Starting phenix.real_space_refine on Thu Oct 29 12:52:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wwl_66314/10_2026/9wwl_66314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wwl_66314/10_2026/9wwl_66314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wwl_66314/10_2026/9wwl_66314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wwl_66314/10_2026/9wwl_66314.map" model { file = "/net/cci-nas-00/data/ceres_data/9wwl_66314/10_2026/9wwl_66314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wwl_66314/10_2026/9wwl_66314.cif" } resolution = 4.0 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= 0.021 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 2 6.06 5 P 136 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 19284 2.51 5 N 5625 2.21 5 O 6311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31475 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8577 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 9862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9862 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1207} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2540 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1399 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "P" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1402 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "E" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 644 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 76} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1567 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1567 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19074 SG CYS D 891 72.674 43.464 60.477 1.00142.41 S ATOM 19641 SG CYS D 968 74.617 46.397 61.836 1.00147.64 S ATOM 19683 SG CYS D 975 71.909 44.770 64.019 1.00150.00 S ATOM 19701 SG CYS D 978 75.052 42.937 63.428 1.00151.13 S ATOM 12555 SG CYS D 60 71.773 112.671 60.888 1.00198.16 S ATOM 12682 SG CYS D 75 72.443 112.773 57.005 1.00193.63 S ATOM 12708 SG CYS D 78 74.410 110.993 57.390 1.00198.78 S Time building chain proxies: 7.23, per 1000 atoms: 0.23 Number of scatterers: 31475 At special positions: 0 Unit cell: (177.1, 156.2, 165, 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 2 29.99 S 116 16.00 P 136 15.00 Mg 1 11.99 O 6311 8.00 N 5625 7.00 C 19284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " Number of angles added : 6 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6860 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 50 sheets defined 46.8% alpha, 14.7% beta 52 base pairs and 106 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.721A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 225 removed outlier: 4.598A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.385A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.719A pdb=" N ARG B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.518A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.644A pdb=" N THR C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.563A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.587A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.759A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.512A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.625A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 589 through 593 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 removed outlier: 3.516A pdb=" N GLN C 612 " --> pdb=" O GLY C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.758A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.501A pdb=" N VAL C 780 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.029A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.649A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1078 Processing helix chain 'C' and resid 1082 through 1092 removed outlier: 3.677A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C1092 " --> pdb=" O LEU C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 3.778A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.648A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 141 through 186 removed outlier: 4.938A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.086A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.998A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.685A pdb=" N VAL D 313 " --> pdb=" O MET D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.003A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.548A pdb=" N MET D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.590A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.966A pdb=" N ARG D 762 " --> pdb=" O LYS D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.696A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.951A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1144 Proline residue: D1127 - end of helix removed outlier: 3.883A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 4.311A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.241A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.554A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.751A pdb=" N VAL D1232 " --> pdb=" O GLU D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'F' and resid 210 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 4.237A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.879A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 335 Processing helix chain 'F' and resid 342 through 363 removed outlier: 4.100A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.508A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 3.704A pdb=" N THR F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.160A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.845A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.897A pdb=" N ASP G 255 " --> pdb=" O ASP G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 removed outlier: 3.585A pdb=" N ARG G 266 " --> pdb=" O ASN G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 278 removed outlier: 3.876A pdb=" N LEU G 275 " --> pdb=" O THR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 284 Processing helix chain 'G' and resid 290 through 304 removed outlier: 3.590A pdb=" N ILE G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP G 295 " --> pdb=" O GLN G 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU G 296 " --> pdb=" O LYS G 292 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 24 Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 38 through 47 removed outlier: 3.633A pdb=" N VAL I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Proline residue: I 44 - end of helix Processing helix chain 'I' and resid 62 through 73 removed outlier: 3.843A pdb=" N ARG I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG I 72 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 97 Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.589A pdb=" N VAL I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 144 removed outlier: 3.821A pdb=" N LYS I 143 " --> pdb=" O GLY I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 163 removed outlier: 4.186A pdb=" N GLU I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 175 Processing helix chain 'I' and resid 177 through 192 Processing helix chain 'I' and resid 196 through 209 removed outlier: 4.264A pdb=" N ALA I 200 " --> pdb=" O ARG I 196 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 23 removed outlier: 3.986A pdb=" N LEU J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 47 removed outlier: 3.699A pdb=" N ALA J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET J 40 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) Proline residue: J 44 - end of helix removed outlier: 3.927A pdb=" N ARG J 47 " --> pdb=" O VAL J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 71 Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.797A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE J 94 " --> pdb=" O MET J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 121 removed outlier: 3.655A pdb=" N ALA J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 144 removed outlier: 3.752A pdb=" N LYS J 143 " --> pdb=" O GLY J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 163 removed outlier: 4.395A pdb=" N GLU J 163 " --> pdb=" O GLY J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.564A pdb=" N ARG J 173 " --> pdb=" O GLN J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 192 Processing helix chain 'J' and resid 196 through 209 removed outlier: 3.599A pdb=" N ALA J 200 " --> pdb=" O ARG J 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 5.637A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.778A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A 145 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.456A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL B 196 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL B 22 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 99 removed outlier: 3.637A pdb=" N VAL B 140 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 97 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 136 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.420A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.627A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 146 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.627A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB7, first strand: chain 'C' and resid 378 through 379 removed outlier: 3.775A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.575A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 204 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.830A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 559 through 562 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.685A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 700 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 7.090A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 885 through 887 removed outlier: 3.971A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C1031 " --> pdb=" O ALA C 886 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 885 through 887 removed outlier: 3.971A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C1031 " --> pdb=" O ALA C 886 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.985A pdb=" N SER C 749 " --> pdb=" O ARG C 877 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG C 877 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS C 751 " --> pdb=" O GLN C 875 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 757 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 7.111A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.514A pdb=" N VAL D 496 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.086A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.813A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.202A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.373A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.159A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE3, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.566A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 929 through 930 removed outlier: 6.450A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 981 through 982 removed outlier: 3.515A pdb=" N LYS D 987 " --> pdb=" O SER D 982 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1051 through 1056 removed outlier: 7.139A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AE8, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.590A pdb=" N GLN D1273 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 4 through 7 removed outlier: 6.930A pdb=" N VAL I 4 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ALA I 33 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU I 6 " --> pdb=" O ALA I 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'I' and resid 52 through 53 removed outlier: 5.296A pdb=" N LEU I 53 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS I 78 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL I 102 " --> pdb=" O CYS I 78 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE I 80 " --> pdb=" O VAL I 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 56 through 57 removed outlier: 3.579A pdb=" N LEU I 57 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY I 60 " --> pdb=" O LEU I 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'J' and resid 29 through 33 removed outlier: 7.894A pdb=" N VAL J 4 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU J 32 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU J 6 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE J 5 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 56 through 57 Processing sheet with id=AF5, first strand: chain 'J' and resid 79 through 82 removed outlier: 5.544A pdb=" N ILE J 80 " --> pdb=" O VAL J 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 1348 hydrogen bonds defined for protein. 3795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 106 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 3.75 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: 10379 1.34 - 1.46: 7166 1.46 - 1.59: 14233 1.59 - 1.71: 270 1.71 - 1.83: 205 Bond restraints: 32253 Sorted by residual: bond pdb=" C3' DC P 60 " pdb=" C2' DC P 60 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DG P 49 " pdb=" C2' DG P 49 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG P 18 " pdb=" C2' DG P 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC O 38 " pdb=" C2' DC O 38 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA P 24 " pdb=" O3' DA P 24 " ideal model delta sigma weight residual 1.435 1.476 -0.041 1.30e-02 5.92e+03 1.01e+01 ... (remaining 32248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 43612 2.42 - 4.83: 550 4.83 - 7.25: 67 7.25 - 9.66: 19 9.66 - 12.08: 10 Bond angle restraints: 44258 Sorted by residual: angle pdb=" O4' DC O 2 " pdb=" C4' DC O 2 " pdb=" C3' DC O 2 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" CA MET C 926 " pdb=" CB MET C 926 " pdb=" CG MET C 926 " ideal model delta sigma weight residual 114.10 123.15 -9.05 2.00e+00 2.50e-01 2.05e+01 angle pdb=" N3 DT P 37 " pdb=" C4 DT P 37 " pdb=" O4 DT P 37 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT O -5 " pdb=" C4 DT O -5 " pdb=" O4 DT O -5 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O4' DA P 11 " pdb=" C4' DA P 11 " pdb=" C3' DA P 11 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 44253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 18281 35.95 - 71.90: 1043 71.90 - 107.85: 33 107.85 - 143.80: 1 143.80 - 179.75: 10 Dihedral angle restraints: 19368 sinusoidal: 8711 harmonic: 10657 Sorted by residual: dihedral pdb=" CA MET I 174 " pdb=" C MET I 174 " pdb=" N PHE I 175 " pdb=" CA PHE I 175 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASP D 339 " pdb=" C ASP D 339 " pdb=" N LEU D 340 " pdb=" CA LEU D 340 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C4' DA P 22 " pdb=" C3' DA P 22 " pdb=" O3' DA P 22 " pdb=" P DT P 23 " ideal model delta sinusoidal sigma weight residual -140.00 39.75 -179.75 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 19365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3505 0.039 - 0.079: 1132 0.079 - 0.118: 390 0.118 - 0.158: 58 0.158 - 0.197: 5 Chirality restraints: 5090 Sorted by residual: chirality pdb=" C3' DC O 8 " pdb=" C4' DC O 8 " pdb=" O3' DC O 8 " pdb=" C2' DC O 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CG LEU D 877 " pdb=" CB LEU D 877 " pdb=" CD1 LEU D 877 " pdb=" CD2 LEU D 877 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" C3' DG O 34 " pdb=" C4' DG O 34 " pdb=" O3' DG O 34 " pdb=" C2' DG O 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 5087 not shown) Planarity restraints: 5321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 421 " -0.240 9.50e-02 1.11e+02 1.07e-01 7.09e+00 pdb=" NE ARG C 421 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 421 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 421 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 421 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 926 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C MET C 926 " 0.037 2.00e-02 2.50e+03 pdb=" O MET C 926 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 927 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1074 " -0.018 2.00e-02 2.50e+03 1.32e-02 4.39e+00 pdb=" CG TRP C1074 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C1074 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C1074 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1074 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C1074 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1074 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1074 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1074 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1074 " -0.001 2.00e-02 2.50e+03 ... (remaining 5318 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 496 2.58 - 3.16: 27704 3.16 - 3.74: 56690 3.74 - 4.32: 70329 4.32 - 4.90: 108974 Nonbonded interactions: 264193 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.003 2.170 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.098 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.131 2.170 nonbonded pdb=" OH TYR D 36 " pdb=" OP1 DG O 22 " model vdw 2.212 3.040 ... (remaining 264188 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.004 0.438 32260 Z= 0.269 Angle : 0.701 12.080 44264 Z= 0.430 Chirality : 0.044 0.197 5090 Planarity : 0.004 0.107 5321 Dihedral : 19.875 179.750 12508 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 0.78 % Allowed : 26.25 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3699 helix: 1.06 (0.14), residues: 1484 sheet: -0.52 (0.26), residues: 413 loop : -0.94 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 572 TYR 0.016 0.001 TYR F 231 PHE 0.020 0.001 PHE D 721 TRP 0.036 0.001 TRP C1074 HIS 0.004 0.001 HIS C1035 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.25 (32253) covalent geometry : angle 0.70037 / 0.43 (44258) hydrogen bonds : bond 0.19447 / 13.39 ( 1469) hydrogen bonds : angle 6.99303 / 4.97 ( 4065) metal coordination : bond 0.20011 / 10.13 ( 7) metal coordination : angle 2.38669 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 1.357 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: B 1 MET cc_start: 0.6742 (tmm) cc_final: 0.6371 (tmm) REVERT: C 154 MET cc_start: 0.9001 (mpp) cc_final: 0.8626 (mpp) REVERT: C 373 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: C 661 MET cc_start: 0.7795 (tpt) cc_final: 0.6763 (tpt) REVERT: C 753 GLU cc_start: 0.7544 (mp0) cc_final: 0.7334 (mp0) REVERT: C 927 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8105 (p0) REVERT: D 155 MET cc_start: 0.9319 (tpp) cc_final: 0.8879 (tpt) REVERT: D 310 MET cc_start: 0.8997 (mmp) cc_final: 0.8781 (mmp) REVERT: D 371 LYS cc_start: 0.9689 (OUTLIER) cc_final: 0.8966 (mtmm) REVERT: D 576 MET cc_start: 0.8805 (tpt) cc_final: 0.8505 (tpt) REVERT: F 525 ASP cc_start: 0.8930 (m-30) cc_final: 0.7790 (t0) REVERT: I 163 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: J 134 MET cc_start: 0.5632 (mtt) cc_final: 0.5412 (ttm) outliers start: 24 outliers final: 8 residues processed: 265 average time/residue: 0.1818 time to fit residues: 81.1443 Evaluate side-chains 237 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 GLN ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.055641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041059 restraints weight = 228802.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042204 restraints weight = 143683.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042998 restraints weight = 102901.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043487 restraints weight = 80669.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043881 restraints weight = 68378.452| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32260 Z= 0.144 Angle : 0.663 12.923 44264 Z= 0.349 Chirality : 0.045 0.341 5090 Planarity : 0.005 0.050 5321 Dihedral : 19.944 179.332 5572 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 2.55 % Allowed : 23.73 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.30 (0.14), residues: 3699 helix: 0.70 (0.13), residues: 1570 sheet: -0.43 (0.25), residues: 423 loop : -0.94 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1044 TYR 0.041 0.001 TYR F 258 PHE 0.012 0.001 PHE I 203 TRP 0.023 0.001 TRP C1074 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (32253) covalent geometry : angle 0.66255 / 0.35 (44258) hydrogen bonds : bond 0.05213 / 3.59 ( 1469) hydrogen bonds : angle 5.66625 / 4.01 ( 4065) metal coordination : bond 0.01040 / 0.51 ( 7) metal coordination : angle 1.67859 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 241 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8522 (tt0) REVERT: B 1 MET cc_start: 0.7010 (tmm) cc_final: 0.6407 (tmm) REVERT: B 95 MET cc_start: 0.8681 (mmm) cc_final: 0.8400 (mmm) REVERT: C 440 MET cc_start: 0.8450 (tmm) cc_final: 0.8240 (tmm) REVERT: C 586 MET cc_start: 0.8981 (ppp) cc_final: 0.8699 (ppp) REVERT: C 710 ASP cc_start: 0.9324 (m-30) cc_final: 0.9098 (p0) REVERT: C 1071 MET cc_start: 0.8571 (ttm) cc_final: 0.8232 (ttp) REVERT: D 92 MET cc_start: 0.8843 (mmm) cc_final: 0.8430 (mmm) REVERT: D 155 MET cc_start: 0.9315 (tpp) cc_final: 0.8937 (tpt) REVERT: D 1155 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: F 525 ASP cc_start: 0.8878 (m-30) cc_final: 0.7824 (t0) REVERT: G 288 ASN cc_start: 0.1404 (OUTLIER) cc_final: 0.1173 (p0) REVERT: I 68 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.9025 (p0) REVERT: J 6 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7579 (mt) REVERT: J 134 MET cc_start: 0.5313 (mtt) cc_final: 0.4958 (ttt) REVERT: J 179 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7861 (tptt) outliers start: 78 outliers final: 23 residues processed: 305 average time/residue: 0.1713 time to fit residues: 89.2253 Evaluate side-chains 250 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [217, 146, 74, 335, 341, 102, 41, 282, 332, 160, 24] chunk 217 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 74 optimal weight: 0.0670 chunk 335 optimal weight: 6.9990 chunk 341 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 282 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 overall best weight: 3.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.054846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.040403 restraints weight = 231069.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041482 restraints weight = 145978.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042253 restraints weight = 105678.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042806 restraints weight = 83450.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.043117 restraints weight = 69998.977| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32260 Z= 0.170 Angle : 0.649 10.750 44264 Z= 0.343 Chirality : 0.045 0.326 5090 Planarity : 0.004 0.056 5321 Dihedral : 19.928 179.531 5550 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Rotamer: Outliers : 3.49 % Allowed : 24.19 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.35 (0.14), residues: 3699 helix: 0.73 (0.13), residues: 1566 sheet: -0.54 (0.24), residues: 432 loop : -1.03 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 350 TYR 0.026 0.001 TYR F 258 PHE 0.021 0.001 PHE B 189 TRP 0.017 0.001 TRP C1074 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (32253) covalent geometry : angle 0.64846 / 0.34 (44258) hydrogen bonds : bond 0.04793 / 3.28 ( 1469) hydrogen bonds : angle 5.42669 / 3.84 ( 4065) metal coordination : bond 0.00488 / 0.22 ( 7) metal coordination : angle 1.87344 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 227 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6802 (tmm) cc_final: 0.6134 (tmm) REVERT: B 95 MET cc_start: 0.8625 (mmm) cc_final: 0.8340 (mmm) REVERT: B 189 PHE cc_start: 0.8930 (m-80) cc_final: 0.8725 (m-80) REVERT: C 586 MET cc_start: 0.9028 (ppp) cc_final: 0.8621 (ppp) REVERT: C 661 MET cc_start: 0.8035 (tpt) cc_final: 0.7046 (tpt) REVERT: C 753 GLU cc_start: 0.7658 (mp0) cc_final: 0.7321 (mp0) REVERT: C 846 LYS cc_start: 0.9342 (mmtp) cc_final: 0.8975 (mmmm) REVERT: C 1028 MET cc_start: 0.8102 (tpp) cc_final: 0.7757 (tpp) REVERT: D 92 MET cc_start: 0.9011 (mmm) cc_final: 0.8763 (mmm) REVERT: D 155 MET cc_start: 0.9324 (tpp) cc_final: 0.8934 (tpt) REVERT: D 559 MET cc_start: 0.9086 (mmm) cc_final: 0.8742 (mmm) REVERT: D 780 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8794 (tm-30) REVERT: D 1155 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: D 1207 LEU cc_start: 0.9462 (tp) cc_final: 0.9256 (pt) REVERT: F 266 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6236 (tm) REVERT: F 282 MET cc_start: 0.8934 (mmt) cc_final: 0.8641 (mmm) REVERT: F 525 ASP cc_start: 0.8888 (m-30) cc_final: 0.7850 (t0) REVERT: G 288 ASN cc_start: 0.0785 (OUTLIER) cc_final: 0.0259 (p0) REVERT: I 68 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.9021 (p0) REVERT: I 163 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7837 (pm20) outliers start: 107 outliers final: 46 residues processed: 313 average time/residue: 0.1689 time to fit residues: 91.0861 Evaluate side-chains 263 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain J residue 167 ASN Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [153, 165, 318, 148, 327, 40, 320, 97, 268, 216, 82] chunk 153 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 148 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 320 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 216 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 443 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040092 restraints weight = 231705.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041178 restraints weight = 147133.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041918 restraints weight = 106413.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042387 restraints weight = 84105.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042777 restraints weight = 71515.390| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32260 Z= 0.191 Angle : 0.662 12.525 44264 Z= 0.348 Chirality : 0.045 0.319 5090 Planarity : 0.004 0.058 5321 Dihedral : 19.919 179.261 5548 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 3.66 % Allowed : 24.65 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 3699 helix: 0.73 (0.13), residues: 1556 sheet: -0.58 (0.24), residues: 420 loop : -1.06 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 350 TYR 0.021 0.001 TYR F 258 PHE 0.014 0.001 PHE B 189 TRP 0.013 0.001 TRP C1074 HIS 0.008 0.001 HIS C1035 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (32253) covalent geometry : angle 0.66148 / 0.35 (44258) hydrogen bonds : bond 0.04616 / 3.16 ( 1469) hydrogen bonds : angle 5.34978 / 3.77 ( 4065) metal coordination : bond 0.00528 / 0.24 ( 7) metal coordination : angle 1.98143 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 225 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.8992 (ttt180) REVERT: A 95 MET cc_start: 0.8830 (tpp) cc_final: 0.8491 (tpp) REVERT: C 297 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.9071 (mm-30) REVERT: C 440 MET cc_start: 0.8458 (tmm) cc_final: 0.8164 (tmm) REVERT: C 516 TYR cc_start: 0.7585 (m-80) cc_final: 0.7159 (m-80) REVERT: C 586 MET cc_start: 0.9076 (ppp) cc_final: 0.8612 (ppp) REVERT: C 661 MET cc_start: 0.8236 (tpt) cc_final: 0.7529 (tpt) REVERT: C 753 GLU cc_start: 0.7704 (mp0) cc_final: 0.7368 (mp0) REVERT: C 846 LYS cc_start: 0.9356 (mmtp) cc_final: 0.8982 (mmmm) REVERT: D 155 MET cc_start: 0.9448 (tpp) cc_final: 0.9030 (tpt) REVERT: D 381 LEU cc_start: 0.9531 (tt) cc_final: 0.9048 (pp) REVERT: D 559 MET cc_start: 0.9112 (mmm) cc_final: 0.8489 (mmm) REVERT: D 780 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8797 (tm-30) REVERT: D 1013 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6331 (mmp80) REVERT: F 282 MET cc_start: 0.8996 (mmt) cc_final: 0.8690 (mmm) REVERT: F 525 ASP cc_start: 0.8910 (m-30) cc_final: 0.7830 (t0) REVERT: G 288 ASN cc_start: 0.0939 (OUTLIER) cc_final: 0.0355 (p0) REVERT: I 68 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8986 (p0) REVERT: I 163 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: J 6 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7196 (mt) REVERT: J 134 MET cc_start: 0.6240 (mmp) cc_final: 0.4974 (ttm) REVERT: J 179 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7993 (tptt) outliers start: 112 outliers final: 66 residues processed: 318 average time/residue: 0.1683 time to fit residues: 91.3308 Evaluate side-chains 287 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [256, 148, 124, 247, 39, 334, 362, 222, 212, 37, 33] chunk 256 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 334 optimal weight: 20.0000 chunk 362 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 0.0370 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 443 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.054106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.039778 restraints weight = 241133.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040858 restraints weight = 149444.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041606 restraints weight = 107276.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.042154 restraints weight = 84705.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.042448 restraints weight = 71173.254| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32260 Z= 0.191 Angle : 0.665 11.244 44264 Z= 0.348 Chirality : 0.045 0.319 5090 Planarity : 0.004 0.058 5321 Dihedral : 19.921 179.073 5546 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.57 % Rotamer: Outliers : 4.41 % Allowed : 24.91 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3699 helix: 0.77 (0.13), residues: 1554 sheet: -0.57 (0.25), residues: 410 loop : -1.06 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 350 TYR 0.025 0.001 TYR D 793 PHE 0.013 0.001 PHE C 430 TRP 0.013 0.001 TRP D 723 HIS 0.004 0.001 HIS D1119 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (32253) covalent geometry : angle 0.66437 / 0.35 (44258) hydrogen bonds : bond 0.04536 / 3.11 ( 1469) hydrogen bonds : angle 5.27231 / 3.71 ( 4065) metal coordination : bond 0.00513 / 0.23 ( 7) metal coordination : angle 2.04141 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 226 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8976 (ttt180) REVERT: B 1 MET cc_start: 0.7239 (tmm) cc_final: 0.6699 (tmm) REVERT: B 189 PHE cc_start: 0.8793 (m-10) cc_final: 0.8169 (m-10) REVERT: C 103 MET cc_start: 0.8880 (ppp) cc_final: 0.8663 (ppp) REVERT: C 154 MET cc_start: 0.8760 (mpp) cc_final: 0.8340 (mpp) REVERT: C 297 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.9073 (mm-30) REVERT: C 440 MET cc_start: 0.8524 (tmm) cc_final: 0.8167 (tmm) REVERT: C 516 TYR cc_start: 0.7644 (m-80) cc_final: 0.7286 (m-80) REVERT: C 586 MET cc_start: 0.9052 (ppp) cc_final: 0.8554 (ppp) REVERT: C 661 MET cc_start: 0.8214 (tpt) cc_final: 0.7650 (tpt) REVERT: C 753 GLU cc_start: 0.7689 (mp0) cc_final: 0.7357 (mp0) REVERT: C 846 LYS cc_start: 0.9368 (mmtp) cc_final: 0.8851 (mmmm) REVERT: C 878 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8441 (tptt) REVERT: D 82 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8931 (m) REVERT: D 485 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.8469 (t0) REVERT: D 559 MET cc_start: 0.9112 (mmm) cc_final: 0.8439 (mmm) REVERT: D 780 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8793 (tm-30) REVERT: D 1013 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6404 (mmp80) REVERT: F 282 MET cc_start: 0.9022 (mmt) cc_final: 0.8741 (mmm) REVERT: F 525 ASP cc_start: 0.8902 (m-30) cc_final: 0.7752 (t0) REVERT: E 77 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: G 288 ASN cc_start: 0.1287 (OUTLIER) cc_final: 0.0815 (p0) REVERT: I 113 ARG cc_start: 0.2642 (tmm160) cc_final: 0.2323 (tpt170) REVERT: I 163 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: J 6 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7096 (mt) REVERT: J 179 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (tptt) outliers start: 135 outliers final: 77 residues processed: 340 average time/residue: 0.1767 time to fit residues: 101.4039 Evaluate side-chains 305 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 216 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 878 LYS Chi-restraints excluded: chain C residue 898 ILE Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 349 TRP Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [73, 95, 171, 301, 39, 350, 325, 309, 64, 289, 293] chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 301 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 325 optimal weight: 50.0000 chunk 309 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 169 ASN C 443 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039998 restraints weight = 240558.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041108 restraints weight = 150162.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041862 restraints weight = 107888.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042326 restraints weight = 85313.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.042724 restraints weight = 72866.819| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32260 Z= 0.159 Angle : 0.676 13.714 44264 Z= 0.346 Chirality : 0.045 0.330 5090 Planarity : 0.004 0.056 5321 Dihedral : 19.922 178.937 5546 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 4.02 % Allowed : 25.79 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.34 (0.14), residues: 3699 helix: 0.80 (0.13), residues: 1550 sheet: -0.52 (0.25), residues: 398 loop : -1.05 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.017 0.001 TYR F 258 PHE 0.012 0.001 PHE C 430 TRP 0.012 0.001 TRP D 723 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (32253) covalent geometry : angle 0.67262 / 0.35 (44258) hydrogen bonds : bond 0.04328 / 2.97 ( 1469) hydrogen bonds : angle 5.18806 / 3.65 ( 4065) metal coordination : bond 0.00934 / 0.29 ( 7) metal coordination : angle 5.76925 / 2.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 228 time to evaluate : 0.865 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 18 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8409 (ttt180) REVERT: A 39 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.9001 (ttt180) REVERT: B 1 MET cc_start: 0.7269 (tmm) cc_final: 0.6676 (tmm) REVERT: B 189 PHE cc_start: 0.8789 (m-10) cc_final: 0.8119 (m-10) REVERT: C 297 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.9053 (mm-30) REVERT: C 439 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7456 (t80) REVERT: C 516 TYR cc_start: 0.7678 (m-80) cc_final: 0.7327 (m-80) REVERT: C 661 MET cc_start: 0.8252 (tpt) cc_final: 0.7752 (tpt) REVERT: C 753 GLU cc_start: 0.7665 (mp0) cc_final: 0.7326 (mp0) REVERT: C 846 LYS cc_start: 0.9188 (mmtp) cc_final: 0.8820 (mmmm) REVERT: C 878 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8403 (tptt) REVERT: D 82 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8941 (m) REVERT: D 155 MET cc_start: 0.9442 (tpp) cc_final: 0.9002 (tpt) REVERT: D 381 LEU cc_start: 0.9479 (tt) cc_final: 0.9002 (pp) REVERT: D 559 MET cc_start: 0.9138 (mmm) cc_final: 0.8422 (mmm) REVERT: D 780 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: D 924 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8824 (p) REVERT: D 1013 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6478 (mmp80) REVERT: F 282 MET cc_start: 0.8934 (mmt) cc_final: 0.8642 (mmt) REVERT: F 525 ASP cc_start: 0.8868 (m-30) cc_final: 0.7722 (t0) REVERT: E 77 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: G 288 ASN cc_start: 0.1841 (OUTLIER) cc_final: 0.1340 (p0) REVERT: I 68 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8988 (p0) REVERT: I 163 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: J 6 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7047 (mt) REVERT: J 179 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7899 (tptt) outliers start: 123 outliers final: 85 residues processed: 333 average time/residue: 0.1707 time to fit residues: 96.6484 Evaluate side-chains 320 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 220 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 878 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 904 ARG Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 349 TRP Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [162, 138, 45, 362, 59, 238, 305, 60, 111, 272, 70] chunk 162 optimal weight: 0.0980 chunk 138 optimal weight: 5.9990 chunk 45 optimal weight: 0.0030 chunk 362 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN G 288 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.054536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040207 restraints weight = 240048.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041296 restraints weight = 149963.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.042081 restraints weight = 108065.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042561 restraints weight = 85240.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042975 restraints weight = 72472.237| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32260 Z= 0.150 Angle : 0.678 13.339 44264 Z= 0.344 Chirality : 0.045 0.334 5090 Planarity : 0.004 0.056 5321 Dihedral : 19.898 178.808 5544 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 3.98 % Allowed : 25.95 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.31 (0.14), residues: 3699 helix: 0.83 (0.13), residues: 1552 sheet: -0.53 (0.25), residues: 405 loop : -1.04 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 47 TYR 0.016 0.001 TYR F 258 PHE 0.015 0.001 PHE B 30 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS C 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (32253) covalent geometry : angle 0.67530 / 0.34 (44258) hydrogen bonds : bond 0.04195 / 2.89 ( 1469) hydrogen bonds : angle 5.11617 / 3.60 ( 4065) metal coordination : bond 0.00740 / 0.28 ( 7) metal coordination : angle 4.77246 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 229 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8442 (ttt180) REVERT: B 1 MET cc_start: 0.7331 (tmm) cc_final: 0.6724 (tmm) REVERT: B 173 LYS cc_start: 0.9173 (tptp) cc_final: 0.8959 (tptp) REVERT: B 189 PHE cc_start: 0.8749 (m-10) cc_final: 0.8078 (m-10) REVERT: C 297 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.9043 (mm-30) REVERT: C 395 ARG cc_start: 0.9620 (OUTLIER) cc_final: 0.9359 (mtm-85) REVERT: C 439 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 440 MET cc_start: 0.8378 (tmm) cc_final: 0.8044 (tmm) REVERT: C 516 TYR cc_start: 0.7710 (m-80) cc_final: 0.7348 (m-80) REVERT: C 661 MET cc_start: 0.8332 (tpt) cc_final: 0.7888 (tpt) REVERT: C 753 GLU cc_start: 0.7714 (mp0) cc_final: 0.7349 (mp0) REVERT: C 787 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8890 (mtm-85) REVERT: C 846 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8857 (mmmm) REVERT: C 878 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8500 (tptt) REVERT: C 1073 CYS cc_start: 0.9071 (m) cc_final: 0.8677 (m) REVERT: D 82 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8936 (m) REVERT: D 155 MET cc_start: 0.9468 (tpp) cc_final: 0.9038 (tpt) REVERT: D 315 ASP cc_start: 0.9057 (m-30) cc_final: 0.8533 (p0) REVERT: D 373 MET cc_start: 0.9433 (ppp) cc_final: 0.9232 (tmm) REVERT: D 381 LEU cc_start: 0.9469 (tt) cc_final: 0.8978 (pp) REVERT: D 485 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.8478 (t0) REVERT: D 541 MET cc_start: 0.9014 (mmm) cc_final: 0.8803 (mmm) REVERT: D 559 MET cc_start: 0.9189 (mmm) cc_final: 0.8403 (mmm) REVERT: D 780 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: D 924 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8832 (p) REVERT: D 1013 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6449 (mmp80) REVERT: F 282 MET cc_start: 0.8947 (mmt) cc_final: 0.8671 (mmt) REVERT: F 525 ASP cc_start: 0.8883 (m-30) cc_final: 0.7718 (t0) REVERT: E 77 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: I 68 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8981 (p0) REVERT: I 163 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: J 6 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7033 (mt) REVERT: J 179 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7904 (tptt) outliers start: 122 outliers final: 89 residues processed: 332 average time/residue: 0.1803 time to fit residues: 100.6698 Evaluate side-chains 325 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 220 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 878 LYS Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 904 ARG Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 349 TRP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [37, 74, 180, 158, 133, 259, 6, 256, 39, 149, 296] chunk 37 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 158 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 256 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN I 10 HIS J 167 ASN ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040115 restraints weight = 232518.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.041199 restraints weight = 147998.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041931 restraints weight = 107151.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.042461 restraints weight = 84938.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.042784 restraints weight = 71885.867| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32260 Z= 0.154 Angle : 0.686 13.350 44264 Z= 0.347 Chirality : 0.045 0.389 5090 Planarity : 0.004 0.056 5321 Dihedral : 19.906 178.584 5544 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.02 % Allowed : 26.02 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.31 (0.14), residues: 3699 helix: 0.84 (0.13), residues: 1555 sheet: -0.55 (0.25), residues: 403 loop : -1.06 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 350 TYR 0.016 0.001 TYR D1142 PHE 0.016 0.001 PHE D 721 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS D1119 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (32253) covalent geometry : angle 0.68390 / 0.35 (44258) hydrogen bonds : bond 0.04163 / 2.86 ( 1469) hydrogen bonds : angle 5.07836 / 3.58 ( 4065) metal coordination : bond 0.00675 / 0.26 ( 7) metal coordination : angle 4.20034 / 2.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 229 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (ttt180) REVERT: B 1 MET cc_start: 0.7379 (tmm) cc_final: 0.6757 (tmm) REVERT: B 189 PHE cc_start: 0.8686 (m-10) cc_final: 0.7999 (m-10) REVERT: C 297 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.9063 (mm-30) REVERT: C 373 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9068 (m-80) REVERT: C 395 ARG cc_start: 0.9610 (OUTLIER) cc_final: 0.9337 (mtm-85) REVERT: C 396 MET cc_start: 0.9429 (tpt) cc_final: 0.9116 (tpp) REVERT: C 439 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7548 (t80) REVERT: C 440 MET cc_start: 0.8371 (tmm) cc_final: 0.7997 (tmm) REVERT: C 516 TYR cc_start: 0.7719 (m-80) cc_final: 0.7384 (m-80) REVERT: C 586 MET cc_start: 0.9075 (ppp) cc_final: 0.8788 (ppp) REVERT: C 612 GLN cc_start: 0.9516 (mm-40) cc_final: 0.8979 (mp10) REVERT: C 661 MET cc_start: 0.8289 (tpt) cc_final: 0.7830 (tpt) REVERT: C 753 GLU cc_start: 0.7708 (mp0) cc_final: 0.7362 (mp0) REVERT: C 787 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8820 (mtm-85) REVERT: C 846 LYS cc_start: 0.9269 (mmtp) cc_final: 0.8872 (mmmm) REVERT: C 878 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8492 (tptt) REVERT: D 82 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8930 (m) REVERT: D 155 MET cc_start: 0.9449 (tpp) cc_final: 0.8956 (tpt) REVERT: D 315 ASP cc_start: 0.9063 (m-30) cc_final: 0.8502 (p0) REVERT: D 373 MET cc_start: 0.9474 (ppp) cc_final: 0.9240 (tmm) REVERT: D 381 LEU cc_start: 0.9440 (tt) cc_final: 0.8954 (pp) REVERT: D 559 MET cc_start: 0.9171 (mmm) cc_final: 0.8327 (mmm) REVERT: D 576 MET cc_start: 0.8836 (tpt) cc_final: 0.8531 (tpt) REVERT: D 780 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8799 (tm-30) REVERT: D 924 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 1013 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6474 (mmp80) REVERT: D 1159 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8838 (tmm-80) REVERT: D 1161 MET cc_start: 0.9106 (ptm) cc_final: 0.8783 (ppp) REVERT: F 282 MET cc_start: 0.8908 (mmt) cc_final: 0.8608 (mmt) REVERT: F 525 ASP cc_start: 0.8862 (m-30) cc_final: 0.7736 (t0) REVERT: E 77 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: I 68 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.9011 (p0) REVERT: I 163 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: J 179 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7695 (tptp) outliers start: 123 outliers final: 91 residues processed: 332 average time/residue: 0.1792 time to fit residues: 100.2333 Evaluate side-chains 328 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 221 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 878 LYS Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 904 ARG Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1159 ARG Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 349 TRP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [76, 21, 122, 269, 345, 32, 342, 64, 12, 297, 24] chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 345 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.054411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040088 restraints weight = 239028.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.041174 restraints weight = 149802.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041966 restraints weight = 108353.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.042424 restraints weight = 85115.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042835 restraints weight = 72817.506| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32260 Z= 0.161 Angle : 0.700 14.493 44264 Z= 0.353 Chirality : 0.045 0.329 5090 Planarity : 0.004 0.056 5321 Dihedral : 19.907 178.644 5544 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.92 % Allowed : 26.18 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3699 helix: 0.84 (0.13), residues: 1552 sheet: -0.58 (0.25), residues: 405 loop : -1.07 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 771 TYR 0.063 0.001 TYR F 258 PHE 0.023 0.001 PHE A 63 TRP 0.013 0.001 TRP C1074 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (32253) covalent geometry : angle 0.69846 / 0.35 (44258) hydrogen bonds : bond 0.04150 / 2.85 ( 1469) hydrogen bonds : angle 5.08207 / 3.59 ( 4065) metal coordination : bond 0.00681 / 0.27 ( 7) metal coordination : angle 3.95463 / 1.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 222 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8442 (ttt180) REVERT: A 62 GLU cc_start: 0.8784 (pm20) cc_final: 0.8581 (pm20) REVERT: A 63 PHE cc_start: 0.9512 (m-10) cc_final: 0.9077 (m-10) REVERT: B 1 MET cc_start: 0.7386 (tmm) cc_final: 0.6740 (tmm) REVERT: B 189 PHE cc_start: 0.8708 (m-10) cc_final: 0.8019 (m-10) REVERT: C 297 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.9065 (mm-30) REVERT: C 373 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.9103 (m-80) REVERT: C 395 ARG cc_start: 0.9620 (OUTLIER) cc_final: 0.9345 (mtm-85) REVERT: C 396 MET cc_start: 0.9450 (tpt) cc_final: 0.9173 (tpp) REVERT: C 439 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7486 (t80) REVERT: C 440 MET cc_start: 0.8354 (tmm) cc_final: 0.7952 (tmm) REVERT: C 516 TYR cc_start: 0.7677 (m-80) cc_final: 0.7326 (m-80) REVERT: C 612 GLN cc_start: 0.9530 (mm-40) cc_final: 0.8982 (mp10) REVERT: C 661 MET cc_start: 0.8310 (tpt) cc_final: 0.7913 (tpt) REVERT: C 753 GLU cc_start: 0.7718 (mp0) cc_final: 0.7361 (mp0) REVERT: C 787 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8791 (mtm-85) REVERT: C 846 LYS cc_start: 0.9287 (mmtp) cc_final: 0.8637 (mmmm) REVERT: C 878 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (tptt) REVERT: D 82 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8926 (m) REVERT: D 155 MET cc_start: 0.9465 (tpp) cc_final: 0.8968 (tpt) REVERT: D 381 LEU cc_start: 0.9451 (tt) cc_final: 0.8958 (pp) REVERT: D 485 ASP cc_start: 0.9357 (m-30) cc_final: 0.8476 (t0) REVERT: D 559 MET cc_start: 0.9181 (mmm) cc_final: 0.8338 (mmm) REVERT: D 576 MET cc_start: 0.8859 (tpt) cc_final: 0.8534 (tpt) REVERT: D 780 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8800 (tm-30) REVERT: D 924 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8847 (p) REVERT: D 1013 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6416 (mmp80) REVERT: D 1159 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8840 (tmm-80) REVERT: D 1161 MET cc_start: 0.9121 (ptm) cc_final: 0.8773 (ppp) REVERT: F 525 ASP cc_start: 0.8879 (m-30) cc_final: 0.7758 (t0) REVERT: E 77 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: I 163 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: J 179 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7738 (tptp) outliers start: 120 outliers final: 92 residues processed: 323 average time/residue: 0.1748 time to fit residues: 95.3864 Evaluate side-chains 327 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 220 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 878 LYS Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 904 ARG Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1159 ARG Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 349 TRP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [204, 352, 283, 361, 368, 198, 342, 314, 212, 149, 120] chunk 204 optimal weight: 2.9990 chunk 352 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 chunk 361 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 314 optimal weight: 50.0000 chunk 212 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 443 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.053211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039205 restraints weight = 235188.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040208 restraints weight = 149609.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040931 restraints weight = 108731.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041398 restraints weight = 86282.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041767 restraints weight = 73566.560| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32260 Z= 0.214 Angle : 0.744 14.124 44264 Z= 0.377 Chirality : 0.046 0.310 5090 Planarity : 0.004 0.059 5321 Dihedral : 19.979 179.494 5544 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.62 % Allowed : 26.48 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 3699 helix: 0.71 (0.13), residues: 1551 sheet: -0.65 (0.25), residues: 399 loop : -1.17 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 771 TYR 0.031 0.002 TYR F 258 PHE 0.024 0.002 PHE D 721 TRP 0.015 0.002 TRP C1074 HIS 0.007 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (32253) covalent geometry : angle 0.74206 / 0.38 (44258) hydrogen bonds : bond 0.04621 / 3.16 ( 1469) hydrogen bonds : angle 5.25020 / 3.69 ( 4065) metal coordination : bond 0.00861 / 0.36 ( 7) metal coordination : angle 4.10848 / 2.00 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 216 time to evaluate : 1.109 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 62 GLU cc_start: 0.8883 (pm20) cc_final: 0.8434 (pm20) REVERT: A 63 PHE cc_start: 0.9587 (m-10) cc_final: 0.9204 (m-10) REVERT: B 1 MET cc_start: 0.7376 (tmm) cc_final: 0.6766 (tmm) REVERT: B 189 PHE cc_start: 0.8700 (m-10) cc_final: 0.7999 (m-10) REVERT: C 154 MET cc_start: 0.8742 (mpp) cc_final: 0.8535 (mpp) REVERT: C 373 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9156 (m-80) REVERT: C 395 ARG cc_start: 0.9622 (OUTLIER) cc_final: 0.9309 (mtm-85) REVERT: C 396 MET cc_start: 0.9485 (tpt) cc_final: 0.9251 (tpp) REVERT: C 439 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7549 (t80) REVERT: C 440 MET cc_start: 0.8405 (tmm) cc_final: 0.8010 (tmm) REVERT: C 516 TYR cc_start: 0.7808 (m-80) cc_final: 0.7475 (m-80) REVERT: C 661 MET cc_start: 0.8425 (tpt) cc_final: 0.8005 (tpt) REVERT: C 753 GLU cc_start: 0.7789 (mp0) cc_final: 0.7463 (mp0) REVERT: C 787 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8840 (mtm-85) REVERT: C 846 LYS cc_start: 0.9344 (mmtp) cc_final: 0.9055 (mmtp) REVERT: C 1076 MET cc_start: 0.8880 (ppp) cc_final: 0.8611 (ppp) REVERT: D 155 MET cc_start: 0.9492 (tpp) cc_final: 0.8991 (tpt) REVERT: D 381 LEU cc_start: 0.9525 (tt) cc_final: 0.9026 (pp) REVERT: D 485 ASP cc_start: 0.9367 (m-30) cc_final: 0.8473 (t0) REVERT: D 576 MET cc_start: 0.8950 (tpt) cc_final: 0.8529 (tpt) REVERT: D 780 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8786 (tm-30) REVERT: D 924 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8911 (p) REVERT: D 1013 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6479 (mmp80) REVERT: D 1159 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8840 (tmm-80) REVERT: D 1161 MET cc_start: 0.9162 (ptm) cc_final: 0.8822 (ppp) REVERT: F 263 MET cc_start: 0.8910 (mtt) cc_final: 0.8294 (mtp) REVERT: F 282 MET cc_start: 0.9021 (mmt) cc_final: 0.8697 (mmp) REVERT: F 525 ASP cc_start: 0.8946 (m-30) cc_final: 0.7827 (t0) REVERT: E 77 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: I 163 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: J 179 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7785 (tmtt) outliers start: 111 outliers final: 91 residues processed: 308 average time/residue: 0.1711 time to fit residues: 88.7262 Evaluate side-chains 316 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 214 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 904 ARG Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1156 VAL Chi-restraints excluded: chain D residue 1159 ARG Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1232 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 349 TRP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 183 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [302, 284, 204, 291, 80, 144, 188, 108, 167, 343, 304] chunk 302 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 291 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 443 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.053328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039085 restraints weight = 244920.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040193 restraints weight = 152283.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040924 restraints weight = 109154.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.041458 restraints weight = 86387.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041744 restraints weight = 73140.957| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 32260 Z= 0.241 Angle : 0.828 59.182 44264 Z= 0.443 Chirality : 0.046 0.380 5090 Planarity : 0.004 0.060 5321 Dihedral : 19.986 179.508 5544 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.49 % Allowed : 26.71 % Favored : 69.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3699 helix: 0.70 (0.13), residues: 1550 sheet: -0.65 (0.25), residues: 399 loop : -1.17 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 771 TYR 0.033 0.002 TYR F 258 PHE 0.024 0.002 PHE C 301 TRP 0.013 0.001 TRP D 723 HIS 0.007 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (32253) covalent geometry : angle 0.82683 / 0.44 (44258) hydrogen bonds : bond 0.04621 / 3.15 ( 1469) hydrogen bonds : angle 5.25066 / 3.69 ( 4065) metal coordination : bond 0.00793 / 0.34 ( 7) metal coordination : angle 4.09880 / 1.99 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5242.06 seconds wall clock time: 91 minutes 32.68 seconds (5492.68 seconds total)