Starting phenix.real_space_refine on Fri Mar 6 17:26:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aof_11843/03_2026/7aof_11843_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aof_11843/03_2026/7aof_11843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aof_11843/03_2026/7aof_11843_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aof_11843/03_2026/7aof_11843_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aof_11843/03_2026/7aof_11843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aof_11843/03_2026/7aof_11843.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 21030 2.51 5 N 5424 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 5573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5573 Classifications: {'peptide': 665} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 641} Chain breaks: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "S" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1360 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 88.711 102.937 62.424 1.00111.55 S ATOM 382 SG CYS A 52 92.441 103.061 61.672 1.00106.51 S ATOM 434 SG CYS A 59 90.886 99.849 63.007 1.00106.93 S ATOM 694 SG CYS A 90 75.616 100.473 109.345 1.00135.81 S ATOM 718 SG CYS A 93 76.868 104.034 109.991 1.00139.72 S ATOM 1016 SG CYS A 130 76.730 101.421 112.791 1.00141.05 S ATOM 1059 SG CYS A 135 73.554 102.962 111.495 1.00143.99 S ATOM 18688 SG CYS B1087 99.143 104.377 76.437 1.00 98.78 S ATOM 18711 SG CYS B1090 95.605 103.182 77.348 1.00101.21 S ATOM 18800 SG CYS B1103 96.072 105.670 74.621 1.00 98.37 S ATOM 18825 SG CYS B1106 96.696 106.749 78.177 1.00102.17 S ATOM 27074 SG CYS I 326 102.516 95.772 38.660 1.00149.52 S ATOM 27387 SG CYS I 363 100.239 92.636 39.608 1.00136.01 S ATOM 27411 SG CYS I 366 103.502 93.325 41.494 1.00142.53 S Time building chain proxies: 7.00, per 1000 atoms: 0.21 Number of scatterers: 32727 At special positions: 0 Unit cell: (163.779, 152.081, 152.081, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 149 16.00 P 3 15.00 Mg 1 11.99 O 6116 8.00 N 5424 7.00 C 21030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" NE2 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7726 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 48 sheets defined 43.6% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.554A pdb=" N LEU A 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.689A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 6.195A pdb=" N LYS A 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.006A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.844A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.614A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 267 " --> pdb=" O TYR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 458 through 471 removed outlier: 3.615A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.181A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.764A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.683A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 712 through 715 Processing helix chain 'A' and resid 727 through 763 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.731A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.638A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.617A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.324A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.519A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1131 through 1136 removed outlier: 3.825A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1171 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.690A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.686A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.525A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.510A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.542A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.567A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.340A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.700A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.623A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.639A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.906A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 4.042A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.533A pdb=" N SER B 799 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.823A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.775A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.324A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.635A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.706A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.968A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.323A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.773A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 157' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.960A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 4.033A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 34 removed outlier: 3.624A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 4.339A pdb=" N ILE E 102 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.774A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 96 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.589A pdb=" N GLY G 113 " --> pdb=" O ARG G 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.213A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.700A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 3.867A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 391 through 396 removed outlier: 4.280A pdb=" N PHE I 395 " --> pdb=" O ASN I 391 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU I 396 " --> pdb=" O LYS I 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 391 through 396' Processing helix chain 'I' and resid 397 through 402 removed outlier: 3.793A pdb=" N TYR I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 421 removed outlier: 4.325A pdb=" N ARG I 408 " --> pdb=" O VAL I 404 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE I 409 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 413 " --> pdb=" O PHE I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 427 removed outlier: 3.983A pdb=" N VAL I 427 " --> pdb=" O GLN I 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 424 through 427' Processing helix chain 'I' and resid 428 through 446 Processing helix chain 'I' and resid 446 through 454 removed outlier: 4.141A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 459 removed outlier: 3.968A pdb=" N LYS I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 501 removed outlier: 3.589A pdb=" N LEU I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 514 Processing helix chain 'I' and resid 522 through 538 Processing helix chain 'I' and resid 545 through 557 Processing helix chain 'I' and resid 561 through 581 removed outlier: 3.603A pdb=" N VAL I 579 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 4.133A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.639A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.778A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.610A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.534A pdb=" N VAL J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 59 through 63 removed outlier: 3.623A pdb=" N ILE S 63 " --> pdb=" O LYS S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 81 removed outlier: 3.594A pdb=" N ASP S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 85 Processing helix chain 'S' and resid 102 through 110 removed outlier: 4.031A pdb=" N THR S 110 " --> pdb=" O MET S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 131 Processing helix chain 'S' and resid 144 through 148 Processing helix chain 'S' and resid 213 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.264A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.580A pdb=" N LYS A 282 " --> pdb=" O ILE B1051 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.535A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.135A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.641A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB3, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB4, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 removed outlier: 3.566A pdb=" N VAL A 998 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 6.398A pdb=" N ASN A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.824A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.824A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.713A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE B 98 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLU B 121 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 100 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 119 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.713A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.954A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.367A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.805A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.816A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.816A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 857 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD3, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.656A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.582A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.829A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.576A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AE2, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.490A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 113 through 115 Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 91 removed outlier: 4.291A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 116 Processing sheet with id=AE7, first strand: chain 'I' and resid 121 through 123 Processing sheet with id=AE8, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.592A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AF1, first strand: chain 'I' and resid 354 through 357 Processing sheet with id=AF2, first strand: chain 'I' and resid 663 through 665 removed outlier: 4.326A pdb=" N ILE I 658 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 668 through 670 1435 hydrogen bonds defined for protein. 3948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10437 1.34 - 1.46: 7462 1.46 - 1.58: 15244 1.58 - 1.70: 12 1.70 - 1.82: 236 Bond restraints: 33391 Sorted by residual: bond pdb=" C LEU E 13 " pdb=" N CYS E 14 " ideal model delta sigma weight residual 1.332 1.304 0.027 1.35e-02 5.49e+03 4.15e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.15e+00 bond pdb=" C ILE C 177 " pdb=" N ASP C 178 " ideal model delta sigma weight residual 1.339 1.414 -0.074 5.57e-02 3.22e+02 1.78e+00 bond pdb=" N ASN B 320 " pdb=" CA ASN B 320 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.40e-01 ... (remaining 33386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 44882 2.24 - 4.48: 254 4.48 - 6.72: 8 6.72 - 8.96: 0 8.96 - 11.20: 2 Bond angle restraints: 45146 Sorted by residual: angle pdb=" CG1 VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG2 VAL E 170 " ideal model delta sigma weight residual 110.80 122.00 -11.20 2.20e+00 2.07e-01 2.59e+01 angle pdb=" CG1 VAL C 111 " pdb=" CB VAL C 111 " pdb=" CG2 VAL C 111 " ideal model delta sigma weight residual 110.80 121.62 -10.82 2.20e+00 2.07e-01 2.42e+01 angle pdb=" CA VAL C 111 " pdb=" CB VAL C 111 " pdb=" CG1 VAL C 111 " ideal model delta sigma weight residual 110.40 116.90 -6.50 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG1 VAL E 170 " ideal model delta sigma weight residual 110.40 116.84 -6.44 1.70e+00 3.46e-01 1.44e+01 angle pdb=" CA VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG2 VAL E 170 " ideal model delta sigma weight residual 110.40 116.81 -6.41 1.70e+00 3.46e-01 1.42e+01 ... (remaining 45141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 19510 17.86 - 35.73: 630 35.73 - 53.59: 119 53.59 - 71.45: 34 71.45 - 89.31: 10 Dihedral angle restraints: 20303 sinusoidal: 8351 harmonic: 11952 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -139.67 53.67 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASN C 245 " pdb=" C ASN C 245 " pdb=" N PRO C 246 " pdb=" CA PRO C 246 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 20300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 5112 0.297 - 0.594: 0 0.594 - 0.892: 0 0.892 - 1.189: 0 1.189 - 1.486: 2 Chirality restraints: 5114 Sorted by residual: chirality pdb=" CB VAL E 170 " pdb=" CA VAL E 170 " pdb=" CG1 VAL E 170 " pdb=" CG2 VAL E 170 " both_signs ideal model delta sigma weight residual False -2.63 -1.14 -1.49 2.00e-01 2.50e+01 5.52e+01 chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.10e+01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 5111 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 41 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C PHE B 41 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE B 41 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 42 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.013 2.00e-02 2.50e+03 1.15e-02 2.32e+00 pdb=" CG PHE A 938 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 459 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C GLN A 459 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN A 459 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 460 " 0.008 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 317 2.57 - 3.15: 28623 3.15 - 3.73: 49790 3.73 - 4.32: 73158 4.32 - 4.90: 122268 Nonbonded interactions: 274156 Sorted by model distance: nonbonded pdb=" N CYS I 366 " pdb="ZN ZN I 801 " model vdw 1.984 2.310 nonbonded pdb=" OD1 ASP A 415 " pdb="MG MG A1301 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.015 2.170 nonbonded pdb=" OE2 GLU I 250 " pdb=" OG SER I 280 " model vdw 2.081 3.040 nonbonded pdb=" O THR B 887 " pdb=" OG SER B 888 " model vdw 2.135 3.040 ... (remaining 274151 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: 2.180 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.002 0.074 33408 Z= 0.118 Angle : 0.459 11.202 45166 Z= 0.264 Chirality : 0.050 1.486 5114 Planarity : 0.002 0.033 5712 Dihedral : 9.854 89.314 12574 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 4.16 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3991 helix: 1.49 (0.14), residues: 1493 sheet: -0.09 (0.23), residues: 534 loop : -0.56 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 250 TYR 0.017 0.001 TYR B 377 PHE 0.026 0.001 PHE A 938 TRP 0.010 0.001 TRP A 365 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00232 (33391) covalent geometry : angle 0.45753 (45146) SS BOND : bond 0.00571 ( 1) SS BOND : angle 1.65910 ( 2) hydrogen bonds : bond 0.14185 ( 1394) hydrogen bonds : angle 6.11192 ( 3948) metal coordination : bond 0.00663 ( 16) metal coordination : angle 2.11088 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 1.440 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 146 LYS cc_start: 0.9210 (ttmt) cc_final: 0.9000 (ttpm) REVERT: A 238 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8334 (mm-40) REVERT: A 1031 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8317 (mm-30) REVERT: B 67 MET cc_start: 0.8226 (mmm) cc_final: 0.7791 (mmm) REVERT: B 159 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8145 (p0) REVERT: B 506 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 719 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: E 18 GLU cc_start: 0.9080 (tp30) cc_final: 0.8673 (tp30) REVERT: E 69 ILE cc_start: 0.9012 (mt) cc_final: 0.8650 (mp) REVERT: E 86 SER cc_start: 0.9536 (m) cc_final: 0.9144 (p) REVERT: G 100 GLN cc_start: 0.8822 (mt0) cc_final: 0.8516 (mp10) REVERT: G 103 ASP cc_start: 0.8719 (p0) cc_final: 0.8382 (p0) REVERT: G 124 PHE cc_start: 0.7903 (m-80) cc_final: 0.7628 (m-80) REVERT: G 131 TYR cc_start: 0.7247 (m-80) cc_final: 0.6882 (m-80) REVERT: I 121 MET cc_start: 0.8477 (mmt) cc_final: 0.7984 (mmt) REVERT: I 195 CYS cc_start: 0.9005 (m) cc_final: 0.8618 (m) REVERT: I 281 TYR cc_start: 0.8519 (t80) cc_final: 0.8235 (t80) REVERT: I 444 ASN cc_start: 0.9005 (t0) cc_final: 0.8404 (p0) REVERT: J 51 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7705 (tp40) REVERT: J 61 ASP cc_start: 0.8268 (t70) cc_final: 0.7908 (t70) REVERT: S 37 LEU cc_start: 0.8072 (mt) cc_final: 0.7797 (tp) outliers start: 67 outliers final: 18 residues processed: 436 average time/residue: 0.7793 time to fit residues: 398.9360 Evaluate side-chains 249 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0030 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 HIS C 129 GLN G 145 GLN I 197 HIS I 567 HIS S 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.045615 restraints weight = 105586.317| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.20 r_work: 0.2580 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33408 Z= 0.187 Angle : 0.580 7.485 45166 Z= 0.306 Chirality : 0.044 0.160 5114 Planarity : 0.004 0.046 5712 Dihedral : 5.534 85.156 4450 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.78 % Allowed : 9.10 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.54 (0.14), residues: 3991 helix: 1.59 (0.14), residues: 1512 sheet: -0.00 (0.23), residues: 526 loop : -0.49 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 90 TYR 0.020 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.014 0.001 TRP A 365 HIS 0.009 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00424 (33391) covalent geometry : angle 0.57692 (45146) SS BOND : bond 0.00295 ( 1) SS BOND : angle 3.25799 ( 2) hydrogen bonds : bond 0.04567 ( 1394) hydrogen bonds : angle 4.88981 ( 3948) metal coordination : bond 0.00682 ( 16) metal coordination : angle 2.58551 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 242 time to evaluate : 1.428 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 44 MET cc_start: 0.8506 (pmm) cc_final: 0.8268 (ppp) REVERT: A 226 MET cc_start: 0.9153 (mmm) cc_final: 0.8738 (mmm) REVERT: A 961 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8607 (t80) REVERT: A 1031 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8915 (mt-10) REVERT: B 67 MET cc_start: 0.8403 (mmm) cc_final: 0.7902 (mmm) REVERT: B 159 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 506 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 719 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: C 247 GLU cc_start: 0.6980 (mp0) cc_final: 0.6684 (mp0) REVERT: E 18 GLU cc_start: 0.9461 (tp30) cc_final: 0.8936 (tp30) REVERT: E 86 SER cc_start: 0.9589 (m) cc_final: 0.9266 (p) REVERT: E 120 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8902 (mp0) REVERT: F 107 GLU cc_start: 0.8932 (mp0) cc_final: 0.8732 (mp0) REVERT: G 100 GLN cc_start: 0.9032 (mt0) cc_final: 0.8558 (mp10) REVERT: G 103 ASP cc_start: 0.8880 (p0) cc_final: 0.8377 (p0) REVERT: G 107 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8379 (mtmt) REVERT: G 124 PHE cc_start: 0.8500 (m-80) cc_final: 0.8084 (m-80) REVERT: G 131 TYR cc_start: 0.7135 (m-80) cc_final: 0.6551 (m-80) REVERT: I 205 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8569 (ptpp) REVERT: I 281 TYR cc_start: 0.9064 (t80) cc_final: 0.8752 (t80) REVERT: I 444 ASN cc_start: 0.9117 (t0) cc_final: 0.8572 (p0) REVERT: I 511 MET cc_start: 0.6944 (mmt) cc_final: 0.6643 (tpp) REVERT: I 569 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8789 (tp40) REVERT: I 573 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8937 (mm) REVERT: I 643 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9234 (tptp) REVERT: I 650 CYS cc_start: 0.8263 (m) cc_final: 0.8016 (m) REVERT: J 21 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8985 (pp) REVERT: J 51 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8154 (tp40) REVERT: J 61 ASP cc_start: 0.8613 (t70) cc_final: 0.8248 (t70) REVERT: S 39 ASP cc_start: 0.8991 (p0) cc_final: 0.8317 (p0) outliers start: 66 outliers final: 21 residues processed: 294 average time/residue: 0.7576 time to fit residues: 264.0285 Evaluate side-chains 240 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 569 GLN Chi-restraints excluded: chain I residue 573 LEU Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 116 optimal weight: 6.9990 chunk 238 optimal weight: 0.2980 chunk 278 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS B 779 GLN I 197 HIS I 567 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.044976 restraints weight = 105861.180| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.12 r_work: 0.2580 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33408 Z= 0.222 Angle : 0.578 10.625 45166 Z= 0.303 Chirality : 0.045 0.166 5114 Planarity : 0.004 0.054 5712 Dihedral : 5.475 83.660 4436 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 2.29 % Allowed : 9.69 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3991 helix: 1.53 (0.14), residues: 1521 sheet: -0.03 (0.23), residues: 519 loop : -0.52 (0.15), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 83 TYR 0.020 0.001 TYR S 134 PHE 0.030 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.008 0.001 HIS I 197 Details of bonding type rmsd covalent geometry : bond 0.00506 (33391) covalent geometry : angle 0.57486 (45146) SS BOND : bond 0.00555 ( 1) SS BOND : angle 1.80183 ( 2) hydrogen bonds : bond 0.04423 ( 1394) hydrogen bonds : angle 4.75479 ( 3948) metal coordination : bond 0.00691 ( 16) metal coordination : angle 2.85715 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 237 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 MET cc_start: 0.9217 (mmm) cc_final: 0.8961 (mmm) REVERT: A 261 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8651 (p0) REVERT: A 631 GLU cc_start: 0.8693 (pp20) cc_final: 0.8447 (pp20) REVERT: A 961 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8674 (t80) REVERT: B 67 MET cc_start: 0.8512 (mmm) cc_final: 0.7974 (mmm) REVERT: B 159 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8267 (p0) REVERT: B 506 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 719 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: E 18 GLU cc_start: 0.9419 (tp30) cc_final: 0.8891 (tp30) REVERT: E 55 ASP cc_start: 0.8298 (t70) cc_final: 0.6993 (t0) REVERT: E 86 SER cc_start: 0.9581 (m) cc_final: 0.9284 (p) REVERT: G 100 GLN cc_start: 0.9055 (mt0) cc_final: 0.8599 (mp10) REVERT: G 103 ASP cc_start: 0.8873 (p0) cc_final: 0.8394 (p0) REVERT: G 107 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8397 (mtmt) REVERT: G 124 PHE cc_start: 0.8439 (m-80) cc_final: 0.8027 (m-80) REVERT: G 131 TYR cc_start: 0.6900 (m-80) cc_final: 0.6244 (m-80) REVERT: G 145 GLN cc_start: 0.8873 (mt0) cc_final: 0.8671 (mt0) REVERT: I 121 MET cc_start: 0.8852 (mmt) cc_final: 0.8279 (mmt) REVERT: I 205 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8638 (ptpp) REVERT: I 281 TYR cc_start: 0.9024 (t80) cc_final: 0.8714 (t80) REVERT: I 444 ASN cc_start: 0.9040 (t0) cc_final: 0.8575 (p0) REVERT: I 511 MET cc_start: 0.6951 (mmt) cc_final: 0.6596 (tpp) REVERT: I 643 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9222 (tptp) REVERT: J 51 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8236 (tp40) REVERT: S 39 ASP cc_start: 0.8828 (p0) cc_final: 0.8550 (p0) REVERT: S 83 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8762 (mtm-85) REVERT: S 141 ASP cc_start: 0.8326 (t0) cc_final: 0.8122 (t0) REVERT: S 146 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8709 (t0) outliers start: 85 outliers final: 33 residues processed: 299 average time/residue: 0.7530 time to fit residues: 267.0215 Evaluate side-chains 250 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 482 PHE Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 389 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 107 ASN A 114 HIS ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.046350 restraints weight = 104217.373| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.12 r_work: 0.2624 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33408 Z= 0.120 Angle : 0.533 9.531 45166 Z= 0.279 Chirality : 0.043 0.162 5114 Planarity : 0.003 0.064 5712 Dihedral : 5.402 83.884 4436 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.13 % Allowed : 9.99 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.54 (0.14), residues: 3991 helix: 1.60 (0.14), residues: 1524 sheet: -0.03 (0.23), residues: 511 loop : -0.50 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 90 TYR 0.024 0.001 TYR A 264 PHE 0.027 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.007 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00266 (33391) covalent geometry : angle 0.52931 (45146) SS BOND : bond 0.01059 ( 1) SS BOND : angle 2.70903 ( 2) hydrogen bonds : bond 0.03851 ( 1394) hydrogen bonds : angle 4.58085 ( 3948) metal coordination : bond 0.00661 ( 16) metal coordination : angle 2.95646 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 235 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8750 (m) REVERT: A 631 GLU cc_start: 0.8739 (pp20) cc_final: 0.8427 (pp20) REVERT: A 961 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8549 (t80) REVERT: B 159 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8294 (p0) REVERT: B 478 ARG cc_start: 0.8475 (ptp-170) cc_final: 0.8273 (ptm160) REVERT: B 506 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 719 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8767 (pt0) REVERT: C 304 ARG cc_start: 0.8619 (tmm160) cc_final: 0.8400 (tmm160) REVERT: E 18 GLU cc_start: 0.9422 (tp30) cc_final: 0.8934 (tp30) REVERT: E 55 ASP cc_start: 0.8344 (t70) cc_final: 0.7904 (t0) REVERT: E 57 MET cc_start: 0.9004 (mmm) cc_final: 0.8655 (mmm) REVERT: E 86 SER cc_start: 0.9582 (m) cc_final: 0.9298 (p) REVERT: E 120 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8847 (mp0) REVERT: G 100 GLN cc_start: 0.9024 (mt0) cc_final: 0.8543 (mp10) REVERT: G 103 ASP cc_start: 0.8786 (p0) cc_final: 0.8333 (p0) REVERT: G 124 PHE cc_start: 0.8463 (m-80) cc_final: 0.8082 (m-80) REVERT: G 131 TYR cc_start: 0.6928 (m-80) cc_final: 0.6226 (m-80) REVERT: I 121 MET cc_start: 0.8857 (mmt) cc_final: 0.8281 (mmt) REVERT: I 205 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8575 (ptpp) REVERT: I 281 TYR cc_start: 0.9009 (t80) cc_final: 0.8679 (t80) REVERT: I 444 ASN cc_start: 0.9003 (t0) cc_final: 0.8516 (p0) REVERT: I 643 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9205 (tptp) REVERT: I 650 CYS cc_start: 0.8342 (m) cc_final: 0.8065 (m) REVERT: J 51 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8243 (tp40) REVERT: S 43 TRP cc_start: 0.9110 (t60) cc_final: 0.8782 (t60) REVERT: S 104 CYS cc_start: 0.9245 (m) cc_final: 0.8467 (p) REVERT: S 141 ASP cc_start: 0.8323 (t0) cc_final: 0.8071 (t0) REVERT: S 146 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8699 (t0) outliers start: 79 outliers final: 31 residues processed: 293 average time/residue: 0.7149 time to fit residues: 250.1067 Evaluate side-chains 252 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 262 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 350 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 389 optimal weight: 0.6980 chunk 332 optimal weight: 5.9990 chunk 390 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN E 92 HIS I 197 HIS I 567 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.046634 restraints weight = 104819.245| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.13 r_work: 0.2633 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33408 Z= 0.118 Angle : 0.528 9.254 45166 Z= 0.274 Chirality : 0.043 0.229 5114 Planarity : 0.003 0.053 5712 Dihedral : 5.338 83.485 4436 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.92 % Allowed : 10.80 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.55 (0.14), residues: 3991 helix: 1.59 (0.14), residues: 1528 sheet: 0.02 (0.23), residues: 513 loop : -0.50 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 126 TYR 0.021 0.001 TYR S 134 PHE 0.028 0.001 PHE A 938 TRP 0.013 0.001 TRP A1054 HIS 0.015 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00264 (33391) covalent geometry : angle 0.52517 (45146) SS BOND : bond 0.00599 ( 1) SS BOND : angle 1.70460 ( 2) hydrogen bonds : bond 0.03706 ( 1394) hydrogen bonds : angle 4.50667 ( 3948) metal coordination : bond 0.00659 ( 16) metal coordination : angle 2.91114 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 GLU cc_start: 0.8747 (pp20) cc_final: 0.8401 (pp20) REVERT: A 1063 GLU cc_start: 0.8190 (pm20) cc_final: 0.7957 (pm20) REVERT: B 67 MET cc_start: 0.8210 (mtp) cc_final: 0.7923 (mmm) REVERT: B 159 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8360 (p0) REVERT: B 421 LYS cc_start: 0.8514 (tmtt) cc_final: 0.8303 (tmtt) REVERT: B 506 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8585 (tm-30) REVERT: B 575 MET cc_start: 0.9433 (mpp) cc_final: 0.9209 (mpt) REVERT: B 719 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: E 18 GLU cc_start: 0.9420 (tp30) cc_final: 0.8968 (tp30) REVERT: E 55 ASP cc_start: 0.8505 (t70) cc_final: 0.7945 (t0) REVERT: E 57 MET cc_start: 0.9147 (mmm) cc_final: 0.8867 (mmm) REVERT: E 67 SER cc_start: 0.9311 (p) cc_final: 0.9110 (p) REVERT: E 86 SER cc_start: 0.9584 (m) cc_final: 0.9300 (p) REVERT: E 144 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: G 100 GLN cc_start: 0.9035 (mt0) cc_final: 0.8574 (mp10) REVERT: G 103 ASP cc_start: 0.8777 (p0) cc_final: 0.8328 (p0) REVERT: G 124 PHE cc_start: 0.8476 (m-80) cc_final: 0.8102 (m-80) REVERT: G 131 TYR cc_start: 0.6827 (m-80) cc_final: 0.6217 (m-80) REVERT: I 205 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8694 (ptpp) REVERT: I 281 TYR cc_start: 0.9026 (t80) cc_final: 0.8686 (t80) REVERT: I 444 ASN cc_start: 0.8977 (t0) cc_final: 0.8483 (p0) REVERT: I 560 MET cc_start: 0.8068 (ptp) cc_final: 0.7423 (ttp) REVERT: I 643 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9208 (tptp) REVERT: I 650 CYS cc_start: 0.8377 (m) cc_final: 0.8066 (m) REVERT: J 17 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8781 (mp0) REVERT: J 51 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8282 (tp40) REVERT: S 43 TRP cc_start: 0.9126 (t60) cc_final: 0.8852 (t60) REVERT: S 104 CYS cc_start: 0.9208 (m) cc_final: 0.8430 (p) REVERT: S 141 ASP cc_start: 0.8346 (t0) cc_final: 0.8084 (t0) REVERT: S 146 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8664 (t0) outliers start: 71 outliers final: 32 residues processed: 284 average time/residue: 0.7320 time to fit residues: 247.8011 Evaluate side-chains 250 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 334 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 355 optimal weight: 0.7980 chunk 119 optimal weight: 0.0000 chunk 145 optimal weight: 0.0170 chunk 137 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 339 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 overall best weight: 0.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 HIS I 197 HIS I 567 HIS S 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.047146 restraints weight = 104268.897| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.13 r_work: 0.2650 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33408 Z= 0.106 Angle : 0.521 10.179 45166 Z= 0.269 Chirality : 0.043 0.172 5114 Planarity : 0.003 0.058 5712 Dihedral : 5.249 83.209 4436 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.84 % Allowed : 11.45 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3991 helix: 1.65 (0.14), residues: 1527 sheet: 0.09 (0.23), residues: 511 loop : -0.50 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 90 TYR 0.026 0.001 TYR A 264 PHE 0.027 0.001 PHE A 938 TRP 0.014 0.001 TRP A1054 HIS 0.008 0.001 HIS I 197 Details of bonding type rmsd covalent geometry : bond 0.00236 (33391) covalent geometry : angle 0.51824 (45146) SS BOND : bond 0.00408 ( 1) SS BOND : angle 1.08982 ( 2) hydrogen bonds : bond 0.03528 ( 1394) hydrogen bonds : angle 4.43390 ( 3948) metal coordination : bond 0.00698 ( 16) metal coordination : angle 2.91202 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 236 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8743 (m) REVERT: A 226 MET cc_start: 0.9090 (mmm) cc_final: 0.8815 (mmm) REVERT: A 631 GLU cc_start: 0.8725 (pp20) cc_final: 0.8345 (pp20) REVERT: B 61 ASN cc_start: 0.9092 (t0) cc_final: 0.8839 (t0) REVERT: B 159 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8368 (p0) REVERT: B 506 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B 575 MET cc_start: 0.9419 (mpp) cc_final: 0.8926 (mpt) REVERT: B 861 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7824 (mm) REVERT: C 304 ARG cc_start: 0.8481 (tmm160) cc_final: 0.8259 (tmm160) REVERT: E 18 GLU cc_start: 0.9415 (tp30) cc_final: 0.8974 (tp30) REVERT: E 55 ASP cc_start: 0.8463 (t70) cc_final: 0.7741 (t0) REVERT: E 57 MET cc_start: 0.9128 (mmm) cc_final: 0.8825 (mmm) REVERT: E 86 SER cc_start: 0.9582 (m) cc_final: 0.9304 (p) REVERT: E 120 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8764 (mp0) REVERT: E 144 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: F 110 LYS cc_start: 0.9567 (mtpt) cc_final: 0.9265 (mtmm) REVERT: G 100 GLN cc_start: 0.8978 (mt0) cc_final: 0.8516 (mp10) REVERT: G 103 ASP cc_start: 0.8783 (p0) cc_final: 0.8377 (p0) REVERT: G 124 PHE cc_start: 0.8480 (m-80) cc_final: 0.8098 (m-80) REVERT: G 131 TYR cc_start: 0.6958 (m-80) cc_final: 0.6384 (m-80) REVERT: I 205 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8666 (ptpp) REVERT: I 281 TYR cc_start: 0.9023 (t80) cc_final: 0.8716 (t80) REVERT: I 444 ASN cc_start: 0.9017 (t0) cc_final: 0.8493 (p0) REVERT: I 643 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9208 (tptp) REVERT: I 650 CYS cc_start: 0.8367 (m) cc_final: 0.8086 (m) REVERT: J 17 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8767 (mp0) REVERT: J 51 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8184 (tp40) REVERT: S 104 CYS cc_start: 0.9171 (m) cc_final: 0.8408 (p) REVERT: S 141 ASP cc_start: 0.8320 (t0) cc_final: 0.8040 (t0) REVERT: S 146 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8624 (OUTLIER) outliers start: 68 outliers final: 33 residues processed: 286 average time/residue: 0.6780 time to fit residues: 232.0719 Evaluate side-chains 257 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 111 optimal weight: 4.9990 chunk 379 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 376 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN B 221 ASN ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.044664 restraints weight = 106395.706| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.14 r_work: 0.2576 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33408 Z= 0.246 Angle : 0.603 11.506 45166 Z= 0.310 Chirality : 0.045 0.220 5114 Planarity : 0.004 0.057 5712 Dihedral : 5.352 82.706 4433 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.34 % Rotamer: Outliers : 1.89 % Allowed : 11.74 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3991 helix: 1.62 (0.14), residues: 1524 sheet: -0.10 (0.23), residues: 519 loop : -0.53 (0.15), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 126 TYR 0.025 0.001 TYR B 377 PHE 0.031 0.001 PHE A 938 TRP 0.015 0.001 TRP S 43 HIS 0.037 0.001 HIS I 197 Details of bonding type rmsd covalent geometry : bond 0.00565 (33391) covalent geometry : angle 0.59991 (45146) SS BOND : bond 0.01742 ( 1) SS BOND : angle 5.07701 ( 2) hydrogen bonds : bond 0.04193 ( 1394) hydrogen bonds : angle 4.59066 ( 3948) metal coordination : bond 0.00745 ( 16) metal coordination : angle 2.85565 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8834 (m) REVERT: A 226 MET cc_start: 0.9125 (mmm) cc_final: 0.8856 (mmm) REVERT: A 631 GLU cc_start: 0.8800 (pp20) cc_final: 0.8427 (pp20) REVERT: B 61 ASN cc_start: 0.9154 (t0) cc_final: 0.8915 (t0) REVERT: B 159 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8468 (p0) REVERT: B 506 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8571 (tm-30) REVERT: C 304 ARG cc_start: 0.8511 (tmm160) cc_final: 0.8261 (tmm160) REVERT: E 18 GLU cc_start: 0.9406 (tp30) cc_final: 0.8926 (tp30) REVERT: E 55 ASP cc_start: 0.8539 (t70) cc_final: 0.7634 (t0) REVERT: E 57 MET cc_start: 0.9169 (mmm) cc_final: 0.8837 (mmm) REVERT: E 86 SER cc_start: 0.9585 (m) cc_final: 0.9289 (p) REVERT: E 120 GLU cc_start: 0.9073 (mp0) cc_final: 0.8794 (mp0) REVERT: E 144 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8780 (pm20) REVERT: G 100 GLN cc_start: 0.9046 (mt0) cc_final: 0.8567 (mp10) REVERT: G 103 ASP cc_start: 0.8850 (p0) cc_final: 0.8410 (p0) REVERT: G 124 PHE cc_start: 0.8495 (m-80) cc_final: 0.8120 (m-80) REVERT: G 131 TYR cc_start: 0.7056 (m-80) cc_final: 0.6674 (m-80) REVERT: I 121 MET cc_start: 0.8817 (mmt) cc_final: 0.8265 (mmt) REVERT: I 205 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8687 (ptpp) REVERT: I 281 TYR cc_start: 0.9011 (t80) cc_final: 0.8796 (t80) REVERT: I 444 ASN cc_start: 0.9014 (t0) cc_final: 0.8499 (p0) REVERT: I 486 LYS cc_start: 0.8716 (mttt) cc_final: 0.8274 (ptpp) REVERT: I 643 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9240 (tptp) REVERT: I 650 CYS cc_start: 0.8439 (m) cc_final: 0.8135 (m) REVERT: J 17 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8902 (mp0) REVERT: J 51 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8178 (tp40) REVERT: S 104 CYS cc_start: 0.9197 (m) cc_final: 0.8471 (p) REVERT: S 141 ASP cc_start: 0.8461 (t0) cc_final: 0.8156 (t0) REVERT: S 146 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8663 (t0) outliers start: 70 outliers final: 41 residues processed: 269 average time/residue: 0.6921 time to fit residues: 222.1078 Evaluate side-chains 261 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 793 PHE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 29 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 391 optimal weight: 0.8980 chunk 215 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.046653 restraints weight = 104327.156| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.14 r_work: 0.2633 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33408 Z= 0.115 Angle : 0.553 12.078 45166 Z= 0.282 Chirality : 0.043 0.217 5114 Planarity : 0.003 0.064 5712 Dihedral : 5.244 83.426 4433 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.59 % Allowed : 12.10 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3991 helix: 1.70 (0.14), residues: 1517 sheet: -0.01 (0.23), residues: 507 loop : -0.51 (0.15), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 90 TYR 0.027 0.001 TYR A 264 PHE 0.028 0.001 PHE A 938 TRP 0.016 0.001 TRP A1054 HIS 0.006 0.001 HIS I 197 Details of bonding type rmsd covalent geometry : bond 0.00259 (33391) covalent geometry : angle 0.54856 (45146) SS BOND : bond 0.00940 ( 1) SS BOND : angle 3.77427 ( 2) hydrogen bonds : bond 0.03605 ( 1394) hydrogen bonds : angle 4.44456 ( 3948) metal coordination : bond 0.00767 ( 16) metal coordination : angle 3.14116 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 1.325 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 149 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8746 (m) REVERT: A 226 MET cc_start: 0.9107 (mmm) cc_final: 0.8824 (mmm) REVERT: A 283 ASP cc_start: 0.8261 (m-30) cc_final: 0.8031 (t0) REVERT: A 631 GLU cc_start: 0.8761 (pp20) cc_final: 0.8363 (pp20) REVERT: B 61 ASN cc_start: 0.9094 (t0) cc_final: 0.8831 (t0) REVERT: B 67 MET cc_start: 0.8772 (mmm) cc_final: 0.8390 (mmm) REVERT: B 159 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8421 (p0) REVERT: B 506 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 575 MET cc_start: 0.9435 (mpp) cc_final: 0.8937 (mpt) REVERT: B 861 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7895 (mm) REVERT: C 304 ARG cc_start: 0.8509 (tmm160) cc_final: 0.8247 (tmm160) REVERT: E 18 GLU cc_start: 0.9418 (tp30) cc_final: 0.8947 (tp30) REVERT: E 86 SER cc_start: 0.9582 (m) cc_final: 0.9293 (p) REVERT: E 120 GLU cc_start: 0.9039 (mp0) cc_final: 0.8782 (mp0) REVERT: E 144 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8826 (pm20) REVERT: F 110 LYS cc_start: 0.9561 (mtpt) cc_final: 0.9225 (mtmm) REVERT: G 100 GLN cc_start: 0.9002 (mt0) cc_final: 0.8527 (mp10) REVERT: G 103 ASP cc_start: 0.8788 (p0) cc_final: 0.8443 (p0) REVERT: G 124 PHE cc_start: 0.8478 (m-80) cc_final: 0.8120 (m-80) REVERT: G 131 TYR cc_start: 0.7206 (m-80) cc_final: 0.6732 (m-80) REVERT: I 205 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8679 (ptpp) REVERT: I 281 TYR cc_start: 0.8977 (t80) cc_final: 0.8735 (t80) REVERT: I 444 ASN cc_start: 0.9011 (t0) cc_final: 0.8439 (p0) REVERT: I 511 MET cc_start: 0.7314 (mmm) cc_final: 0.6960 (tpp) REVERT: I 643 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9202 (tptp) REVERT: I 650 CYS cc_start: 0.8316 (m) cc_final: 0.8004 (m) REVERT: I 795 ASN cc_start: 0.8341 (m-40) cc_final: 0.8042 (m110) REVERT: J 51 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8104 (tp40) REVERT: S 104 CYS cc_start: 0.9175 (m) cc_final: 0.8491 (p) REVERT: S 141 ASP cc_start: 0.8379 (t0) cc_final: 0.8078 (t0) REVERT: S 146 ASP cc_start: 0.9008 (m-30) cc_final: 0.8672 (OUTLIER) outliers start: 59 outliers final: 34 residues processed: 274 average time/residue: 0.7328 time to fit residues: 238.6207 Evaluate side-chains 251 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 187 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 333 optimal weight: 0.0020 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 372 optimal weight: 0.4980 chunk 357 optimal weight: 7.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 ASN I 567 HIS J 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.046565 restraints weight = 104007.422| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.13 r_work: 0.2633 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33408 Z= 0.125 Angle : 0.567 13.230 45166 Z= 0.287 Chirality : 0.043 0.275 5114 Planarity : 0.003 0.064 5712 Dihedral : 5.206 82.801 4433 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.38 % Allowed : 12.58 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.60 (0.14), residues: 3991 helix: 1.72 (0.14), residues: 1516 sheet: -0.07 (0.23), residues: 509 loop : -0.49 (0.15), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 126 TYR 0.028 0.001 TYR S 134 PHE 0.028 0.001 PHE A 938 TRP 0.016 0.001 TRP A1054 HIS 0.005 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00286 (33391) covalent geometry : angle 0.56351 (45146) SS BOND : bond 0.00881 ( 1) SS BOND : angle 3.19565 ( 2) hydrogen bonds : bond 0.03600 ( 1394) hydrogen bonds : angle 4.45703 ( 3948) metal coordination : bond 0.00681 ( 16) metal coordination : angle 3.05160 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 1.299 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 149 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8747 (m) REVERT: A 226 MET cc_start: 0.9086 (mmm) cc_final: 0.8769 (mmm) REVERT: A 283 ASP cc_start: 0.8266 (m-30) cc_final: 0.8024 (t0) REVERT: A 631 GLU cc_start: 0.8760 (pp20) cc_final: 0.8348 (pp20) REVERT: B 61 ASN cc_start: 0.9102 (t0) cc_final: 0.8803 (t0) REVERT: B 67 MET cc_start: 0.8690 (mmm) cc_final: 0.8471 (mmm) REVERT: B 159 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8465 (p0) REVERT: B 506 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 575 MET cc_start: 0.9431 (mpp) cc_final: 0.8942 (mpt) REVERT: B 861 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 304 ARG cc_start: 0.8534 (tmm160) cc_final: 0.8280 (tmm160) REVERT: E 18 GLU cc_start: 0.9425 (tp30) cc_final: 0.8949 (tp30) REVERT: E 86 SER cc_start: 0.9582 (m) cc_final: 0.9295 (p) REVERT: E 120 GLU cc_start: 0.9038 (mp0) cc_final: 0.8780 (mp0) REVERT: E 144 GLU cc_start: 0.9211 (pt0) cc_final: 0.8859 (pm20) REVERT: F 110 LYS cc_start: 0.9557 (mtpt) cc_final: 0.9199 (mtmm) REVERT: F 122 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8837 (pp20) REVERT: G 100 GLN cc_start: 0.9046 (mt0) cc_final: 0.8568 (mp10) REVERT: G 103 ASP cc_start: 0.8872 (p0) cc_final: 0.8502 (p0) REVERT: G 124 PHE cc_start: 0.8486 (m-80) cc_final: 0.8124 (m-80) REVERT: G 131 TYR cc_start: 0.7192 (m-80) cc_final: 0.6677 (m-80) REVERT: I 205 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8685 (ptpp) REVERT: I 281 TYR cc_start: 0.8990 (t80) cc_final: 0.8749 (t80) REVERT: I 444 ASN cc_start: 0.8950 (t0) cc_final: 0.8407 (p0) REVERT: I 486 LYS cc_start: 0.8736 (mttt) cc_final: 0.8316 (ptpp) REVERT: I 643 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9210 (tptp) REVERT: I 650 CYS cc_start: 0.8294 (m) cc_final: 0.8044 (m) REVERT: J 51 GLN cc_start: 0.8714 (tp40) cc_final: 0.8084 (tp40) REVERT: S 43 TRP cc_start: 0.9172 (t60) cc_final: 0.8918 (t60) REVERT: S 104 CYS cc_start: 0.9216 (m) cc_final: 0.8515 (p) REVERT: S 141 ASP cc_start: 0.8403 (t0) cc_final: 0.8108 (t0) REVERT: S 146 ASP cc_start: 0.9001 (m-30) cc_final: 0.8602 (OUTLIER) outliers start: 51 outliers final: 31 residues processed: 263 average time/residue: 0.7456 time to fit residues: 233.2151 Evaluate side-chains 244 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 793 PHE Chi-restraints excluded: chain S residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 293 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 335 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 197 HIS I 567 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.045181 restraints weight = 105509.451| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.14 r_work: 0.2593 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33408 Z= 0.202 Angle : 0.610 13.868 45166 Z= 0.309 Chirality : 0.044 0.255 5114 Planarity : 0.004 0.099 5712 Dihedral : 5.293 82.144 4431 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.49 % Rotamer: Outliers : 1.24 % Allowed : 12.66 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.56 (0.14), residues: 3991 helix: 1.70 (0.14), residues: 1513 sheet: -0.13 (0.23), residues: 528 loop : -0.51 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 90 TYR 0.029 0.001 TYR A 264 PHE 0.030 0.001 PHE A 938 TRP 0.017 0.001 TRP S 43 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00465 (33391) covalent geometry : angle 0.60654 (45146) SS BOND : bond 0.01052 ( 1) SS BOND : angle 3.34196 ( 2) hydrogen bonds : bond 0.03986 ( 1394) hydrogen bonds : angle 4.54564 ( 3948) metal coordination : bond 0.00675 ( 16) metal coordination : angle 2.99499 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 1.354 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 149 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8799 (m) REVERT: A 226 MET cc_start: 0.9123 (mmm) cc_final: 0.8809 (mmm) REVERT: A 283 ASP cc_start: 0.8316 (m-30) cc_final: 0.8044 (t0) REVERT: A 631 GLU cc_start: 0.8792 (pp20) cc_final: 0.8389 (pp20) REVERT: B 61 ASN cc_start: 0.9089 (t0) cc_final: 0.8831 (t0) REVERT: B 67 MET cc_start: 0.8750 (mmm) cc_final: 0.8351 (mmm) REVERT: B 159 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8532 (p0) REVERT: B 506 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 861 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8047 (mm) REVERT: C 304 ARG cc_start: 0.8536 (tmm160) cc_final: 0.8267 (tmm160) REVERT: E 18 GLU cc_start: 0.9400 (tp30) cc_final: 0.8892 (tp30) REVERT: E 57 MET cc_start: 0.8664 (mmm) cc_final: 0.8399 (mmm) REVERT: E 86 SER cc_start: 0.9583 (m) cc_final: 0.9286 (p) REVERT: E 120 GLU cc_start: 0.9058 (mp0) cc_final: 0.8808 (mp0) REVERT: E 144 GLU cc_start: 0.9235 (pt0) cc_final: 0.8904 (pm20) REVERT: F 122 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8826 (pp20) REVERT: G 100 GLN cc_start: 0.9077 (mt0) cc_final: 0.8600 (mp10) REVERT: G 103 ASP cc_start: 0.8935 (p0) cc_final: 0.8535 (p0) REVERT: G 124 PHE cc_start: 0.8491 (m-80) cc_final: 0.8122 (m-80) REVERT: G 131 TYR cc_start: 0.7113 (m-80) cc_final: 0.6667 (m-80) REVERT: I 121 MET cc_start: 0.8815 (mmt) cc_final: 0.8259 (mmt) REVERT: I 205 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8706 (ptpp) REVERT: I 281 TYR cc_start: 0.9004 (t80) cc_final: 0.8737 (t80) REVERT: I 444 ASN cc_start: 0.9000 (t0) cc_final: 0.8440 (p0) REVERT: I 486 LYS cc_start: 0.8739 (mttt) cc_final: 0.8322 (ptpp) REVERT: I 643 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9228 (tptp) REVERT: I 650 CYS cc_start: 0.8200 (m) cc_final: 0.7958 (m) REVERT: J 51 GLN cc_start: 0.8837 (tp40) cc_final: 0.8244 (tp40) REVERT: S 43 TRP cc_start: 0.9159 (t60) cc_final: 0.8899 (t60) REVERT: S 104 CYS cc_start: 0.9199 (m) cc_final: 0.8547 (p) REVERT: S 141 ASP cc_start: 0.8443 (t0) cc_final: 0.8161 (t0) REVERT: S 146 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8642 (t0) outliers start: 46 outliers final: 34 residues processed: 254 average time/residue: 0.7615 time to fit residues: 228.7156 Evaluate side-chains 251 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 793 PHE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 49 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 207 optimal weight: 0.2980 chunk 373 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 197 HIS I 567 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.044941 restraints weight = 105790.614| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.13 r_work: 0.2582 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33408 Z= 0.220 Angle : 0.619 14.244 45166 Z= 0.315 Chirality : 0.045 0.272 5114 Planarity : 0.004 0.058 5712 Dihedral : 5.349 82.241 4431 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.29 % Rotamer: Outliers : 1.40 % Allowed : 12.72 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3991 helix: 1.59 (0.14), residues: 1529 sheet: -0.16 (0.23), residues: 528 loop : -0.53 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 126 TYR 0.023 0.001 TYR B 377 PHE 0.030 0.001 PHE A 938 TRP 0.014 0.001 TRP A1054 HIS 0.010 0.001 HIS I 197 Details of bonding type rmsd covalent geometry : bond 0.00503 (33391) covalent geometry : angle 0.61551 (45146) SS BOND : bond 0.00969 ( 1) SS BOND : angle 3.20390 ( 2) hydrogen bonds : bond 0.04071 ( 1394) hydrogen bonds : angle 4.58027 ( 3948) metal coordination : bond 0.00686 ( 16) metal coordination : angle 3.00113 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8379.99 seconds wall clock time: 144 minutes 52.19 seconds (8692.19 seconds total)