% beta 41 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 151 removed outlier: 4.058A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.632A pdb=" N GLY A 237 " --> pdb=" O CYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.121A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 300 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 removed outlier: 3.521A pdb=" N LEU A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.560A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.511A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 4.029A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 723 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.360A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.919A pdb=" N SER A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 901' Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.529A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.727A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.879A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.017A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.206A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.791A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1198 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1281 through 1296 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.944A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.963A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1432 removed outlier: 3.902A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1446 Processing helix chain 'A' and resid 1453 through 1459 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 4.388A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 247 through 253 removed outlier: 4.362A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.760A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 4.242A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.503A pdb=" N GLN B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.522A pdb=" N SER B 659 " --> pdb=" O ASP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.947A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 4.264A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.895A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1018 removed outlier: 3.509A pdb=" N ILE B1011 " --> pdb=" O ASN B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 242 through 271 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.114A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.531A pdb=" N LEU H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.585A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.751A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.703A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.241A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 38 through 42 Processing helix chain 'Q' and resid 156 through 161 Processing helix chain 'Q' and resid 162 through 165 Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 175 through 180 removed outlier: 3.932A pdb=" N GLN Q 179 " --> pdb=" O SER Q 175 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG Q 180 " --> pdb=" O ILE Q 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 175 through 180' Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 24 through 35 Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 123 through 136 removed outlier: 3.669A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 26 removed outlier: 3.682A pdb=" N LYS W 15 " --> pdb=" O PRO W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 40 Processing helix chain 'W' and resid 45 through 53 Processing helix chain 'W' and resid 55 through 70 Processing helix chain 'W' and resid 95 through 124 removed outlier: 3.918A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 145 Processing helix chain 'W' and resid 166 through 184 removed outlier: 4.135A pdb=" N LYS W 170 " --> pdb=" O SER W 166 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS W 171 " --> pdb=" O ALA W 167 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA W 173 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG W 179 " --> pdb=" O THR W 175 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 194 Processing helix chain 'X' and resid 76 through 91 removed outlier: 3.630A pdb=" N LYS X 80 " --> pdb=" O GLY X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 106 removed outlier: 3.595A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 122 Processing helix chain 'X' and resid 122 through 127 removed outlier: 3.870A pdb=" N ASN X 127 " --> pdb=" O ALA X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 162 Processing helix chain 'X' and resid 168 through 175 Processing helix chain 'X' and resid 177 through 186 removed outlier: 4.066A pdb=" N ALA X 181 " --> pdb=" O ASN X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 213 through 223 Processing helix chain 'X' and resid 229 through 240 removed outlier: 3.730A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.539A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 3.640A pdb=" N LEU A 90 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.507A pdb=" N SER A 194 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.562A pdb=" N ARG A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.640A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.645A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.937A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.539A pdb=" N THR A 527 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.192A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 61 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL H 59 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP H 8 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL H 116 " --> pdb=" O MET H 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.628A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.922A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1138 through 1142 removed outlier: 4.090A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS A1310 " --> pdb=" O ILE A1335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1256 through 1259 removed outlier: 3.952A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A1175 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 4.279A pdb=" N ILE A1321 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1471 through 1475 removed outlier: 3.825A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 107 " --> pdb=" O ASP A1472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A1474 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 105 " --> pdb=" O LEU A1474 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.109A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.206A pdb=" N SER B 94 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC3, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'B' and resid 197 through 200 Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 220 removed outlier: 4.080A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.770A pdb=" N ARG B 623 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC8, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.577A pdb=" N GLU B 551 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 576 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 602 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.551A pdb=" N VAL B 750 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS L 46 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 removed outlier: 6.022A pdb=" N GLY B 997 " --> pdb=" O THR B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 3.582A pdb=" N ALA B 936 " --> pdb=" O GLN B1049 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD5, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD6, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.488A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.992A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 50 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.725A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 removed outlier: 11.323A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.551A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.722A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.545A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 92 removed outlier: 3.690A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG G 151 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE8, first strand: chain 'I' and resid 36 through 38 Processing sheet with id=AE9, first strand: chain 'I' and resid 94 through 97 removed outlier: 3.588A pdb=" N VAL I 95 " --> pdb=" O VAL I 113 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 30 through 33 Processing sheet with id=AF2, first strand: chain 'Q' and resid 24 through 26 removed outlier: 10.935A pdb=" N GLN R 91 " --> pdb=" O GLN R 112 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLN R 112 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU R 93 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR R 97 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU R 106 " --> pdb=" O THR R 97 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER R 99 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU R 104 " --> pdb=" O SER R 99 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 104 through 116 current: chain 'Q' and resid 143 through 149 removed outlier: 4.027A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA Q 45 " --> pdb=" O LEU R 7 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 24 through 26 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 91 through 99 current: chain 'R' and resid 52 through 58 removed outlier: 3.937A pdb=" N GLY R 41 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU Q 136 " --> pdb=" O THR Q 128 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR Q 128 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE Q 138 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER Q 123 " --> pdb=" O VAL R 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL R 23 " --> pdb=" O SER Q 123 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL R 18 " --> pdb=" O VAL R 111 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG R 113 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU R 20 " --> pdb=" O ARG R 113 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU R 115 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS R 22 " --> pdb=" O GLU R 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 104 through 116 current: chain 'Q' and resid 143 through 149 removed outlier: 4.027A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA Q 45 " --> pdb=" O LEU R 7 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 42 through 44 Processing sheet with id=AF5, first strand: chain 'W' and resid 127 through 129 removed outlier: 3.693A pdb=" N CYS W 129 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER W 134 " --> pdb=" O CYS W 129 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 130 through 133 Processing sheet with id=AF7, first strand: chain 'X' and resid 166 through 167 1558 hydrogen bonds defined for protein. 4341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 13.06 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12486 1.34 - 1.47: 9146 1.47 - 1.60: 16908 1.60 - 1.73: 169 1.73 - 1.86: 343 Bond restraints: 39052 Sorted by residual: bond pdb=" C5' DG N 74 " pdb=" C4' DG N 74 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.89e+01 bond pdb=" C5' DG N 64 " pdb=" C4' DG N 64 " ideal model delta sigma weight residual 1.512 1.541 -0.029 7.00e-03 2.04e+04 1.76e+01 bond pdb=" C2 DG T 37 " pdb=" N2 DG T 37 " ideal model delta sigma weight residual 1.341 1.301 0.040 1.00e-02 1.00e+04 1.60e+01 bond pdb=" C2 DG N 64 " pdb=" N2 DG N 64 " ideal model delta sigma weight residual 1.341 1.303 0.038 1.00e-02 1.00e+04 1.41e+01 bond pdb=" P DG T 27 " pdb=" O5' DG T 27 " ideal model delta sigma weight residual 1.593 1.630 -0.037 1.00e-02 1.00e+04 1.38e+01 ... (remaining 39047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 51155 1.93 - 3.85: 1515 3.85 - 5.78: 335 5.78 - 7.71: 116 7.71 - 9.64: 10 Bond angle restraints: 53131 Sorted by residual: angle pdb=" O5' DG N 69 " pdb=" C5' DG N 69 " pdb=" C4' DG N 69 " ideal model delta sigma weight residual 109.40 113.78 -4.38 8.00e-01 1.56e+00 2.99e+01 angle pdb=" O5' DG T 34 " pdb=" C5' DG T 34 " pdb=" C4' DG T 34 " ideal model delta sigma weight residual 109.40 113.70 -4.30 8.00e-01 1.56e+00 2.89e+01 angle pdb=" C3' DG T 27 " pdb=" O3' DG T 27 " pdb=" P DG T 28 " ideal model delta sigma weight residual 119.70 125.67 -5.97 1.20e+00 6.94e-01 2.47e+01 angle pdb=" C3' DG N 70 " pdb=" O3' DG N 70 " pdb=" P DC N 71 " ideal model delta sigma weight residual 119.70 125.56 -5.86 1.20e+00 6.94e-01 2.38e+01 angle pdb=" CA ASN A1129 " pdb=" C ASN A1129 " pdb=" N ILE A1130 " ideal model delta sigma weight residual 115.27 121.74 -6.47 1.34e+00 5.57e-01 2.33e+01 ... (remaining 53126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 23017 35.28 - 70.57: 651 70.57 - 105.85: 42 105.85 - 141.13: 1 141.13 - 176.41: 3 Dihedral angle restraints: 23714 sinusoidal: 10568 harmonic: 13146 Sorted by residual: dihedral pdb=" CA THR A 463 " pdb=" C THR A 463 " pdb=" N LEU A 464 " pdb=" CA LEU A 464 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLU A1434 " pdb=" C GLU A1434 " pdb=" N THR A1435 " pdb=" CA THR A1435 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA PHE H 88 " pdb=" C PHE H 88 " pdb=" N GLU H 89 " pdb=" CA GLU H 89 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 23711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 5764 0.129 - 0.259: 74 0.259 - 0.388: 5 0.388 - 0.518: 16 0.518 - 0.647: 68 Chirality restraints: 5927 Sorted by residual: chirality pdb=" P DT N 57 " pdb=" OP1 DT N 57 " pdb=" OP2 DT N 57 " pdb=" O5' DT N 57 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DG T 28 " pdb=" OP1 DG T 28 " pdb=" OP2 DG T 28 " pdb=" O5' DG T 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DT T 21 " pdb=" OP1 DT T 21 " pdb=" OP2 DT T 21 " pdb=" O5' DT T 21 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 5924 not shown) Planarity restraints: 6556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG N 69 " 0.079 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" N9 DG N 69 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DG N 69 " -0.080 2.00e-02 2.50e+03 pdb=" N7 DG N 69 " -0.089 2.00e-02 2.50e+03 pdb=" C5 DG N 69 " -0.014 2.00e-02 2.50e+03 pdb=" C6 DG N 69 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG N 69 " 0.068 2.00e-02 2.50e+03 pdb=" N1 DG N 69 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DG N 69 " 0.021 2.00e-02 2.50e+03 pdb=" N2 DG N 69 " -0.116 2.00e-02 2.50e+03 pdb=" N3 DG N 69 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DG N 69 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 64 " 0.082 2.00e-02 2.50e+03 5.73e-02 9.87e+01 pdb=" N9 DG N 64 " 0.050 2.00e-02 2.50e+03 pdb=" C8 DG N 64 " -0.086 2.00e-02 2.50e+03 pdb=" N7 DG N 64 " -0.086 2.00e-02 2.50e+03 pdb=" C5 DG N 64 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DG N 64 " 0.019 2.00e-02 2.50e+03 pdb=" O6 DG N 64 " 0.100 2.00e-02 2.50e+03 pdb=" N1 DG N 64 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG N 64 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG N 64 " -0.067 2.00e-02 2.50e+03 pdb=" N3 DG N 64 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG N 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 74 " 0.058 2.00e-02 2.50e+03 4.74e-02 6.75e+01 pdb=" N9 DG N 74 " 0.014 2.00e-02 2.50e+03 pdb=" C8 DG N 74 " -0.085 2.00e-02 2.50e+03 pdb=" N7 DG N 74 " -0.056 2.00e-02 2.50e+03 pdb=" C5 DG N 74 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG N 74 " 0.027 2.00e-02 2.50e+03 pdb=" O6 DG N 74 " 0.057 2.00e-02 2.50e+03 pdb=" N1 DG N 74 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG N 74 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG N 74 " -0.084 2.00e-02 2.50e+03 pdb=" N3 DG N 74 " 0.039 2.00e-02 2.50e+03 pdb=" C4 DG N 74 " 0.025 2.00e-02 2.50e+03 ... (remaining 6553 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 100 2.38 - 3.01: 21666 3.01 - 3.64: 59332 3.64 - 4.27: 85295 4.27 - 4.90: 140722 Nonbonded interactions: 307115 Sorted by model distance: nonbonded pdb=" O3' A P 14 " pdb="MG MG P 101 " model vdw 1.747 2.170 nonbonded pdb=" CD2 LEU B 747 " pdb=" OP1 DG T 49 " model vdw 1.765 3.460 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG P 101 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR C 15 " pdb=" OD1 ASN C 18 " model vdw 1.996 3.040 nonbonded pdb=" OG SER B 31 " pdb=" OH TYR B 766 " model vdw 2.003 3.040 ... (remaining 307110 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 47.270 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.006 0.686 39085 Z= 0.308 Angle : 0.832 23.961 53164 Z= 0.457 Chirality : 0.080 0.647 5927 Planarity : 0.007 0.228 6556 Dihedral : 15.613 176.412 15202 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.29 (0.13), residues: 4460 helix: 1.47 (0.13), residues: 1594 sheet: -0.25 (0.21), residues: 651 loop : -0.58 (0.14), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 358 TYR 0.043 0.001 TYR A 145 PHE 0.040 0.002 PHE B1086 TRP 0.017 0.001 TRP A1192 HIS 0.014 0.001 HIS B 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.29 (39052) covalent geometry : angle 0.81876 / 0.46 (53131) hydrogen bonds : bond 0.18009 / 12.48 ( 1625) hydrogen bonds : angle 7.27462 / 5.11 ( 4555) metal coordination : bond 0.12015 / 9.17 ( 33) metal coordination : angle 6.07419 / 4.50 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 716 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8601 (t70) cc_final: 0.8252 (t0) REVERT: A 186 ARG cc_start: 0.7388 (tpt170) cc_final: 0.6933 (tpp-160) REVERT: A 355 MET cc_start: 0.9244 (mmm) cc_final: 0.8043 (mmm) REVERT: A 365 THR cc_start: 0.8971 (t) cc_final: 0.8710 (m) REVERT: A 561 MET cc_start: 0.8987 (mmt) cc_final: 0.8644 (mmt) REVERT: A 565 MET cc_start: 0.8861 (tpt) cc_final: 0.8500 (tpt) REVERT: A 818 GLU cc_start: 0.8628 (pm20) cc_final: 0.8407 (tt0) REVERT: A 845 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 861 GLN cc_start: 0.8803 (pt0) cc_final: 0.8589 (pt0) REVERT: A 1036 ASN cc_start: 0.8462 (m-40) cc_final: 0.8002 (t0) REVERT: A 1038 THR cc_start: 0.9052 (m) cc_final: 0.8696 (t) REVERT: A 1050 CYS cc_start: 0.8692 (t) cc_final: 0.8477 (t) REVERT: A 1093 GLN cc_start: 0.9085 (mt0) cc_final: 0.8628 (tt0) REVERT: A 1192 TRP cc_start: 0.8712 (p90) cc_final: 0.8417 (p90) REVERT: A 1288 ILE cc_start: 0.9550 (mm) cc_final: 0.9168 (tp) REVERT: A 1293 LEU cc_start: 0.9413 (tt) cc_final: 0.9086 (mm) REVERT: A 1309 MET cc_start: 0.8495 (mtp) cc_final: 0.8201 (mtt) REVERT: A 1322 ILE cc_start: 0.8905 (mt) cc_final: 0.8676 (mt) REVERT: A 1434 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 60 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8903 (tm-30) REVERT: B 155 MET cc_start: 0.8311 (ptm) cc_final: 0.7945 (ptm) REVERT: B 172 CYS cc_start: 0.9255 (m) cc_final: 0.8749 (m) REVERT: B 230 ARG cc_start: 0.7881 (tpt170) cc_final: 0.7384 (tpp80) REVERT: B 299 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 300 MET cc_start: 0.9062 (tpt) cc_final: 0.8652 (tpp) REVERT: B 315 ASN cc_start: 0.9122 (m-40) cc_final: 0.8563 (m-40) REVERT: B 346 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8250 (tt0) REVERT: B 422 PHE cc_start: 0.8556 (t80) cc_final: 0.7972 (t80) REVERT: B 683 GLN cc_start: 0.8647 (mm110) cc_final: 0.8446 (mm110) REVERT: B 709 SER cc_start: 0.8887 (m) cc_final: 0.8663 (m) REVERT: B 908 MET cc_start: 0.8644 (ttm) cc_final: 0.8342 (ttm) REVERT: B 942 LYS cc_start: 0.7946 (mttp) cc_final: 0.7692 (mttt) REVERT: B 983 GLU cc_start: 0.9003 (tt0) cc_final: 0.8748 (tt0) REVERT: B 1093 CYS cc_start: 0.8551 (t) cc_final: 0.8087 (t) REVERT: B 1127 ILE cc_start: 0.8823 (pt) cc_final: 0.8319 (pt) REVERT: B 1136 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6787 (tm-30) REVERT: B 1155 CYS cc_start: 0.9077 (t) cc_final: 0.8777 (t) REVERT: B 1172 MET cc_start: 0.8896 (mmp) cc_final: 0.8502 (mmp) REVERT: C 157 GLN cc_start: 0.9103 (mt0) cc_final: 0.8832 (mt0) REVERT: C 265 HIS cc_start: 0.8826 (t70) cc_final: 0.8347 (t70) REVERT: D 34 ASN cc_start: 0.9258 (m110) cc_final: 0.8790 (t0) REVERT: E 91 CYS cc_start: 0.9386 (m) cc_final: 0.9137 (m) REVERT: E 108 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8414 (tm-30) REVERT: E 116 GLN cc_start: 0.9458 (tp-100) cc_final: 0.8811 (tp40) REVERT: F 96 GLU cc_start: 0.8861 (pp20) cc_final: 0.8620 (pp20) REVERT: F 100 ARG cc_start: 0.9020 (tpp80) cc_final: 0.8707 (tpp80) REVERT: G 3 TYR cc_start: 0.8791 (m-80) cc_final: 0.8496 (m-10) REVERT: G 21 ASN cc_start: 0.8432 (t0) cc_final: 0.8005 (t0) REVERT: G 60 GLN cc_start: 0.8470 (mm110) cc_final: 0.8080 (mt0) REVERT: H 9 ILE cc_start: 0.8661 (mt) cc_final: 0.7962 (mm) REVERT: H 37 MET cc_start: 0.8385 (mtp) cc_final: 0.8108 (mtp) REVERT: H 43 VAL cc_start: 0.9253 (t) cc_final: 0.8996 (p) REVERT: H 56 PHE cc_start: 0.8109 (p90) cc_final: 0.7803 (p90) REVERT: H 89 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7453 (tm-30) REVERT: H 103 GLU cc_start: 0.8928 (pm20) cc_final: 0.8692 (pm20) REVERT: H 124 ARG cc_start: 0.7395 (ttp-170) cc_final: 0.7133 (ttp80) REVERT: I 74 GLN cc_start: 0.8807 (pt0) cc_final: 0.8568 (pt0) REVERT: J 48 MET cc_start: 0.9059 (tpp) cc_final: 0.8698 (tpt) REVERT: J 54 ASP cc_start: 0.8085 (p0) cc_final: 0.7541 (p0) REVERT: K 31 CYS cc_start: 0.8138 (t) cc_final: 0.7895 (t) REVERT: K 53 ASP cc_start: 0.9082 (t70) cc_final: 0.8746 (t0) REVERT: K 102 GLU cc_start: 0.8953 (tt0) cc_final: 0.8692 (mt-10) REVERT: L 18 ILE cc_start: 0.8959 (tp) cc_final: 0.8383 (tp) REVERT: L 41 TYR cc_start: 0.7738 (t80) cc_final: 0.7360 (t80) REVERT: L 44 MET cc_start: 0.8352 (mmm) cc_final: 0.7834 (mmm) REVERT: Q 98 TRP cc_start: 0.7250 (m100) cc_final: 0.6288 (m100) REVERT: Q 99 LEU cc_start: 0.7125 (tt) cc_final: 0.6711 (tt) REVERT: Q 124 TYR cc_start: 0.8555 (m-80) cc_final: 0.8162 (m-80) REVERT: Q 141 HIS cc_start: 0.8256 (m90) cc_final: 0.7766 (m90) REVERT: R 144 GLN cc_start: 0.7354 (pt0) cc_final: 0.7009 (pt0) outliers start: 0 outliers final: 0 residues processed: 716 average time/residue: 0.2293 time to fit residues: 278.5773 Evaluate side-chains 591 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.0470 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 50.0000 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 601 ASN A 671 ASN A 703 GLN A 791 GLN A1077 ASN A1462 GLN B 111 ASN B 139 GLN B 344 GLN B 503 ASN B 654 GLN B 716 HIS ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN B1094 GLN C 194 HIS C 217 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Q 145 ASN Q 168 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.140979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083909 restraints weight = 77574.088| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.01 r_work: 0.2874 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39085 Z= 0.156 Angle : 0.667 11.131 53164 Z= 0.348 Chirality : 0.046 0.399 5927 Planarity : 0.005 0.070 6556 Dihedral : 13.568 175.963 6003 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.27 % Allowed : 7.53 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.28 (0.13), residues: 4460 helix: 1.47 (0.13), residues: 1602 sheet: -0.12 (0.21), residues: 617 loop : -0.66 (0.14), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 14 TYR 0.020 0.002 TYR A 875 PHE 0.026 0.002 PHE E 73 TRP 0.014 0.001 TRP A1210 HIS 0.016 0.001 HIS A1417 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (39052) covalent geometry : angle 0.65964 / 0.35 (53131) hydrogen bonds : bond 0.04721 / 3.13 ( 1625) hydrogen bonds : angle 5.60182 / 3.98 ( 4555) metal coordination : bond 0.00737 / 0.50 ( 33) metal coordination : angle 4.12339 / 2.86 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 646 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8924 (t70) cc_final: 0.8687 (t0) REVERT: A 51 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7790 (mtm-85) REVERT: A 57 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 99 PHE cc_start: 0.8340 (m-10) cc_final: 0.8003 (m-80) REVERT: A 186 ARG cc_start: 0.7332 (tpt170) cc_final: 0.6927 (tpp-160) REVERT: A 321 GLU cc_start: 0.8992 (tp30) cc_final: 0.8779 (tp30) REVERT: A 561 MET cc_start: 0.9172 (mmt) cc_final: 0.8807 (mmm) REVERT: A 565 MET cc_start: 0.9106 (tpt) cc_final: 0.8839 (tpt) REVERT: A 791 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8772 (mm-40) REVERT: A 845 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8844 (tm-30) REVERT: A 1036 ASN cc_start: 0.8704 (m-40) cc_final: 0.8318 (t0) REVERT: A 1038 THR cc_start: 0.9126 (m) cc_final: 0.8770 (t) REVERT: A 1093 GLN cc_start: 0.9145 (mt0) cc_final: 0.8799 (tt0) REVERT: A 1192 TRP cc_start: 0.8729 (p90) cc_final: 0.8398 (p90) REVERT: A 1215 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8262 (tp30) REVERT: A 1284 PHE cc_start: 0.8914 (t80) cc_final: 0.8689 (t80) REVERT: A 1293 LEU cc_start: 0.9401 (tt) cc_final: 0.9056 (mm) REVERT: A 1322 ILE cc_start: 0.8874 (mt) cc_final: 0.8635 (mt) REVERT: A 1434 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 1440 MET cc_start: 0.9265 (mmt) cc_final: 0.8897 (mmp) REVERT: B 172 CYS cc_start: 0.9402 (m) cc_final: 0.8881 (m) REVERT: B 230 ARG cc_start: 0.8185 (tpt170) cc_final: 0.7776 (tpp80) REVERT: B 236 TRP cc_start: 0.7720 (m-10) cc_final: 0.7412 (m-10) REVERT: B 299 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8805 (tm-30) REVERT: B 300 MET cc_start: 0.8910 (tpt) cc_final: 0.8418 (tpt) REVERT: B 346 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8389 (tt0) REVERT: B 422 PHE cc_start: 0.8451 (t80) cc_final: 0.7833 (t80) REVERT: B 669 GLU cc_start: 0.8808 (tt0) cc_final: 0.8394 (mt-10) REVERT: B 796 MET cc_start: 0.8889 (mtm) cc_final: 0.8393 (mtm) REVERT: B 1093 CYS cc_start: 0.8858 (t) cc_final: 0.8547 (t) REVERT: B 1155 CYS cc_start: 0.9461 (t) cc_final: 0.9057 (t) REVERT: B 1172 MET cc_start: 0.8906 (mmp) cc_final: 0.8520 (mmp) REVERT: C 27 ASP cc_start: 0.8751 (m-30) cc_final: 0.8375 (t70) REVERT: C 157 GLN cc_start: 0.9003 (mt0) cc_final: 0.8740 (mt0) REVERT: C 265 HIS cc_start: 0.8961 (t70) cc_final: 0.8528 (t70) REVERT: E 18 MET cc_start: 0.9630 (mmt) cc_final: 0.9333 (mmm) REVERT: E 72 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8477 (tpp) REVERT: E 108 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8662 (tm-30) REVERT: E 116 GLN cc_start: 0.9441 (tp-100) cc_final: 0.8790 (tp40) REVERT: E 120 ASP cc_start: 0.8594 (p0) cc_final: 0.8081 (p0) REVERT: E 130 PHE cc_start: 0.8184 (m-80) cc_final: 0.7907 (m-80) REVERT: E 151 MET cc_start: 0.8890 (mtp) cc_final: 0.8557 (mtp) REVERT: F 96 GLU cc_start: 0.9096 (pp20) cc_final: 0.8726 (pp20) REVERT: F 100 ARG cc_start: 0.9135 (tpp80) cc_final: 0.8755 (tpp80) REVERT: G 3 TYR cc_start: 0.8618 (m-80) cc_final: 0.8212 (m-10) REVERT: G 60 GLN cc_start: 0.8422 (mm110) cc_final: 0.8167 (mt0) REVERT: G 73 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7507 (mmmt) REVERT: H 8 ASP cc_start: 0.7024 (t0) cc_final: 0.6368 (t0) REVERT: H 20 LYS cc_start: 0.8857 (tppt) cc_final: 0.8579 (tppt) REVERT: H 31 GLU cc_start: 0.8446 (pm20) cc_final: 0.8123 (pm20) REVERT: H 37 MET cc_start: 0.9036 (mtp) cc_final: 0.8698 (mtp) REVERT: H 89 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7891 (tm-30) REVERT: H 100 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7365 (mt-10) REVERT: H 103 GLU cc_start: 0.8894 (pm20) cc_final: 0.8650 (pm20) REVERT: H 107 GLU cc_start: 0.8589 (tp30) cc_final: 0.8328 (tp30) REVERT: I 23 MET cc_start: 0.4081 (tmm) cc_final: 0.3773 (tmm) REVERT: I 37 TYR cc_start: 0.5870 (OUTLIER) cc_final: 0.5026 (t80) REVERT: J 54 ASP cc_start: 0.8598 (p0) cc_final: 0.8044 (p0) REVERT: K 24 ASP cc_start: 0.8793 (t0) cc_final: 0.8545 (t0) REVERT: K 31 CYS cc_start: 0.8644 (t) cc_final: 0.8097 (t) REVERT: K 53 ASP cc_start: 0.9209 (t70) cc_final: 0.8883 (t0) REVERT: K 102 GLU cc_start: 0.9150 (tt0) cc_final: 0.8941 (mt-10) REVERT: L 18 ILE cc_start: 0.9083 (tp) cc_final: 0.8652 (tp) REVERT: L 41 TYR cc_start: 0.7721 (t80) cc_final: 0.7487 (t80) REVERT: L 44 MET cc_start: 0.8999 (mmm) cc_final: 0.8090 (mmm) REVERT: Q 28 ILE cc_start: 0.4506 (OUTLIER) cc_final: 0.4180 (tp) REVERT: Q 98 TRP cc_start: 0.7352 (m100) cc_final: 0.6638 (m100) REVERT: Q 99 LEU cc_start: 0.6650 (tt) cc_final: 0.6427 (tt) REVERT: Q 124 TYR cc_start: 0.8760 (m-80) cc_final: 0.8416 (m-80) REVERT: Q 125 TYR cc_start: 0.8179 (m-80) cc_final: 0.7947 (m-10) REVERT: Q 138 PHE cc_start: 0.6868 (m-80) cc_final: 0.6573 (m-10) REVERT: Q 141 HIS cc_start: 0.8289 (m90) cc_final: 0.7934 (m90) REVERT: R 144 GLN cc_start: 0.7203 (pt0) cc_final: 0.6761 (pt0) REVERT: W 168 MET cc_start: 0.8211 (ptp) cc_final: 0.7628 (ppp) outliers start: 51 outliers final: 26 residues processed: 665 average time/residue: 0.2188 time to fit residues: 247.1965 Evaluate side-chains 604 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 574 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain R residue 96 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 417 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 145 optimal weight: 0.4980 chunk 440 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 376 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 360 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 GLN B 98 HIS B 111 ASN B 139 GLN B 790 GLN B 817 GLN B 980 HIS B 992 ASN E 129 GLN G 93 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN W 143 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.141006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.084051 restraints weight = 77251.852| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.99 r_work: 0.2882 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39085 Z= 0.139 Angle : 0.624 11.949 53164 Z= 0.323 Chirality : 0.045 0.377 5927 Planarity : 0.004 0.053 6556 Dihedral : 13.613 177.291 6003 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.68 % Allowed : 10.03 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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 (0.13), residues: 4460 helix: 1.43 (0.13), residues: 1610 sheet: -0.04 (0.21), residues: 615 loop : -0.69 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 70 TYR 0.025 0.001 TYR H 118 PHE 0.029 0.001 PHE H 56 TRP 0.014 0.001 TRP R 31 HIS 0.012 0.001 HIS A1044 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (39052) covalent geometry : angle 0.61553 / 0.32 (53131) hydrogen bonds : bond 0.04026 / 2.67 ( 1625) hydrogen bonds : angle 5.13736 / 3.66 ( 4555) metal coordination : bond 0.00540 / 0.37 ( 33) metal coordination : angle 4.09207 / 2.78 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 635 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8899 (t70) cc_final: 0.8647 (t0) REVERT: A 186 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6874 (tpp-160) REVERT: A 321 GLU cc_start: 0.9001 (tp30) cc_final: 0.8763 (tp30) REVERT: A 470 MET cc_start: 0.9462 (mtm) cc_final: 0.9234 (mtm) REVERT: A 845 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8893 (tm-30) REVERT: A 1036 ASN cc_start: 0.8744 (m-40) cc_final: 0.8360 (t0) REVERT: A 1038 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8842 (t) REVERT: A 1093 GLN cc_start: 0.9123 (mt0) cc_final: 0.8870 (tt0) REVERT: A 1215 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8301 (tp30) REVERT: A 1293 LEU cc_start: 0.9449 (tt) cc_final: 0.9081 (mm) REVERT: A 1302 GLU cc_start: 0.8728 (pm20) cc_final: 0.8363 (pm20) REVERT: A 1322 ILE cc_start: 0.8921 (mt) cc_final: 0.8684 (mt) REVERT: B 168 ASP cc_start: 0.7990 (t0) cc_final: 0.7751 (t0) REVERT: B 172 CYS cc_start: 0.9410 (m) cc_final: 0.8829 (m) REVERT: B 230 ARG cc_start: 0.8183 (tpt170) cc_final: 0.7761 (tpp80) REVERT: B 236 TRP cc_start: 0.7700 (m-10) cc_final: 0.7344 (m-10) REVERT: B 299 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8820 (tm-30) REVERT: B 300 MET cc_start: 0.8879 (tpt) cc_final: 0.8581 (tpp) REVERT: B 346 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8262 (tt0) REVERT: B 365 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9115 (tt) REVERT: B 386 ASP cc_start: 0.9284 (t0) cc_final: 0.8615 (p0) REVERT: B 669 GLU cc_start: 0.8900 (tt0) cc_final: 0.8504 (mt-10) REVERT: B 916 TYR cc_start: 0.8048 (m-80) cc_final: 0.7825 (m-80) REVERT: B 992 ASN cc_start: 0.9448 (OUTLIER) cc_final: 0.9114 (t0) REVERT: B 1092 ASP cc_start: 0.8973 (m-30) cc_final: 0.8688 (m-30) REVERT: B 1155 CYS cc_start: 0.9419 (t) cc_final: 0.9085 (t) REVERT: B 1172 MET cc_start: 0.8941 (mmp) cc_final: 0.8572 (mmp) REVERT: C 27 ASP cc_start: 0.8750 (m-30) cc_final: 0.8359 (t70) REVERT: C 157 GLN cc_start: 0.9022 (mt0) cc_final: 0.8757 (mt0) REVERT: C 265 HIS cc_start: 0.8954 (t70) cc_final: 0.8505 (t70) REVERT: E 72 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8631 (tpp) REVERT: E 108 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8693 (tm-30) REVERT: E 116 GLN cc_start: 0.9418 (tp-100) cc_final: 0.8674 (tp40) REVERT: E 120 ASP cc_start: 0.8456 (p0) cc_final: 0.7925 (p0) REVERT: E 129 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: E 203 TYR cc_start: 0.8286 (t80) cc_final: 0.7974 (t80) REVERT: F 96 GLU cc_start: 0.9069 (pp20) cc_final: 0.8797 (pp20) REVERT: F 100 ARG cc_start: 0.9160 (tpp80) cc_final: 0.8746 (tpp80) REVERT: F 106 ILE cc_start: 0.8883 (mt) cc_final: 0.8613 (tt) REVERT: G 3 TYR cc_start: 0.8711 (m-80) cc_final: 0.8275 (m-10) REVERT: G 60 GLN cc_start: 0.8500 (mm110) cc_final: 0.8240 (mt0) REVERT: G 73 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7483 (mmmt) REVERT: H 8 ASP cc_start: 0.7251 (t0) cc_final: 0.6408 (t0) REVERT: H 9 ILE cc_start: 0.9073 (mt) cc_final: 0.8811 (mt) REVERT: H 20 LYS cc_start: 0.8971 (tppt) cc_final: 0.8630 (tppt) REVERT: H 37 MET cc_start: 0.9091 (mtp) cc_final: 0.8742 (mtp) REVERT: H 56 PHE cc_start: 0.7869 (p90) cc_final: 0.7619 (p90) REVERT: H 89 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7851 (tm-30) REVERT: H 100 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7320 (mt-10) REVERT: H 103 GLU cc_start: 0.8893 (pm20) cc_final: 0.8612 (pm20) REVERT: H 107 GLU cc_start: 0.8658 (tp30) cc_final: 0.8415 (tp30) REVERT: I 23 MET cc_start: 0.4390 (tmm) cc_final: 0.3952 (tmm) REVERT: I 37 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5009 (t80) REVERT: J 54 ASP cc_start: 0.8639 (p0) cc_final: 0.8125 (p0) REVERT: K 24 ASP cc_start: 0.8825 (t0) cc_final: 0.8469 (t0) REVERT: K 31 CYS cc_start: 0.8670 (t) cc_final: 0.8118 (t) REVERT: K 38 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8766 (mm-30) REVERT: K 53 ASP cc_start: 0.9225 (t70) cc_final: 0.8970 (t70) REVERT: K 102 GLU cc_start: 0.9162 (tt0) cc_final: 0.8947 (mt-10) REVERT: L 18 ILE cc_start: 0.9116 (tp) cc_final: 0.8778 (tp) REVERT: L 44 MET cc_start: 0.8955 (mmm) cc_final: 0.8047 (mmt) REVERT: Q 28 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4458 (tp) REVERT: Q 94 GLU cc_start: 0.7039 (tp30) cc_final: 0.6337 (tp30) REVERT: Q 98 TRP cc_start: 0.7364 (m100) cc_final: 0.6685 (m100) REVERT: Q 124 TYR cc_start: 0.8769 (m-80) cc_final: 0.8410 (m-80) REVERT: Q 125 TYR cc_start: 0.8144 (m-10) cc_final: 0.7842 (m-10) REVERT: Q 180 ARG cc_start: 0.6516 (tmt170) cc_final: 0.6210 (tmt170) REVERT: R 144 GLN cc_start: 0.7136 (pt0) cc_final: 0.6671 (pt0) REVERT: W 168 MET cc_start: 0.8262 (ptp) cc_final: 0.7653 (ppp) outliers start: 67 outliers final: 32 residues processed: 661 average time/residue: 0.2065 time to fit residues: 233.3979 Evaluate side-chains 616 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 577 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 422 optimal weight: 10.0000 chunk 375 optimal weight: 0.9980 chunk 386 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 56 optimal weight: 0.0370 chunk 95 optimal weight: 0.6980 chunk 315 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 173 optimal weight: 0.3980 chunk 229 optimal weight: 0.0040 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS A 601 ASN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN B 265 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN B1021 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS K 69 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 HIS ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.084312 restraints weight = 76779.902| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.06 r_work: 0.2868 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39085 Z= 0.121 Angle : 0.605 12.413 53164 Z= 0.313 Chirality : 0.044 0.359 5927 Planarity : 0.004 0.061 6556 Dihedral : 13.568 178.186 6003 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.73 % Allowed : 12.12 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.24 (0.13), residues: 4460 helix: 1.39 (0.13), residues: 1615 sheet: 0.01 (0.21), residues: 623 loop : -0.70 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 938 TYR 0.018 0.001 TYR A 875 PHE 0.021 0.001 PHE Q 138 TRP 0.020 0.001 TRP A1210 HIS 0.007 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (39052) covalent geometry : angle 0.59789 / 0.31 (53131) hydrogen bonds : bond 0.03698 / 2.44 ( 1625) hydrogen bonds : angle 4.92584 / 3.51 ( 4555) metal coordination : bond 0.00597 / 0.39 ( 33) metal coordination : angle 3.76581 / 2.54 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 649 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8803 (t70) cc_final: 0.8566 (t0) REVERT: A 45 GLU cc_start: 0.7921 (pm20) cc_final: 0.7639 (pm20) REVERT: A 51 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: A 85 PHE cc_start: 0.7729 (m-80) cc_final: 0.7505 (m-80) REVERT: A 186 ARG cc_start: 0.7341 (tpt170) cc_final: 0.7045 (tpt-90) REVERT: A 238 MET cc_start: 0.6770 (ptt) cc_final: 0.6456 (ptt) REVERT: A 248 MET cc_start: 0.8841 (tpp) cc_final: 0.8532 (mmm) REVERT: A 282 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 321 GLU cc_start: 0.9005 (tp30) cc_final: 0.8796 (tp30) REVERT: A 329 MET cc_start: 0.8374 (mmm) cc_final: 0.8169 (mmm) REVERT: A 337 LYS cc_start: 0.8557 (tppt) cc_final: 0.8073 (tptp) REVERT: A 810 PHE cc_start: 0.9304 (m-80) cc_final: 0.9072 (m-10) REVERT: A 845 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8889 (tm-30) REVERT: A 1036 ASN cc_start: 0.8677 (m-40) cc_final: 0.8293 (t0) REVERT: A 1038 THR cc_start: 0.9083 (m) cc_final: 0.8782 (t) REVERT: A 1093 GLN cc_start: 0.9070 (mt0) cc_final: 0.8839 (tt0) REVERT: A 1192 TRP cc_start: 0.8732 (p90) cc_final: 0.8393 (p90) REVERT: A 1215 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8332 (tp30) REVERT: A 1293 LEU cc_start: 0.9467 (tt) cc_final: 0.9125 (mm) REVERT: A 1302 GLU cc_start: 0.8731 (pm20) cc_final: 0.8367 (pm20) REVERT: A 1322 ILE cc_start: 0.8974 (mt) cc_final: 0.8745 (mt) REVERT: A 1434 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8430 (mp0) REVERT: B 168 ASP cc_start: 0.7972 (t0) cc_final: 0.7699 (t0) REVERT: B 172 CYS cc_start: 0.9406 (m) cc_final: 0.8863 (m) REVERT: B 230 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7715 (tpp80) REVERT: B 236 TRP cc_start: 0.7619 (m-10) cc_final: 0.7062 (m-10) REVERT: B 299 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8788 (tm-30) REVERT: B 300 MET cc_start: 0.8821 (tpt) cc_final: 0.8531 (tpp) REVERT: B 313 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7902 (pp20) REVERT: B 346 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8193 (tt0) REVERT: B 422 PHE cc_start: 0.8380 (t80) cc_final: 0.7717 (t80) REVERT: B 581 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: B 669 GLU cc_start: 0.8846 (tt0) cc_final: 0.8468 (mt-10) REVERT: B 916 TYR cc_start: 0.8012 (m-80) cc_final: 0.7599 (m-80) REVERT: B 1151 MET cc_start: 0.9180 (ptm) cc_final: 0.8050 (ppp) REVERT: B 1155 CYS cc_start: 0.9380 (t) cc_final: 0.8969 (t) REVERT: B 1171 MET cc_start: 0.9532 (mmm) cc_final: 0.9322 (mpp) REVERT: B 1172 MET cc_start: 0.8851 (mmp) cc_final: 0.8462 (mmp) REVERT: C 17 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: C 27 ASP cc_start: 0.8643 (m-30) cc_final: 0.8289 (t70) REVERT: C 157 GLN cc_start: 0.9004 (mt0) cc_final: 0.8764 (mt0) REVERT: C 265 HIS cc_start: 0.8923 (t70) cc_final: 0.8487 (t70) REVERT: D 26 PHE cc_start: 0.6625 (m-80) cc_final: 0.6412 (m-80) REVERT: E 72 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8571 (tpp) REVERT: E 108 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8715 (tm-30) REVERT: E 116 GLN cc_start: 0.9413 (tp-100) cc_final: 0.8666 (tp40) REVERT: E 120 ASP cc_start: 0.8409 (p0) cc_final: 0.7821 (p0) REVERT: F 96 GLU cc_start: 0.9120 (pp20) cc_final: 0.8571 (tm-30) REVERT: F 100 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8708 (tpp80) REVERT: F 106 ILE cc_start: 0.8797 (mt) cc_final: 0.8540 (tt) REVERT: G 3 TYR cc_start: 0.8648 (m-80) cc_final: 0.8242 (m-10) REVERT: G 60 GLN cc_start: 0.8431 (mm110) cc_final: 0.8224 (mt0) REVERT: G 73 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7464 (mmmt) REVERT: H 7 GLU cc_start: 0.8966 (tp30) cc_final: 0.8738 (tp30) REVERT: H 8 ASP cc_start: 0.7220 (t0) cc_final: 0.6571 (t0) REVERT: H 20 LYS cc_start: 0.8968 (tppt) cc_final: 0.8685 (tppt) REVERT: H 37 MET cc_start: 0.9105 (mtp) cc_final: 0.8732 (mtp) REVERT: H 89 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7738 (tm-30) REVERT: H 103 GLU cc_start: 0.8857 (pm20) cc_final: 0.8558 (pm20) REVERT: H 107 GLU cc_start: 0.8664 (tp30) cc_final: 0.8443 (tp30) REVERT: H 145 MET cc_start: 0.8179 (mtp) cc_final: 0.7962 (mtp) REVERT: I 37 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.4974 (t80) REVERT: J 54 ASP cc_start: 0.8633 (p0) cc_final: 0.8116 (p0) REVERT: K 24 ASP cc_start: 0.8798 (t0) cc_final: 0.8438 (t0) REVERT: K 31 CYS cc_start: 0.8596 (t) cc_final: 0.8006 (t) REVERT: K 53 ASP cc_start: 0.9258 (t70) cc_final: 0.8990 (t70) REVERT: K 102 GLU cc_start: 0.9154 (tt0) cc_final: 0.8928 (mt-10) REVERT: L 44 MET cc_start: 0.8955 (mmm) cc_final: 0.8743 (mmt) REVERT: L 55 PHE cc_start: 0.9027 (m-80) cc_final: 0.8810 (m-80) REVERT: Q 28 ILE cc_start: 0.4717 (OUTLIER) cc_final: 0.4470 (tp) REVERT: Q 49 ARG cc_start: 0.7994 (ttt180) cc_final: 0.7603 (mmt180) REVERT: Q 124 TYR cc_start: 0.8773 (m-80) cc_final: 0.8414 (m-80) REVERT: Q 125 TYR cc_start: 0.8102 (m-10) cc_final: 0.7779 (m-10) REVERT: Q 169 LYS cc_start: 0.8145 (pptt) cc_final: 0.7849 (tptt) REVERT: R 144 GLN cc_start: 0.7017 (pt0) cc_final: 0.6574 (pt0) REVERT: W 168 MET cc_start: 0.8321 (ptp) cc_final: 0.7741 (ppp) outliers start: 69 outliers final: 36 residues processed: 681 average time/residue: 0.2063 time to fit residues: 239.8339 Evaluate side-chains 642 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 600 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain W residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 24 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 417 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 673 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 315 ASN B 683 GLN B 699 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 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 = 0.3937 r_free = 0.3937 target = 0.134383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075724 restraints weight = 78338.345| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.99 r_work: 0.2732 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 39085 Z= 0.332 Angle : 0.743 12.829 53164 Z= 0.379 Chirality : 0.047 0.335 5927 Planarity : 0.005 0.054 6556 Dihedral : 13.642 178.921 6003 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.73 % Allowed : 13.32 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.02 (0.13), residues: 4460 helix: 1.25 (0.13), residues: 1613 sheet: -0.15 (0.20), residues: 645 loop : -0.86 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 324 TYR 0.030 0.002 TYR B 766 PHE 0.029 0.002 PHE H 56 TRP 0.018 0.002 TRP A 479 HIS 0.012 0.002 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.33 (39052) covalent geometry : angle 0.73312 / 0.38 (53131) hydrogen bonds : bond 0.04259 / 2.82 ( 1625) hydrogen bonds : angle 4.99056 / 3.55 ( 4555) metal coordination : bond 0.01344 / 0.82 ( 33) metal coordination : angle 4.85114 / 3.12 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 574 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8963 (t70) cc_final: 0.8715 (t0) REVERT: A 186 ARG cc_start: 0.7423 (tpt170) cc_final: 0.7141 (tpt-90) REVERT: A 238 MET cc_start: 0.7237 (ptt) cc_final: 0.6962 (ptt) REVERT: A 241 ARG cc_start: 0.9125 (ptm160) cc_final: 0.8635 (tmm-80) REVERT: A 282 ASP cc_start: 0.9050 (t70) cc_final: 0.8681 (t0) REVERT: A 321 GLU cc_start: 0.9114 (tp30) cc_final: 0.8899 (tp30) REVERT: A 337 LYS cc_start: 0.8848 (tppt) cc_final: 0.8279 (tptp) REVERT: A 347 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 450 MET cc_start: 0.9521 (ttm) cc_final: 0.9251 (mtm) REVERT: A 561 MET cc_start: 0.9274 (mmt) cc_final: 0.8889 (mmt) REVERT: A 791 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8897 (mm-40) REVERT: A 845 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8909 (tm-30) REVERT: A 868 MET cc_start: 0.8708 (mmp) cc_final: 0.8102 (mtt) REVERT: A 879 VAL cc_start: 0.9552 (t) cc_final: 0.9201 (p) REVERT: A 1004 LEU cc_start: 0.9303 (tp) cc_final: 0.8908 (tp) REVERT: A 1036 ASN cc_start: 0.8834 (m-40) cc_final: 0.8506 (m-40) REVERT: A 1038 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8962 (t) REVERT: A 1063 GLU cc_start: 0.8755 (pm20) cc_final: 0.8551 (pt0) REVERT: A 1093 GLN cc_start: 0.9244 (mt0) cc_final: 0.8960 (tt0) REVERT: A 1102 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8259 (mpp) REVERT: A 1192 TRP cc_start: 0.8736 (p90) cc_final: 0.8399 (p90) REVERT: A 1215 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8242 (tp30) REVERT: A 1293 LEU cc_start: 0.9505 (tt) cc_final: 0.9194 (mm) REVERT: A 1302 GLU cc_start: 0.8841 (pm20) cc_final: 0.8474 (pm20) REVERT: A 1322 ILE cc_start: 0.8959 (mt) cc_final: 0.8736 (mt) REVERT: A 1364 GLU cc_start: 0.8688 (tp30) cc_final: 0.8415 (tm-30) REVERT: A 1434 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8785 (mt-10) REVERT: B 172 CYS cc_start: 0.9501 (m) cc_final: 0.8947 (m) REVERT: B 206 TYR cc_start: 0.8415 (m-10) cc_final: 0.7976 (m-10) REVERT: B 230 ARG cc_start: 0.8216 (tpt170) cc_final: 0.7717 (tpp80) REVERT: B 236 TRP cc_start: 0.7780 (m-10) cc_final: 0.7314 (m-10) REVERT: B 265 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8771 (pm20) REVERT: B 299 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8846 (tm-30) REVERT: B 300 MET cc_start: 0.9082 (tpt) cc_final: 0.8774 (tpp) REVERT: B 368 MET cc_start: 0.9572 (ttp) cc_final: 0.9219 (ttt) REVERT: B 422 PHE cc_start: 0.8573 (t80) cc_final: 0.7895 (t80) REVERT: B 581 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: B 669 GLU cc_start: 0.8996 (tt0) cc_final: 0.8568 (mt-10) REVERT: B 796 MET cc_start: 0.9202 (mtm) cc_final: 0.8846 (mtm) REVERT: B 916 TYR cc_start: 0.8144 (m-80) cc_final: 0.7709 (m-80) REVERT: B 1172 MET cc_start: 0.9025 (mmp) cc_final: 0.8718 (mmp) REVERT: C 27 ASP cc_start: 0.8862 (m-30) cc_final: 0.8532 (t70) REVERT: C 62 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8997 (mm-30) REVERT: C 157 GLN cc_start: 0.9310 (mt0) cc_final: 0.8590 (mt0) REVERT: C 265 HIS cc_start: 0.8944 (t70) cc_final: 0.8473 (t70) REVERT: D 30 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: D 34 ASN cc_start: 0.7576 (t0) cc_final: 0.7367 (t0) REVERT: E 16 THR cc_start: 0.9311 (m) cc_final: 0.9005 (p) REVERT: E 72 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8576 (tpp) REVERT: E 108 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8914 (tm-30) REVERT: E 116 GLN cc_start: 0.9416 (tp-100) cc_final: 0.8551 (tp40) REVERT: E 120 ASP cc_start: 0.8412 (p0) cc_final: 0.7723 (p0) REVERT: E 134 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8722 (tp30) REVERT: F 96 GLU cc_start: 0.9178 (pp20) cc_final: 0.8911 (pp20) REVERT: F 100 ARG cc_start: 0.9359 (tpp80) cc_final: 0.8867 (tpp80) REVERT: F 115 TYR cc_start: 0.8977 (p90) cc_final: 0.8549 (p90) REVERT: G 3 TYR cc_start: 0.8666 (m-80) cc_final: 0.8262 (m-10) REVERT: G 60 GLN cc_start: 0.8695 (mm110) cc_final: 0.8370 (mt0) REVERT: G 73 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7477 (mmmt) REVERT: H 8 ASP cc_start: 0.7713 (t0) cc_final: 0.7083 (t70) REVERT: H 37 MET cc_start: 0.9163 (mtp) cc_final: 0.8799 (mtp) REVERT: H 48 TYR cc_start: 0.9247 (t80) cc_final: 0.8862 (t80) REVERT: H 56 PHE cc_start: 0.8458 (p90) cc_final: 0.8039 (p90) REVERT: H 89 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7712 (tm-30) REVERT: I 37 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5254 (t80) REVERT: I 74 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8810 (pt0) REVERT: J 54 ASP cc_start: 0.8731 (p0) cc_final: 0.7894 (p0) REVERT: J 57 GLU cc_start: 0.8905 (mp0) cc_final: 0.7878 (mp0) REVERT: K 24 ASP cc_start: 0.8894 (t0) cc_final: 0.8473 (t0) REVERT: K 31 CYS cc_start: 0.8697 (t) cc_final: 0.8216 (t) REVERT: L 44 MET cc_start: 0.8989 (mmm) cc_final: 0.8137 (mmt) REVERT: L 55 PHE cc_start: 0.9046 (m-80) cc_final: 0.8616 (m-80) REVERT: Q 28 ILE cc_start: 0.5180 (tt) cc_final: 0.4948 (tp) REVERT: Q 98 TRP cc_start: 0.7619 (m100) cc_final: 0.6871 (m100) REVERT: Q 124 TYR cc_start: 0.8766 (m-80) cc_final: 0.8440 (m-80) REVERT: Q 125 TYR cc_start: 0.8069 (m-10) cc_final: 0.7730 (m-10) REVERT: Q 178 GLN cc_start: 0.6771 (mm-40) cc_final: 0.6561 (mp10) REVERT: R 144 GLN cc_start: 0.7085 (pt0) cc_final: 0.6659 (pt0) REVERT: W 168 MET cc_start: 0.8340 (ptp) cc_final: 0.7765 (ppp) outliers start: 109 outliers final: 70 residues processed: 643 average time/residue: 0.2065 time to fit residues: 227.1512 Evaluate side-chains 617 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 539 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain W residue 161 VAL Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 54 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 389 optimal weight: 20.0000 chunk 331 optimal weight: 6.9990 chunk 72 optimal weight: 0.0470 chunk 252 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 422 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A1032 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079625 restraints weight = 76705.507| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.00 r_work: 0.2816 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39085 Z= 0.149 Angle : 0.630 12.714 53164 Z= 0.323 Chirality : 0.044 0.353 5927 Planarity : 0.004 0.059 6556 Dihedral : 13.627 178.276 6003 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.05 % Allowed : 15.25 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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 (0.13), residues: 4460 helix: 1.35 (0.13), residues: 1611 sheet: -0.04 (0.21), residues: 633 loop : -0.71 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 37 TYR 0.025 0.001 TYR B 766 PHE 0.024 0.001 PHE H 56 TRP 0.017 0.001 TRP A1210 HIS 0.009 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (39052) covalent geometry : angle 0.62214 / 0.32 (53131) hydrogen bonds : bond 0.03668 / 2.44 ( 1625) hydrogen bonds : angle 4.78604 / 3.39 ( 4555) metal coordination : bond 0.00633 / 0.41 ( 33) metal coordination : angle 4.13893 / 2.74 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 605 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8885 (t70) cc_final: 0.8641 (t0) REVERT: A 186 ARG cc_start: 0.7408 (tpt170) cc_final: 0.7115 (tpt-90) REVERT: A 241 ARG cc_start: 0.9137 (ptm160) cc_final: 0.8633 (tmm-80) REVERT: A 274 ASP cc_start: 0.8774 (t70) cc_final: 0.8477 (t70) REVERT: A 275 ASP cc_start: 0.9145 (m-30) cc_final: 0.8490 (p0) REVERT: A 282 ASP cc_start: 0.9064 (t70) cc_final: 0.8678 (t0) REVERT: A 337 LYS cc_start: 0.8797 (tppt) cc_final: 0.7497 (tptp) REVERT: A 370 ASP cc_start: 0.8877 (t70) cc_final: 0.8655 (t70) REVERT: A 561 MET cc_start: 0.9226 (mmt) cc_final: 0.9022 (mmt) REVERT: A 565 MET cc_start: 0.9474 (tpp) cc_final: 0.9264 (tpt) REVERT: A 845 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8927 (tm-30) REVERT: A 868 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7805 (mtt) REVERT: A 1036 ASN cc_start: 0.8786 (m-40) cc_final: 0.8343 (t0) REVERT: A 1038 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8887 (t) REVERT: A 1086 MET cc_start: 0.9576 (mmp) cc_final: 0.9368 (mmm) REVERT: A 1192 TRP cc_start: 0.8712 (p90) cc_final: 0.8349 (p90) REVERT: A 1293 LEU cc_start: 0.9512 (tt) cc_final: 0.9196 (mm) REVERT: A 1302 GLU cc_start: 0.8844 (pm20) cc_final: 0.8453 (pm20) REVERT: A 1322 ILE cc_start: 0.8971 (mt) cc_final: 0.8735 (mt) REVERT: A 1361 ASP cc_start: 0.8666 (t0) cc_final: 0.8439 (t0) REVERT: A 1364 GLU cc_start: 0.8590 (tp30) cc_final: 0.8328 (tm-30) REVERT: A 1434 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8694 (mt-10) REVERT: B 172 CYS cc_start: 0.9449 (m) cc_final: 0.8895 (m) REVERT: B 230 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7504 (tpp80) REVERT: B 236 TRP cc_start: 0.7721 (m-10) cc_final: 0.7254 (m-10) REVERT: B 299 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8784 (tm-30) REVERT: B 300 MET cc_start: 0.9005 (tpt) cc_final: 0.8700 (tpp) REVERT: B 346 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8256 (tt0) REVERT: B 368 MET cc_start: 0.9534 (ttp) cc_final: 0.9197 (ttt) REVERT: B 422 PHE cc_start: 0.8544 (t80) cc_final: 0.7810 (t80) REVERT: B 669 GLU cc_start: 0.8904 (tt0) cc_final: 0.8359 (mt-10) REVERT: B 789 ASN cc_start: 0.9100 (p0) cc_final: 0.8683 (p0) REVERT: B 916 TYR cc_start: 0.8070 (m-80) cc_final: 0.7676 (m-80) REVERT: B 1172 MET cc_start: 0.8936 (mmp) cc_final: 0.8609 (mmp) REVERT: C 27 ASP cc_start: 0.8769 (m-30) cc_final: 0.8429 (t70) REVERT: C 62 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9047 (mm-30) REVERT: C 157 GLN cc_start: 0.9138 (mt0) cc_final: 0.8645 (mt0) REVERT: C 265 HIS cc_start: 0.8962 (t70) cc_final: 0.8488 (t70) REVERT: D 30 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: E 16 THR cc_start: 0.9273 (m) cc_final: 0.8969 (p) REVERT: E 72 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: E 91 CYS cc_start: 0.9554 (m) cc_final: 0.9315 (p) REVERT: E 108 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8726 (tm-30) REVERT: E 116 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8695 (tp40) REVERT: E 120 ASP cc_start: 0.8376 (p0) cc_final: 0.7786 (p0) REVERT: E 134 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8730 (tp30) REVERT: F 100 ARG cc_start: 0.9321 (tpp80) cc_final: 0.8790 (tpp80) REVERT: F 115 TYR cc_start: 0.8984 (p90) cc_final: 0.8533 (p90) REVERT: G 3 TYR cc_start: 0.8592 (m-80) cc_final: 0.8189 (m-10) REVERT: G 60 GLN cc_start: 0.8682 (mm110) cc_final: 0.8386 (mt0) REVERT: G 73 LYS cc_start: 0.7794 (mmtt) cc_final: 0.7486 (mmmt) REVERT: H 8 ASP cc_start: 0.7483 (t0) cc_final: 0.6947 (t70) REVERT: H 37 MET cc_start: 0.9146 (mtp) cc_final: 0.8797 (mtp) REVERT: H 48 TYR cc_start: 0.9189 (t80) cc_final: 0.8904 (t80) REVERT: H 56 PHE cc_start: 0.8247 (p90) cc_final: 0.7804 (p90) REVERT: H 89 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7806 (tm-30) REVERT: I 37 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5138 (t80) REVERT: J 31 GLU cc_start: 0.9131 (mp0) cc_final: 0.8831 (mp0) REVERT: K 24 ASP cc_start: 0.8879 (t0) cc_final: 0.8470 (t0) REVERT: K 31 CYS cc_start: 0.8661 (t) cc_final: 0.8102 (t) REVERT: L 44 MET cc_start: 0.8988 (mmm) cc_final: 0.8455 (mmm) REVERT: L 55 PHE cc_start: 0.9004 (m-80) cc_final: 0.8758 (m-80) REVERT: Q 28 ILE cc_start: 0.5174 (tt) cc_final: 0.4947 (tp) REVERT: Q 98 TRP cc_start: 0.7622 (m100) cc_final: 0.6937 (m100) REVERT: Q 124 TYR cc_start: 0.8758 (m-80) cc_final: 0.8391 (m-80) REVERT: Q 125 TYR cc_start: 0.8081 (m-10) cc_final: 0.7689 (m-10) REVERT: Q 178 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6759 (mp10) REVERT: R 144 GLN cc_start: 0.7046 (pt0) cc_final: 0.6625 (pt0) REVERT: W 168 MET cc_start: 0.8363 (ptp) cc_final: 0.7741 (ppp) REVERT: X 120 MET cc_start: 0.6144 (mmm) cc_final: 0.5925 (mmm) outliers start: 82 outliers final: 51 residues processed: 648 average time/residue: 0.2072 time to fit residues: 229.5295 Evaluate side-chains 622 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 566 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain W residue 161 VAL Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 353 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 390 optimal weight: 50.0000 chunk 308 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 402 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.135240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.076805 restraints weight = 77618.370| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.98 r_work: 0.2758 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 39085 Z= 0.243 Angle : 0.677 12.342 53164 Z= 0.345 Chirality : 0.045 0.349 5927 Planarity : 0.004 0.046 6556 Dihedral : 13.612 178.710 6003 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.55 % Allowed : 15.47 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.13 (0.13), residues: 4460 helix: 1.29 (0.13), residues: 1619 sheet: -0.14 (0.20), residues: 641 loop : -0.73 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.029 0.002 TYR B 766 PHE 0.048 0.002 PHE E 75 TRP 0.017 0.001 TRP A1210 HIS 0.010 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (39052) covalent geometry : angle 0.66826 / 0.34 (53131) hydrogen bonds : bond 0.03783 / 2.51 ( 1625) hydrogen bonds : angle 4.78660 / 3.39 ( 4555) metal coordination : bond 0.00989 / 0.61 ( 33) metal coordination : angle 4.38910 / 2.83 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 569 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8941 (t70) cc_final: 0.8689 (t0) REVERT: A 186 ARG cc_start: 0.7314 (tpt170) cc_final: 0.7030 (tpt-90) REVERT: A 241 ARG cc_start: 0.9150 (ptm160) cc_final: 0.8647 (tmm-80) REVERT: A 248 MET cc_start: 0.9099 (tpp) cc_final: 0.8857 (tpp) REVERT: A 275 ASP cc_start: 0.9172 (m-30) cc_final: 0.8517 (p0) REVERT: A 282 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8667 (t0) REVERT: A 337 LYS cc_start: 0.8918 (tppt) cc_final: 0.7911 (mmmm) REVERT: A 347 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 370 ASP cc_start: 0.8877 (t70) cc_final: 0.8638 (t70) REVERT: A 450 MET cc_start: 0.9407 (ttm) cc_final: 0.9194 (mtm) REVERT: A 561 MET cc_start: 0.9281 (mmt) cc_final: 0.8836 (mmt) REVERT: A 565 MET cc_start: 0.9508 (tpp) cc_final: 0.9269 (tpt) REVERT: A 845 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8967 (tm-30) REVERT: A 868 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8071 (mtt) REVERT: A 974 ASP cc_start: 0.8571 (t0) cc_final: 0.8321 (t0) REVERT: A 1036 ASN cc_start: 0.8850 (m-40) cc_final: 0.8549 (m-40) REVERT: A 1038 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8974 (t) REVERT: A 1093 GLN cc_start: 0.9218 (mt0) cc_final: 0.8909 (tt0) REVERT: A 1192 TRP cc_start: 0.8656 (p90) cc_final: 0.8322 (p90) REVERT: A 1215 GLU cc_start: 0.8210 (tp30) cc_final: 0.7858 (tp30) REVERT: A 1262 MET cc_start: 0.8768 (ppp) cc_final: 0.8039 (ppp) REVERT: A 1302 GLU cc_start: 0.8900 (pm20) cc_final: 0.8522 (pm20) REVERT: A 1322 ILE cc_start: 0.8943 (mt) cc_final: 0.8713 (mt) REVERT: A 1361 ASP cc_start: 0.8734 (t0) cc_final: 0.8530 (t0) REVERT: A 1364 GLU cc_start: 0.8699 (tp30) cc_final: 0.8304 (tm-30) REVERT: A 1434 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8731 (mt-10) REVERT: B 172 CYS cc_start: 0.9494 (m) cc_final: 0.8905 (m) REVERT: B 230 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7521 (tpp80) REVERT: B 236 TRP cc_start: 0.7754 (m-10) cc_final: 0.7329 (m-10) REVERT: B 299 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8834 (tm-30) REVERT: B 300 MET cc_start: 0.9078 (tpt) cc_final: 0.8774 (tpp) REVERT: B 346 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8233 (tt0) REVERT: B 368 MET cc_start: 0.9578 (ttp) cc_final: 0.9248 (ttt) REVERT: B 422 PHE cc_start: 0.8599 (t80) cc_final: 0.7877 (t80) REVERT: B 669 GLU cc_start: 0.8987 (tt0) cc_final: 0.8609 (mt-10) REVERT: B 796 MET cc_start: 0.9194 (mtm) cc_final: 0.8874 (mtm) REVERT: B 916 TYR cc_start: 0.8174 (m-80) cc_final: 0.7699 (m-80) REVERT: B 1171 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.8340 (mmm) REVERT: B 1172 MET cc_start: 0.8998 (mmp) cc_final: 0.8680 (mmp) REVERT: C 17 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: C 27 ASP cc_start: 0.8836 (m-30) cc_final: 0.8480 (t70) REVERT: C 62 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8955 (mm-30) REVERT: C 157 GLN cc_start: 0.9238 (mt0) cc_final: 0.8704 (mt0) REVERT: C 265 HIS cc_start: 0.8943 (t70) cc_final: 0.8475 (t70) REVERT: E 16 THR cc_start: 0.9298 (m) cc_final: 0.8975 (p) REVERT: E 72 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8786 (tpp) REVERT: E 98 ASN cc_start: 0.9355 (t0) cc_final: 0.8982 (p0) REVERT: E 108 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8944 (tm-30) REVERT: E 116 GLN cc_start: 0.9377 (tp-100) cc_final: 0.8691 (tp40) REVERT: E 120 ASP cc_start: 0.8358 (p0) cc_final: 0.7775 (p0) REVERT: E 134 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8750 (tp30) REVERT: E 151 MET cc_start: 0.8933 (mtp) cc_final: 0.8719 (mtp) REVERT: F 100 ARG cc_start: 0.9407 (tpp80) cc_final: 0.8918 (tpp80) REVERT: F 115 TYR cc_start: 0.8984 (p90) cc_final: 0.8547 (p90) REVERT: F 122 GLU cc_start: 0.8558 (pm20) cc_final: 0.8213 (pm20) REVERT: G 3 TYR cc_start: 0.8586 (m-80) cc_final: 0.8210 (m-10) REVERT: G 60 GLN cc_start: 0.8742 (mm110) cc_final: 0.8448 (mt0) REVERT: G 73 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7609 (mmmt) REVERT: H 8 ASP cc_start: 0.7660 (t0) cc_final: 0.7064 (t70) REVERT: H 37 MET cc_start: 0.9157 (mtp) cc_final: 0.8776 (mtp) REVERT: H 56 PHE cc_start: 0.8316 (p90) cc_final: 0.7914 (p90) REVERT: I 37 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5296 (t80) REVERT: I 68 ILE cc_start: 0.8353 (mm) cc_final: 0.8073 (mm) REVERT: J 31 GLU cc_start: 0.9148 (mp0) cc_final: 0.8852 (mp0) REVERT: J 54 ASP cc_start: 0.9016 (p0) cc_final: 0.8748 (p0) REVERT: J 57 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8995 (mm-30) REVERT: K 24 ASP cc_start: 0.8920 (t0) cc_final: 0.8497 (t0) REVERT: K 31 CYS cc_start: 0.8685 (t) cc_final: 0.8144 (t) REVERT: K 38 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8928 (mm-30) REVERT: L 44 MET cc_start: 0.8980 (mmm) cc_final: 0.8089 (mmt) REVERT: L 55 PHE cc_start: 0.9059 (m-80) cc_final: 0.8663 (m-80) REVERT: Q 28 ILE cc_start: 0.5174 (tt) cc_final: 0.4953 (tp) REVERT: Q 98 TRP cc_start: 0.7636 (m100) cc_final: 0.6988 (m100) REVERT: Q 124 TYR cc_start: 0.8787 (m-80) cc_final: 0.8417 (m-80) REVERT: Q 125 TYR cc_start: 0.8092 (m-10) cc_final: 0.7739 (m-10) REVERT: Q 178 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6801 (mp10) REVERT: W 168 MET cc_start: 0.8337 (ptp) cc_final: 0.7736 (ppp) outliers start: 102 outliers final: 71 residues processed: 624 average time/residue: 0.2041 time to fit residues: 217.2741 Evaluate side-chains 625 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 547 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain W residue 161 VAL Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 337 optimal weight: 6.9990 chunk 421 optimal weight: 30.0000 chunk 419 optimal weight: 0.5980 chunk 389 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 278 optimal weight: 0.8980 chunk 209 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 HIS B 98 HIS B 111 ASN ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.137785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079947 restraints weight = 76377.340| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.98 r_work: 0.2827 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39085 Z= 0.135 Angle : 0.643 12.877 53164 Z= 0.328 Chirality : 0.045 0.362 5927 Planarity : 0.004 0.042 6556 Dihedral : 13.589 178.553 6003 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.17 % Allowed : 16.62 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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 (0.13), residues: 4460 helix: 1.29 (0.13), residues: 1626 sheet: -0.04 (0.21), residues: 623 loop : -0.68 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 44 TYR 0.024 0.001 TYR B 766 PHE 0.024 0.001 PHE D 26 TRP 0.017 0.001 TRP A1210 HIS 0.012 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (39052) covalent geometry : angle 0.63500 / 0.33 (53131) hydrogen bonds : bond 0.03514 / 2.33 ( 1625) hydrogen bonds : angle 4.68735 / 3.33 ( 4555) metal coordination : bond 0.00532 / 0.36 ( 33) metal coordination : angle 4.01916 / 2.67 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 604 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8859 (t70) cc_final: 0.8613 (t0) REVERT: A 186 ARG cc_start: 0.7311 (tpt170) cc_final: 0.7017 (tpt-90) REVERT: A 241 ARG cc_start: 0.9098 (ptm160) cc_final: 0.8604 (tmm-80) REVERT: A 274 ASP cc_start: 0.8784 (t70) cc_final: 0.8516 (t70) REVERT: A 275 ASP cc_start: 0.9157 (m-30) cc_final: 0.8485 (p0) REVERT: A 279 LYS cc_start: 0.9072 (tppp) cc_final: 0.8818 (tppp) REVERT: A 282 ASP cc_start: 0.9060 (t70) cc_final: 0.8623 (t0) REVERT: A 337 LYS cc_start: 0.8932 (tppt) cc_final: 0.7975 (tppt) REVERT: A 561 MET cc_start: 0.9214 (mmt) cc_final: 0.8805 (mmm) REVERT: A 818 GLU cc_start: 0.9000 (pm20) cc_final: 0.8142 (tm-30) REVERT: A 845 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8953 (tm-30) REVERT: A 868 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: A 974 ASP cc_start: 0.8524 (t0) cc_final: 0.8282 (t0) REVERT: A 1036 ASN cc_start: 0.8802 (m-40) cc_final: 0.8558 (m-40) REVERT: A 1038 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8922 (t) REVERT: A 1192 TRP cc_start: 0.8626 (p90) cc_final: 0.8303 (p90) REVERT: A 1215 GLU cc_start: 0.8230 (tp30) cc_final: 0.7913 (tp30) REVERT: A 1262 MET cc_start: 0.8706 (ppp) cc_final: 0.8135 (ppp) REVERT: A 1302 GLU cc_start: 0.8876 (pm20) cc_final: 0.8513 (pm20) REVERT: A 1322 ILE cc_start: 0.8976 (mt) cc_final: 0.8756 (mt) REVERT: A 1361 ASP cc_start: 0.8693 (t0) cc_final: 0.8435 (t0) REVERT: A 1364 GLU cc_start: 0.8536 (tp30) cc_final: 0.8305 (tm-30) REVERT: A 1434 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8610 (mt-10) REVERT: B 168 ASP cc_start: 0.8120 (t0) cc_final: 0.7857 (t0) REVERT: B 172 CYS cc_start: 0.9431 (m) cc_final: 0.8829 (m) REVERT: B 230 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7519 (tpp80) REVERT: B 236 TRP cc_start: 0.7783 (m-10) cc_final: 0.7298 (m-10) REVERT: B 278 PHE cc_start: 0.8574 (m-10) cc_final: 0.8339 (m-80) REVERT: B 299 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8777 (tm-30) REVERT: B 300 MET cc_start: 0.9040 (tpt) cc_final: 0.8721 (tpp) REVERT: B 346 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8295 (tt0) REVERT: B 368 MET cc_start: 0.9535 (ttp) cc_final: 0.9178 (ttt) REVERT: B 384 ASP cc_start: 0.8992 (t0) cc_final: 0.8770 (t0) REVERT: B 422 PHE cc_start: 0.8587 (t80) cc_final: 0.7822 (t80) REVERT: B 501 LEU cc_start: 0.9464 (tp) cc_final: 0.9142 (tp) REVERT: B 669 GLU cc_start: 0.8878 (tt0) cc_final: 0.8332 (mt-10) REVERT: B 789 ASN cc_start: 0.9113 (p0) cc_final: 0.8682 (p0) REVERT: B 796 MET cc_start: 0.9134 (mtm) cc_final: 0.8894 (mtm) REVERT: B 916 TYR cc_start: 0.8240 (m-80) cc_final: 0.7809 (m-80) REVERT: B 1151 MET cc_start: 0.9186 (ptm) cc_final: 0.8749 (ppp) REVERT: B 1171 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.8304 (mmm) REVERT: B 1172 MET cc_start: 0.8939 (mmp) cc_final: 0.8601 (mmp) REVERT: C 17 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: C 27 ASP cc_start: 0.8744 (m-30) cc_final: 0.8439 (t70) REVERT: C 62 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8931 (mm-30) REVERT: C 157 GLN cc_start: 0.9107 (mt0) cc_final: 0.8686 (mt0) REVERT: C 265 HIS cc_start: 0.8956 (t70) cc_final: 0.8491 (t70) REVERT: E 16 THR cc_start: 0.9291 (m) cc_final: 0.8980 (p) REVERT: E 72 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8825 (tpp) REVERT: E 91 CYS cc_start: 0.9578 (m) cc_final: 0.9352 (p) REVERT: E 98 ASN cc_start: 0.9285 (t0) cc_final: 0.8928 (p0) REVERT: E 108 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8700 (tm-30) REVERT: E 116 GLN cc_start: 0.9347 (tp-100) cc_final: 0.8330 (tp40) REVERT: E 120 ASP cc_start: 0.8214 (p0) cc_final: 0.7435 (p0) REVERT: E 134 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8754 (tp30) REVERT: E 151 MET cc_start: 0.8864 (mtp) cc_final: 0.8663 (mtp) REVERT: F 100 ARG cc_start: 0.9451 (tpp80) cc_final: 0.8898 (tpp80) REVERT: F 115 TYR cc_start: 0.8964 (p90) cc_final: 0.8528 (p90) REVERT: G 3 TYR cc_start: 0.8521 (m-80) cc_final: 0.8139 (m-10) REVERT: G 60 GLN cc_start: 0.8732 (mm110) cc_final: 0.8459 (mt0) REVERT: G 73 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7658 (mmmt) REVERT: H 8 ASP cc_start: 0.7471 (t0) cc_final: 0.6974 (t70) REVERT: H 37 MET cc_start: 0.9119 (mtp) cc_final: 0.8762 (mtp) REVERT: H 56 PHE cc_start: 0.8258 (p90) cc_final: 0.7911 (p90) REVERT: I 37 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5218 (t80) REVERT: I 68 ILE cc_start: 0.8394 (mm) cc_final: 0.8114 (mm) REVERT: J 31 GLU cc_start: 0.9149 (mp0) cc_final: 0.8850 (mp0) REVERT: J 48 MET cc_start: 0.9436 (tpt) cc_final: 0.8944 (tpt) REVERT: J 54 ASP cc_start: 0.9000 (p0) cc_final: 0.8646 (p0) REVERT: J 57 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8850 (mm-30) REVERT: K 24 ASP cc_start: 0.8954 (t0) cc_final: 0.8543 (t0) REVERT: K 31 CYS cc_start: 0.8615 (t) cc_final: 0.8064 (t) REVERT: L 44 MET cc_start: 0.9002 (mmm) cc_final: 0.8470 (mmm) REVERT: L 55 PHE cc_start: 0.9052 (m-80) cc_final: 0.8681 (m-80) REVERT: Q 28 ILE cc_start: 0.5350 (tt) cc_final: 0.5105 (tp) REVERT: Q 98 TRP cc_start: 0.7650 (m100) cc_final: 0.7035 (m100) REVERT: Q 124 TYR cc_start: 0.8751 (m-80) cc_final: 0.8354 (m-80) REVERT: Q 125 TYR cc_start: 0.8049 (m-10) cc_final: 0.7642 (m-10) REVERT: Q 169 LYS cc_start: 0.8163 (pptt) cc_final: 0.7748 (tptt) REVERT: Q 178 GLN cc_start: 0.7268 (mm110) cc_final: 0.6946 (mp10) REVERT: W 168 MET cc_start: 0.8351 (ptp) cc_final: 0.7719 (ppp) outliers start: 87 outliers final: 64 residues processed: 645 average time/residue: 0.2074 time to fit residues: 228.4686 Evaluate side-chains 641 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 571 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain W residue 161 VAL Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 71 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 362 optimal weight: 0.0050 chunk 94 optimal weight: 0.8980 chunk 366 optimal weight: 0.5980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN G 28 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS I 74 GLN ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.136995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079193 restraints weight = 76708.974| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.98 r_work: 0.2814 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39085 Z= 0.164 Angle : 0.656 14.531 53164 Z= 0.333 Chirality : 0.044 0.357 5927 Planarity : 0.004 0.055 6556 Dihedral : 13.576 179.100 6003 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.02 % Allowed : 17.02 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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 (0.13), residues: 4460 helix: 1.28 (0.13), residues: 1627 sheet: -0.02 (0.21), residues: 622 loop : -0.68 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 109 TYR 0.031 0.001 TYR E 203 PHE 0.018 0.001 PHE A 592 TRP 0.022 0.001 TRP A1210 HIS 0.008 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (39052) covalent geometry : angle 0.64875 / 0.33 (53131) hydrogen bonds : bond 0.03569 / 2.37 ( 1625) hydrogen bonds : angle 4.68272 / 3.32 ( 4555) metal coordination : bond 0.00639 / 0.41 ( 33) metal coordination : angle 3.98598 / 2.58 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 597 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8853 (t70) cc_final: 0.8612 (t0) REVERT: A 186 ARG cc_start: 0.7308 (tpt170) cc_final: 0.7016 (tpt-90) REVERT: A 241 ARG cc_start: 0.9118 (ptm160) cc_final: 0.8622 (tmm-80) REVERT: A 248 MET cc_start: 0.9094 (tpp) cc_final: 0.8863 (tpp) REVERT: A 274 ASP cc_start: 0.8782 (t70) cc_final: 0.8516 (t70) REVERT: A 275 ASP cc_start: 0.9166 (m-30) cc_final: 0.8573 (p0) REVERT: A 282 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8628 (t0) REVERT: A 337 LYS cc_start: 0.8919 (tppt) cc_final: 0.7894 (tppt) REVERT: A 347 GLU cc_start: 0.8228 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 818 GLU cc_start: 0.9006 (pm20) cc_final: 0.8104 (tm-30) REVERT: A 845 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9013 (tm-30) REVERT: A 868 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7829 (mtt) REVERT: A 974 ASP cc_start: 0.8508 (t0) cc_final: 0.8261 (t0) REVERT: A 1036 ASN cc_start: 0.8828 (m-40) cc_final: 0.8420 (t0) REVERT: A 1038 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8960 (t) REVERT: A 1192 TRP cc_start: 0.8627 (p90) cc_final: 0.8297 (p90) REVERT: A 1215 GLU cc_start: 0.8186 (tp30) cc_final: 0.7949 (tp30) REVERT: A 1226 LEU cc_start: 0.9341 (pt) cc_final: 0.9022 (pt) REVERT: A 1262 MET cc_start: 0.8730 (ppp) cc_final: 0.8165 (ppp) REVERT: A 1302 GLU cc_start: 0.8890 (pm20) cc_final: 0.8519 (pm20) REVERT: A 1322 ILE cc_start: 0.8999 (mt) cc_final: 0.8788 (mt) REVERT: A 1364 GLU cc_start: 0.8565 (tp30) cc_final: 0.8342 (tm-30) REVERT: B 39 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9066 (mm) REVERT: B 108 MET cc_start: 0.9307 (mmp) cc_final: 0.9062 (mmm) REVERT: B 172 CYS cc_start: 0.9453 (m) cc_final: 0.8891 (m) REVERT: B 230 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7492 (tpp80) REVERT: B 236 TRP cc_start: 0.7756 (m-10) cc_final: 0.7262 (m-10) REVERT: B 299 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8789 (tm-30) REVERT: B 300 MET cc_start: 0.9036 (tpt) cc_final: 0.8726 (tpp) REVERT: B 346 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8241 (tt0) REVERT: B 368 MET cc_start: 0.9541 (ttp) cc_final: 0.9184 (ttt) REVERT: B 384 ASP cc_start: 0.9004 (t0) cc_final: 0.8770 (t0) REVERT: B 422 PHE cc_start: 0.8626 (t80) cc_final: 0.7864 (t80) REVERT: B 501 LEU cc_start: 0.9471 (tp) cc_final: 0.9144 (tp) REVERT: B 669 GLU cc_start: 0.8899 (tt0) cc_final: 0.8330 (mt-10) REVERT: B 789 ASN cc_start: 0.9113 (p0) cc_final: 0.8676 (p0) REVERT: B 796 MET cc_start: 0.9162 (mtm) cc_final: 0.8887 (mtm) REVERT: B 916 TYR cc_start: 0.8245 (m-80) cc_final: 0.7799 (m-80) REVERT: B 1151 MET cc_start: 0.9207 (ptm) cc_final: 0.8658 (ppp) REVERT: B 1171 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: B 1172 MET cc_start: 0.8941 (mmp) cc_final: 0.8602 (mmp) REVERT: C 17 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: C 27 ASP cc_start: 0.8794 (m-30) cc_final: 0.8466 (t70) REVERT: C 62 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8830 (mm-30) REVERT: C 157 GLN cc_start: 0.9154 (mt0) cc_final: 0.8670 (mt0) REVERT: C 265 HIS cc_start: 0.8939 (t70) cc_final: 0.8491 (t70) REVERT: E 16 THR cc_start: 0.9286 (m) cc_final: 0.8977 (p) REVERT: E 72 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8801 (tpp) REVERT: E 91 CYS cc_start: 0.9578 (m) cc_final: 0.9344 (p) REVERT: E 98 ASN cc_start: 0.9318 (t0) cc_final: 0.8971 (p0) REVERT: E 108 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8725 (tm-30) REVERT: E 110 MET cc_start: 0.8327 (ttt) cc_final: 0.8124 (ttt) REVERT: E 116 GLN cc_start: 0.9305 (tp-100) cc_final: 0.8303 (tp40) REVERT: E 120 ASP cc_start: 0.8183 (p0) cc_final: 0.7358 (p0) REVERT: E 134 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8780 (tp30) REVERT: F 100 ARG cc_start: 0.9427 (tpp80) cc_final: 0.8853 (tpp80) REVERT: F 115 TYR cc_start: 0.8962 (p90) cc_final: 0.8535 (p90) REVERT: F 122 GLU cc_start: 0.8610 (pm20) cc_final: 0.8165 (pm20) REVERT: G 1 MET cc_start: 0.8919 (ppp) cc_final: 0.8626 (tmm) REVERT: G 3 TYR cc_start: 0.8487 (m-80) cc_final: 0.8028 (m-10) REVERT: G 60 GLN cc_start: 0.8724 (mm110) cc_final: 0.8454 (mt0) REVERT: G 73 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7567 (mmmt) REVERT: H 8 ASP cc_start: 0.7552 (t0) cc_final: 0.6981 (t70) REVERT: H 37 MET cc_start: 0.9115 (mtp) cc_final: 0.8735 (mtp) REVERT: H 56 PHE cc_start: 0.8316 (p90) cc_final: 0.7870 (p90) REVERT: I 37 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5323 (t80) REVERT: I 67 GLN cc_start: 0.9117 (pp30) cc_final: 0.8822 (pp30) REVERT: J 31 GLU cc_start: 0.9129 (mp0) cc_final: 0.8818 (mp0) REVERT: J 54 ASP cc_start: 0.9039 (p0) cc_final: 0.8683 (p0) REVERT: J 57 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8831 (mm-30) REVERT: K 24 ASP cc_start: 0.8982 (t0) cc_final: 0.8567 (t0) REVERT: K 31 CYS cc_start: 0.8645 (t) cc_final: 0.8090 (t) REVERT: L 15 MET cc_start: 0.8964 (tpp) cc_final: 0.8764 (tpp) REVERT: L 44 MET cc_start: 0.8992 (mmm) cc_final: 0.8236 (mmm) REVERT: L 55 PHE cc_start: 0.9089 (m-80) cc_final: 0.8558 (m-80) REVERT: Q 28 ILE cc_start: 0.5358 (tt) cc_final: 0.5112 (tp) REVERT: Q 31 PHE cc_start: 0.6941 (m-10) cc_final: 0.6725 (m-10) REVERT: Q 48 GLU cc_start: 0.5238 (mp0) cc_final: 0.5022 (mp0) REVERT: Q 124 TYR cc_start: 0.8756 (m-80) cc_final: 0.8365 (m-80) REVERT: Q 125 TYR cc_start: 0.8065 (m-10) cc_final: 0.7712 (m-10) REVERT: Q 169 LYS cc_start: 0.8163 (pptt) cc_final: 0.7749 (tptt) REVERT: Q 178 GLN cc_start: 0.7017 (mm110) cc_final: 0.6726 (mp10) REVERT: W 168 MET cc_start: 0.8350 (ptp) cc_final: 0.7729 (ppp) outliers start: 81 outliers final: 64 residues processed: 637 average time/residue: 0.1955 time to fit residues: 213.5546 Evaluate side-chains 645 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 573 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain W residue 161 VAL Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 410 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 chunk 132 optimal weight: 0.4980 chunk 285 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 441 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 437 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 HIS ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.137772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080245 restraints weight = 76313.722| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.98 r_work: 0.2822 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39085 Z= 0.139 Angle : 0.656 14.647 53164 Z= 0.333 Chirality : 0.044 0.360 5927 Planarity : 0.004 0.048 6556 Dihedral : 13.573 179.145 6003 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.00 % Allowed : 17.40 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.17 (0.13), residues: 4460 helix: 1.25 (0.13), residues: 1626 sheet: 0.00 (0.21), residues: 612 loop : -0.68 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.027 0.001 TYR B 766 PHE 0.025 0.001 PHE D 26 TRP 0.040 0.002 TRP Q 98 HIS 0.013 0.001 HIS Q 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (39052) covalent geometry : angle 0.64925 / 0.33 (53131) hydrogen bonds : bond 0.03460 / 2.30 ( 1625) hydrogen bonds : angle 4.65608 / 3.30 ( 4555) metal coordination : bond 0.00502 / 0.33 ( 33) metal coordination : angle 3.75225 / 2.42 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 615 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8821 (t70) cc_final: 0.8577 (t0) REVERT: A 186 ARG cc_start: 0.7305 (tpt170) cc_final: 0.7010 (tpt-90) REVERT: A 241 ARG cc_start: 0.9099 (ptm160) cc_final: 0.8615 (tmm-80) REVERT: A 274 ASP cc_start: 0.8777 (t70) cc_final: 0.8533 (t70) REVERT: A 275 ASP cc_start: 0.9156 (m-30) cc_final: 0.8559 (p0) REVERT: A 279 LYS cc_start: 0.9067 (tppp) cc_final: 0.8846 (tppp) REVERT: A 282 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8630 (t0) REVERT: A 337 LYS cc_start: 0.8935 (tppt) cc_final: 0.7920 (tppt) REVERT: A 347 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 450 MET cc_start: 0.9346 (ttm) cc_final: 0.9123 (ttm) REVERT: A 561 MET cc_start: 0.9178 (mmt) cc_final: 0.8783 (mmm) REVERT: A 818 GLU cc_start: 0.8988 (pm20) cc_final: 0.8112 (tm-30) REVERT: A 845 GLU cc_start: 0.9294 (tm-30) cc_final: 0.9008 (tm-30) REVERT: A 868 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7712 (mtt) REVERT: A 974 ASP cc_start: 0.8501 (t0) cc_final: 0.8257 (t0) REVERT: A 1036 ASN cc_start: 0.8830 (m-40) cc_final: 0.8425 (t0) REVERT: A 1038 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 1192 TRP cc_start: 0.8607 (p90) cc_final: 0.8270 (p90) REVERT: A 1221 MET cc_start: 0.9212 (mmm) cc_final: 0.8833 (mmm) REVERT: A 1262 MET cc_start: 0.8706 (ppp) cc_final: 0.8153 (ppp) REVERT: A 1302 GLU cc_start: 0.8905 (pm20) cc_final: 0.8539 (pm20) REVERT: A 1322 ILE cc_start: 0.9010 (mt) cc_final: 0.8797 (mt) REVERT: A 1364 GLU cc_start: 0.8582 (tp30) cc_final: 0.8298 (tm-30) REVERT: B 108 MET cc_start: 0.9282 (mmp) cc_final: 0.9048 (mmm) REVERT: B 155 MET cc_start: 0.8793 (ptm) cc_final: 0.8347 (ptm) REVERT: B 172 CYS cc_start: 0.9440 (m) cc_final: 0.8871 (m) REVERT: B 230 ARG cc_start: 0.8179 (tpt170) cc_final: 0.7502 (tpp80) REVERT: B 236 TRP cc_start: 0.7776 (m-10) cc_final: 0.7230 (m-10) REVERT: B 299 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8781 (tm-30) REVERT: B 300 MET cc_start: 0.9003 (tpt) cc_final: 0.8688 (tpp) REVERT: B 346 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8215 (tt0) REVERT: B 368 MET cc_start: 0.9538 (ttp) cc_final: 0.9175 (ttt) REVERT: B 384 ASP cc_start: 0.8975 (t0) cc_final: 0.8740 (t0) REVERT: B 422 PHE cc_start: 0.8573 (t80) cc_final: 0.7832 (t80) REVERT: B 501 LEU cc_start: 0.9452 (tp) cc_final: 0.9236 (tp) REVERT: B 669 GLU cc_start: 0.8912 (tt0) cc_final: 0.8344 (mt-10) REVERT: B 789 ASN cc_start: 0.9094 (p0) cc_final: 0.8661 (p0) REVERT: B 796 MET cc_start: 0.9144 (mtm) cc_final: 0.8923 (mtm) REVERT: B 916 TYR cc_start: 0.8243 (m-80) cc_final: 0.7801 (m-80) REVERT: B 1151 MET cc_start: 0.9169 (ptm) cc_final: 0.8714 (ppp) REVERT: B 1171 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: B 1172 MET cc_start: 0.8935 (mmp) cc_final: 0.8593 (mmp) REVERT: C 27 ASP cc_start: 0.8739 (m-30) cc_final: 0.8435 (t70) REVERT: C 62 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 157 GLN cc_start: 0.9101 (mt0) cc_final: 0.8715 (mt0) REVERT: C 265 HIS cc_start: 0.8941 (t70) cc_final: 0.8493 (t70) REVERT: E 3 ASP cc_start: 0.8024 (m-30) cc_final: 0.7697 (t70) REVERT: E 16 THR cc_start: 0.9276 (m) cc_final: 0.8961 (p) REVERT: E 65 ASN cc_start: 0.9341 (m-40) cc_final: 0.8886 (m110) REVERT: E 72 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8820 (tpp) REVERT: E 91 CYS cc_start: 0.9582 (m) cc_final: 0.9345 (p) REVERT: E 98 ASN cc_start: 0.9321 (t0) cc_final: 0.9014 (p0) REVERT: E 108 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8701 (tm-30) REVERT: E 116 GLN cc_start: 0.9301 (tp-100) cc_final: 0.8361 (tp40) REVERT: E 120 ASP cc_start: 0.8135 (p0) cc_final: 0.7329 (p0) REVERT: E 134 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8781 (tp30) REVERT: F 100 ARG cc_start: 0.9406 (tpp80) cc_final: 0.8818 (tpp80) REVERT: F 106 ILE cc_start: 0.8925 (mt) cc_final: 0.8659 (tt) REVERT: F 115 TYR cc_start: 0.8973 (p90) cc_final: 0.8521 (p90) REVERT: F 122 GLU cc_start: 0.8631 (pm20) cc_final: 0.8177 (pm20) REVERT: G 1 MET cc_start: 0.8864 (ppp) cc_final: 0.8595 (tmm) REVERT: G 3 TYR cc_start: 0.8440 (m-80) cc_final: 0.7984 (m-10) REVERT: G 60 GLN cc_start: 0.8720 (mm110) cc_final: 0.8455 (mt0) REVERT: G 73 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7592 (mmmt) REVERT: H 8 ASP cc_start: 0.7537 (t0) cc_final: 0.6975 (t70) REVERT: H 37 MET cc_start: 0.9108 (mtp) cc_final: 0.8731 (mtp) REVERT: H 56 PHE cc_start: 0.8295 (p90) cc_final: 0.7879 (p90) REVERT: I 37 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5338 (t80) REVERT: I 67 GLN cc_start: 0.9141 (pp30) cc_final: 0.8860 (pp30) REVERT: J 31 GLU cc_start: 0.9119 (mp0) cc_final: 0.8802 (mp0) REVERT: J 54 ASP cc_start: 0.9024 (p0) cc_final: 0.8670 (p0) REVERT: J 57 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8803 (mm-30) REVERT: K 24 ASP cc_start: 0.8999 (t0) cc_final: 0.8579 (t0) REVERT: K 31 CYS cc_start: 0.8633 (t) cc_final: 0.8084 (t) REVERT: K 38 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8877 (mm-30) REVERT: K 93 ASP cc_start: 0.8953 (m-30) cc_final: 0.8568 (t0) REVERT: L 15 MET cc_start: 0.8926 (tpp) cc_final: 0.8726 (tpp) REVERT: L 44 MET cc_start: 0.8989 (mmm) cc_final: 0.8464 (mmm) REVERT: L 55 PHE cc_start: 0.9079 (m-80) cc_final: 0.8557 (m-80) REVERT: Q 28 ILE cc_start: 0.5322 (tt) cc_final: 0.5072 (tp) REVERT: Q 124 TYR cc_start: 0.8797 (m-80) cc_final: 0.8441 (m-80) REVERT: Q 125 TYR cc_start: 0.8062 (m-10) cc_final: 0.7718 (m-10) REVERT: Q 169 LYS cc_start: 0.8158 (pptt) cc_final: 0.7751 (tptt) REVERT: W 168 MET cc_start: 0.8359 (ptp) cc_final: 0.7719 (ppp) outliers start: 80 outliers final: 64 residues processed: 648 average time/residue: 0.2005 time to fit residues: 223.2734 Evaluate side-chains 659 residues out of total 4001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 589 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 141 HIS Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain W residue 161 VAL Chi-restraints excluded: chain X residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 359 optimal weight: 0.8980 chunk 414 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 245 optimal weight: 0.5980 chunk 302 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 673 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN Q 44 GLN ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076919 restraints weight = 77433.865| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.98 r_work: 0.2765 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 39085 Z= 0.233 Angle : 0.698 11.725 53164 Z= 0.356 Chirality : 0.045 0.352 5927 Planarity : 0.004 0.046 6556 Dihedral : 13.600 179.383 6003 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.10 % Allowed : 17.85 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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 (0.13), residues: 4460 helix: 1.23 (0.13), residues: 1626 sheet: -0.08 (0.21), residues: 634 loop : -0.73 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 40 TYR 0.034 0.002 TYR B 766 PHE 0.021 0.002 PHE D 26 TRP 0.037 0.002 TRP R 31 HIS 0.029 0.001 HIS Q 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (39052) covalent geometry : angle 0.69184 / 0.36 (53131) hydrogen bonds : bond 0.03672 / 2.45 ( 1625) hydrogen bonds : angle 4.70734 / 3.33 ( 4555) metal coordination : bond 0.00951 / 0.59 ( 33) metal coordination : angle 3.87027 / 2.52 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11252.83 seconds wall clock time: 193 minutes 5.94 seconds (11585.94 seconds total)