Starting phenix.real_space_refine on Sun Jul 5 09:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji2_61492/07_2026/9ji2_61492.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji2_61492/07_2026/9ji2_61492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ji2_61492/07_2026/9ji2_61492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji2_61492/07_2026/9ji2_61492.map" model { file = "/net/cci-nas-00/data/ceres_data/9ji2_61492/07_2026/9ji2_61492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji2_61492/07_2026/9ji2_61492.cif" } resolution = 3.38 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= -0.001 sd= 0.032 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 102 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 16732 2.51 5 N 4856 2.21 5 O 5431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27219 Number of models: 1 Model: "" Number of chains: 9 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: 9870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9870 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1207} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 46 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: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1057 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "P" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1047 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} 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: "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 19082 SG CYS D 891 19.407 45.589 106.549 1.00 78.18 S ATOM 19649 SG CYS D 968 22.197 47.400 104.717 1.00 74.20 S ATOM 19691 SG CYS D 975 21.373 48.271 108.386 1.00 74.38 S ATOM 19709 SG CYS D 978 22.952 44.945 107.554 1.00 70.41 S ATOM 12682 SG CYS D 75 36.569 101.721 70.033 1.00108.95 S ATOM 12708 SG CYS D 78 38.053 99.603 70.767 1.00107.66 S Time building chain proxies: 4.87, per 1000 atoms: 0.18 Number of scatterers: 27219 At special positions: 0 Unit cell: (122.4, 158.4, 193.2, 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 95 16.00 P 102 15.00 Mg 1 11.99 O 5431 8.00 N 4856 7.00 C 16732 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: 1.76 Conformation dependent library (CDL) restraints added in 907.3 milliseconds 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 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " 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 78 " Number of angles added : 6 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5980 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 40 sheets defined 42.9% alpha, 15.0% beta 21 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 226 removed outlier: 4.224A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.655A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.682A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) 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 203 through 224 removed outlier: 3.907A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.933A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 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 242 removed outlier: 3.759A 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 290 through 301 removed outlier: 3.878A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.729A 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 removed outlier: 3.745A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 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: 4.061A 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 588 through 593 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.506A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.396A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 Processing helix chain 'D' and resid 16 through 24 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 130 Processing helix chain 'D' and resid 141 through 185 removed outlier: 5.107A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 4.114A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.644A 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 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.025A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.552A pdb=" N ASN D 396 " --> pdb=" O GLY D 393 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 393 through 397' Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.357A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) 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 492 removed outlier: 4.382A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (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 558 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: 3.833A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.845A 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 726 removed outlier: 3.642A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 736 removed outlier: 3.527A pdb=" N VAL D 736 " --> pdb=" O MET D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 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: 3.608A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.756A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 975 through 980 removed outlier: 3.616A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.741A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1145 Proline residue: D1127 - end of helix removed outlier: 3.875A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 4.217A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.285A 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: 3.753A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1239 removed outlier: 3.516A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D1238 " --> pdb=" O THR D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1255 removed outlier: 3.642A pdb=" N VAL D1252 " --> pdb=" O LEU D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.573A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1281 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: 4.550A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.542A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 303 " --> pdb=" O ASN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.746A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (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 418 removed outlier: 3.803A pdb=" N ARG F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.626A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 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 521 Processing helix chain 'F' and resid 523 through 527 removed outlier: 3.770A pdb=" N LEU F 527 " --> pdb=" O ARG F 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.933A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.689A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 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: 6.202A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.809A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.707A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.572A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLN B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 196 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL B 22 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.982A 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 95 removed outlier: 3.801A pdb=" N LEU B 138 " --> pdb=" O MET B 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.801A pdb=" N LEU B 138 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.804A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.518A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.968A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (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 376 through 379 removed outlier: 6.422A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 191 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: 6.774A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (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 558 through 562 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.662A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.937A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.760A 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 1007 through 1008 removed outlier: 6.909A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.394A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.576A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.631A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.808A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD5, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.615A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 4.891A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 328 through 329 removed outlier: 3.537A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.051A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1051 through 1056 removed outlier: 7.152A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1181 through 1182 Processing sheet with id=AE4, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.611A pdb=" N GLN D1273 " --> pdb=" O GLU E 105 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 2.39 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: 8584 1.34 - 1.46: 4325 1.46 - 1.58: 14606 1.58 - 1.70: 202 1.70 - 1.82: 168 Bond restraints: 27885 Sorted by residual: bond pdb=" C3' DT P 31 " pdb=" C2' DT P 31 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DC P 6 " pdb=" C2' DC P 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG P 36 " pdb=" C2' DG P 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC O 25 " pdb=" C2' DC O 25 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA O 43 " pdb=" C2' DA O 43 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 27880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 37517 2.02 - 4.03: 634 4.03 - 6.05: 52 6.05 - 8.06: 7 8.06 - 10.08: 5 Bond angle restraints: 38215 Sorted by residual: angle pdb=" O4' DG O 35 " pdb=" C4' DG O 35 " pdb=" C3' DG O 35 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT P 5 " pdb=" C4 DT P 5 " pdb=" O4 DT P 5 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT O 41 " pdb=" C4 DT O 41 " pdb=" O4 DT O 41 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT P 13 " pdb=" C4 DT P 13 " pdb=" O4 DT P 13 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT P 44 " pdb=" C4 DT P 44 " pdb=" O4 DT P 44 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 38210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 15846 34.90 - 69.80: 865 69.80 - 104.70: 39 104.70 - 139.61: 1 139.61 - 174.51: 8 Dihedral angle restraints: 16759 sinusoidal: 7461 harmonic: 9298 Sorted by residual: dihedral pdb=" CA ARG C 231 " pdb=" C ARG C 231 " pdb=" N GLN C 232 " pdb=" CA GLN C 232 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA HIS C 451 " pdb=" C HIS C 451 " pdb=" N LYS C 452 " pdb=" CA LYS C 452 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DG P 18 " pdb=" C3' DG P 18 " pdb=" O3' DG P 18 " pdb=" P DG P 19 " ideal model delta sinusoidal sigma weight residual -140.00 34.51 -174.51 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 16756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2782 0.032 - 0.065: 980 0.065 - 0.097: 390 0.097 - 0.130: 193 0.130 - 0.162: 19 Chirality restraints: 4364 Sorted by residual: chirality pdb=" CB THR D1173 " pdb=" CA THR D1173 " pdb=" OG1 THR D1173 " pdb=" CG2 THR D1173 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA ASP B 188 " pdb=" N ASP B 188 " pdb=" C ASP B 188 " pdb=" CB ASP B 188 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CB VAL C 475 " pdb=" CA VAL C 475 " pdb=" CG1 VAL C 475 " pdb=" CG2 VAL C 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 4361 not shown) Planarity restraints: 4661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D1199 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO D1200 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D1200 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D1200 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 35 " 0.033 2.00e-02 2.50e+03 1.34e-02 5.35e+00 pdb=" N9 DG O 35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG O 35 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG O 35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG O 35 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG O 35 " 0.009 2.00e-02 2.50e+03 pdb=" O6 DG O 35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG O 35 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG O 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG O 35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG O 35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG O 35 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO D 434 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " 0.030 5.00e-02 4.00e+02 ... (remaining 4658 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 393 2.64 - 3.20: 24517 3.20 - 3.77: 43738 3.77 - 4.33: 56588 4.33 - 4.90: 92633 Nonbonded interactions: 217869 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.148 2.170 nonbonded pdb=" OD2 ASP D1048 " pdb=" OH TYR D1077 " model vdw 2.195 3.040 nonbonded pdb=" O2 DC O 10 " pdb=" N2 DG P 42 " model vdw 2.203 3.120 nonbonded pdb=" OG1 THR B 74 " pdb=" OE2 GLU D 608 " model vdw 2.222 3.040 ... (remaining 217864 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) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 26.970 Find NCS groups from input model: 0.240 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27891 Z= 0.242 Angle : 0.596 10.081 38221 Z= 0.382 Chirality : 0.043 0.162 4364 Planarity : 0.004 0.081 4661 Dihedral : 19.283 174.507 10779 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.19 % Allowed : 21.66 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.08 (0.15), residues: 3230 helix: 1.62 (0.15), residues: 1270 sheet: -1.02 (0.28), residues: 350 loop : -1.24 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 465 TYR 0.016 0.001 TYR B 176 PHE 0.014 0.001 PHE D 512 TRP 0.013 0.001 TRP C 938 HIS 0.003 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.24 (27885) covalent geometry : angle 0.59538 / 0.38 (38215) hydrogen bonds : bond 0.13608 / 9.51 ( 1174) hydrogen bonds : angle 5.73111 / 4.18 ( 3285) metal coordination : bond 0.00265 / 0.14 ( 6) metal coordination : angle 1.53938 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8455 (t0) cc_final: 0.8254 (t0) REVERT: C 819 ARG cc_start: 0.8551 (mpp80) cc_final: 0.8259 (mtm-85) REVERT: D 310 MET cc_start: 0.8957 (mmm) cc_final: 0.8705 (mmm) REVERT: F 282 MET cc_start: 0.7997 (mmm) cc_final: 0.7765 (mmm) outliers start: 5 outliers final: 2 residues processed: 207 average time/residue: 0.1653 time to fit residues: 54.6375 Evaluate side-chains 187 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 442 GLN C 679 ASN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072712 restraints weight = 68477.675| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.93 r_work: 0.3015 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27891 Z= 0.161 Angle : 0.569 6.992 38221 Z= 0.310 Chirality : 0.043 0.242 4364 Planarity : 0.004 0.052 4661 Dihedral : 18.081 174.255 4664 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.97 % Allowed : 20.48 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3230 helix: 1.70 (0.15), residues: 1262 sheet: -0.91 (0.28), residues: 347 loop : -1.17 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 465 TYR 0.014 0.001 TYR B 176 PHE 0.013 0.001 PHE D1186 TRP 0.010 0.001 TRP C 938 HIS 0.007 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (27885) covalent geometry : angle 0.56926 / 0.31 (38215) hydrogen bonds : bond 0.04109 / 2.76 ( 1174) hydrogen bonds : angle 4.85415 / 3.54 ( 3285) metal coordination : bond 0.00805 / 0.46 ( 6) metal coordination : angle 1.21780 / 0.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.8654 (mmt) cc_final: 0.8432 (mmm) REVERT: C 404 MET cc_start: 0.8578 (ttt) cc_final: 0.8316 (ptm) REVERT: C 869 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9181 (m) REVERT: C 926 MET cc_start: 0.8928 (tpp) cc_final: 0.8625 (tpp) REVERT: D 858 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7775 (ttpt) REVERT: E 105 GLU cc_start: 0.8259 (pp20) cc_final: 0.8051 (pp20) outliers start: 53 outliers final: 29 residues processed: 232 average time/residue: 0.1706 time to fit residues: 63.4540 Evaluate side-chains 208 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain F residue 422 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 114 optimal weight: 0.0270 chunk 198 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 323 optimal weight: 40.0000 chunk 318 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 679 ASN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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 = 0.3705 r_free = 0.3705 target = 0.101542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073058 restraints weight = 68228.416| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.93 r_work: 0.3022 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27891 Z= 0.127 Angle : 0.537 7.077 38221 Z= 0.293 Chirality : 0.042 0.242 4364 Planarity : 0.004 0.047 4661 Dihedral : 18.100 173.212 4664 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.12 % Allowed : 20.88 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.10 (0.15), residues: 3230 helix: 1.72 (0.15), residues: 1266 sheet: -0.80 (0.28), residues: 346 loop : -1.11 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 286 TYR 0.010 0.001 TYR D1142 PHE 0.013 0.001 PHE D1186 TRP 0.010 0.001 TRP C 938 HIS 0.008 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (27885) covalent geometry : angle 0.53680 / 0.29 (38215) hydrogen bonds : bond 0.03820 / 2.56 ( 1174) hydrogen bonds : angle 4.61341 / 3.37 ( 3285) metal coordination : bond 0.00472 / 0.26 ( 6) metal coordination : angle 1.05649 / 0.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 PHE cc_start: 0.8391 (m-80) cc_final: 0.8164 (m-80) REVERT: C 107 PHE cc_start: 0.8482 (m-80) cc_final: 0.8155 (m-80) REVERT: C 404 MET cc_start: 0.8609 (ttt) cc_final: 0.8235 (ptm) REVERT: C 869 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9160 (m) REVERT: C 926 MET cc_start: 0.8959 (tpp) cc_final: 0.8633 (tpp) REVERT: D 541 MET cc_start: 0.8490 (mmm) cc_final: 0.8215 (ttt) REVERT: D 554 GLU cc_start: 0.8315 (tp30) cc_final: 0.7980 (tt0) REVERT: D 858 LYS cc_start: 0.8372 (ttpt) cc_final: 0.7775 (ttpt) REVERT: D 963 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8241 (mtp180) REVERT: F 315 MET cc_start: 0.8851 (mtt) cc_final: 0.8597 (mmm) REVERT: F 507 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8712 (tm-30) REVERT: F 511 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8261 (mmp) outliers start: 57 outliers final: 30 residues processed: 246 average time/residue: 0.1681 time to fit residues: 67.3419 Evaluate side-chains 214 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain F residue 511 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 5 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 302 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 321 optimal weight: 30.0000 chunk 148 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 442 GLN C 679 ASN ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** 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 = 0.3670 r_free = 0.3670 target = 0.099539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.070868 restraints weight = 70082.768| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.97 r_work: 0.2975 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27891 Z= 0.208 Angle : 0.582 10.724 38221 Z= 0.313 Chirality : 0.043 0.239 4364 Planarity : 0.004 0.052 4661 Dihedral : 18.145 173.268 4664 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.68 % Allowed : 21.26 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.01 (0.15), residues: 3230 helix: 1.65 (0.15), residues: 1264 sheet: -0.86 (0.28), residues: 362 loop : -1.15 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 242 TYR 0.012 0.001 TYR D1142 PHE 0.012 0.001 PHE D1186 TRP 0.008 0.001 TRP C 938 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (27885) covalent geometry : angle 0.58194 / 0.31 (38215) hydrogen bonds : bond 0.04046 / 2.72 ( 1174) hydrogen bonds : angle 4.64517 / 3.37 ( 3285) metal coordination : bond 0.01253 / 0.71 ( 6) metal coordination : angle 1.32018 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 185 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8555 (m-80) cc_final: 0.8227 (m-80) REVERT: C 404 MET cc_start: 0.8640 (ttt) cc_final: 0.8288 (ptm) REVERT: C 869 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9158 (m) REVERT: D 554 GLU cc_start: 0.8367 (tp30) cc_final: 0.8136 (tt0) REVERT: D 858 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8167 (tptp) REVERT: F 507 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8747 (tm-30) REVERT: E 105 GLU cc_start: 0.8285 (pp20) cc_final: 0.8041 (pp20) outliers start: 72 outliers final: 49 residues processed: 248 average time/residue: 0.1499 time to fit residues: 61.1479 Evaluate side-chains 224 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 814 LEU 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 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 423 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 315 optimal weight: 40.0000 chunk 240 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.100126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071548 restraints weight = 69649.056| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.96 r_work: 0.2992 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27891 Z= 0.150 Angle : 0.550 8.673 38221 Z= 0.296 Chirality : 0.043 0.248 4364 Planarity : 0.004 0.051 4661 Dihedral : 18.146 174.673 4664 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.75 % Allowed : 21.44 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.08 (0.15), residues: 3230 helix: 1.68 (0.15), residues: 1271 sheet: -0.80 (0.28), residues: 359 loop : -1.10 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.010 0.001 TYR D1142 PHE 0.013 0.001 PHE D1186 TRP 0.010 0.001 TRP C 938 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (27885) covalent geometry : angle 0.54997 / 0.30 (38215) hydrogen bonds : bond 0.03805 / 2.55 ( 1174) hydrogen bonds : angle 4.52378 / 3.28 ( 3285) metal coordination : bond 0.00732 / 0.39 ( 6) metal coordination : angle 1.44367 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 189 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8605 (m-80) cc_final: 0.8265 (m-80) REVERT: C 160 MET cc_start: 0.8640 (tmm) cc_final: 0.8435 (tmm) REVERT: C 219 ARG cc_start: 0.7362 (mpp-170) cc_final: 0.7156 (mpp-170) REVERT: C 230 ARG cc_start: 0.3973 (tpt90) cc_final: 0.3620 (tpt90) REVERT: C 404 MET cc_start: 0.8646 (ttt) cc_final: 0.8252 (ptm) REVERT: D 541 MET cc_start: 0.8510 (mmm) cc_final: 0.8271 (mtp) REVERT: D 576 MET cc_start: 0.8596 (tpp) cc_final: 0.8313 (ttt) REVERT: D 858 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8149 (tptp) REVERT: F 349 TRP cc_start: 0.8393 (m100) cc_final: 0.7734 (m100) REVERT: E 99 ILE cc_start: 0.9273 (mm) cc_final: 0.8752 (mt) REVERT: E 105 GLU cc_start: 0.8226 (pp20) cc_final: 0.7824 (pp20) outliers start: 74 outliers final: 55 residues processed: 256 average time/residue: 0.1507 time to fit residues: 64.6028 Evaluate side-chains 234 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 136 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 188 optimal weight: 0.3980 chunk 267 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 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 = 0.3696 r_free = 0.3696 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072617 restraints weight = 69806.093| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.98 r_work: 0.3014 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27891 Z= 0.117 Angle : 0.539 9.419 38221 Z= 0.288 Chirality : 0.042 0.249 4364 Planarity : 0.004 0.052 4661 Dihedral : 18.105 176.017 4664 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.49 % Allowed : 22.37 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3230 helix: 1.74 (0.15), residues: 1278 sheet: -0.71 (0.28), residues: 346 loop : -1.04 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 421 TYR 0.025 0.001 TYR E 56 PHE 0.014 0.001 PHE C 99 TRP 0.011 0.001 TRP C 938 HIS 0.004 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (27885) covalent geometry : angle 0.53880 / 0.29 (38215) hydrogen bonds : bond 0.03595 / 2.40 ( 1174) hydrogen bonds : angle 4.41405 / 3.21 ( 3285) metal coordination : bond 0.00428 / 0.22 ( 6) metal coordination : angle 1.30054 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8600 (m-80) cc_final: 0.8271 (m-80) REVERT: C 230 ARG cc_start: 0.4157 (tpt90) cc_final: 0.3841 (tpt90) REVERT: C 404 MET cc_start: 0.8649 (ttt) cc_final: 0.8196 (ptm) REVERT: C 519 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8056 (p) REVERT: C 875 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: D 373 MET cc_start: 0.9020 (tpp) cc_final: 0.8788 (mmm) REVERT: D 541 MET cc_start: 0.8466 (mmm) cc_final: 0.8177 (ttm) REVERT: D 858 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8109 (tptp) REVERT: F 349 TRP cc_start: 0.8370 (m100) cc_final: 0.7733 (m100) REVERT: E 56 TYR cc_start: 0.8398 (t80) cc_final: 0.8191 (t80) REVERT: E 105 GLU cc_start: 0.8184 (pp20) cc_final: 0.7780 (pp20) outliers start: 67 outliers final: 51 residues processed: 253 average time/residue: 0.1614 time to fit residues: 67.0824 Evaluate side-chains 239 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 423 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 19 optimal weight: 5.9990 chunk 319 optimal weight: 30.0000 chunk 323 optimal weight: 30.0000 chunk 156 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071454 restraints weight = 69556.947| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.96 r_work: 0.2992 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27891 Z= 0.161 Angle : 0.556 10.032 38221 Z= 0.297 Chirality : 0.042 0.242 4364 Planarity : 0.004 0.052 4661 Dihedral : 18.104 177.076 4664 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.97 % Allowed : 21.96 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3230 helix: 1.75 (0.15), residues: 1280 sheet: -0.76 (0.28), residues: 363 loop : -1.04 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 465 TYR 0.013 0.001 TYR E 56 PHE 0.012 0.001 PHE D1186 TRP 0.009 0.001 TRP C 938 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (27885) covalent geometry : angle 0.55624 / 0.30 (38215) hydrogen bonds : bond 0.03729 / 2.51 ( 1174) hydrogen bonds : angle 4.42736 / 3.20 ( 3285) metal coordination : bond 0.00833 / 0.46 ( 6) metal coordination : angle 1.43285 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 185 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8590 (ttp) cc_final: 0.8337 (ttp) REVERT: B 71 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: C 103 MET cc_start: 0.7627 (ttp) cc_final: 0.7248 (ttp) REVERT: C 107 PHE cc_start: 0.8643 (m-80) cc_final: 0.8318 (m-80) REVERT: C 404 MET cc_start: 0.8597 (ttt) cc_final: 0.8191 (ptm) REVERT: C 875 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: D 541 MET cc_start: 0.8473 (mmm) cc_final: 0.8273 (mtp) REVERT: D 858 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8133 (tptp) REVERT: D 895 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8492 (mtp180) REVERT: F 341 TYR cc_start: 0.8454 (m-80) cc_final: 0.7968 (m-80) REVERT: F 349 TRP cc_start: 0.8385 (m100) cc_final: 0.7742 (m100) REVERT: E 56 TYR cc_start: 0.8356 (t80) cc_final: 0.8018 (t80) REVERT: E 105 GLU cc_start: 0.8241 (pp20) cc_final: 0.7804 (pp20) outliers start: 80 outliers final: 58 residues processed: 257 average time/residue: 0.1555 time to fit residues: 66.4707 Evaluate side-chains 240 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 895 ARG Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 264 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069301 restraints weight = 69268.715| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.92 r_work: 0.2947 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 27891 Z= 0.247 Angle : 0.635 10.242 38221 Z= 0.336 Chirality : 0.045 0.276 4364 Planarity : 0.005 0.056 4661 Dihedral : 18.211 177.700 4664 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.79 % Allowed : 22.67 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.01 (0.15), residues: 3230 helix: 1.60 (0.15), residues: 1271 sheet: -0.82 (0.28), residues: 351 loop : -1.16 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 465 TYR 0.015 0.002 TYR C1083 PHE 0.015 0.002 PHE D 226 TRP 0.007 0.001 TRP C 938 HIS 0.007 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (27885) covalent geometry : angle 0.63400 / 0.34 (38215) hydrogen bonds : bond 0.04231 / 2.87 ( 1174) hydrogen bonds : angle 4.63062 / 3.34 ( 3285) metal coordination : bond 0.01419 / 0.79 ( 6) metal coordination : angle 2.27176 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 181 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8631 (ttp) cc_final: 0.8352 (ttp) REVERT: B 71 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: C 107 PHE cc_start: 0.8717 (m-80) cc_final: 0.8382 (m-80) REVERT: C 208 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8152 (tmm-80) REVERT: C 404 MET cc_start: 0.8632 (ttt) cc_final: 0.8167 (ptm) REVERT: C 875 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: C 926 MET cc_start: 0.9113 (mmm) cc_final: 0.8730 (tpp) REVERT: D 541 MET cc_start: 0.8540 (mmm) cc_final: 0.8327 (mtp) REVERT: D 858 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8163 (tptp) REVERT: D 895 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8519 (mtp180) REVERT: F 341 TYR cc_start: 0.8476 (m-80) cc_final: 0.8102 (m-80) REVERT: F 349 TRP cc_start: 0.8416 (m100) cc_final: 0.7767 (m100) REVERT: E 56 TYR cc_start: 0.8482 (t80) cc_final: 0.8268 (t80) REVERT: E 105 GLU cc_start: 0.8267 (pp20) cc_final: 0.7882 (pp20) outliers start: 75 outliers final: 61 residues processed: 249 average time/residue: 0.1522 time to fit residues: 62.0754 Evaluate side-chains 240 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 895 ARG Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 120 optimal weight: 0.0050 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 320 optimal weight: 30.0000 chunk 61 optimal weight: 0.0060 chunk 40 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 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 = 0.3686 r_free = 0.3686 target = 0.100531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.072251 restraints weight = 69511.847| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.95 r_work: 0.3008 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27891 Z= 0.113 Angle : 0.567 10.434 38221 Z= 0.300 Chirality : 0.042 0.263 4364 Planarity : 0.004 0.049 4661 Dihedral : 18.152 178.588 4664 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.78 % Allowed : 23.63 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3230 helix: 1.74 (0.15), residues: 1281 sheet: -0.65 (0.29), residues: 329 loop : -1.06 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 465 TYR 0.011 0.001 TYR C 344 PHE 0.015 0.001 PHE D1186 TRP 0.012 0.001 TRP C 938 HIS 0.006 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (27885) covalent geometry : angle 0.56627 / 0.30 (38215) hydrogen bonds : bond 0.03595 / 2.40 ( 1174) hydrogen bonds : angle 4.39148 / 3.19 ( 3285) metal coordination : bond 0.00287 / 0.14 ( 6) metal coordination : angle 1.74091 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8483 (ttp) cc_final: 0.8252 (ttp) REVERT: C 103 MET cc_start: 0.7469 (ttp) cc_final: 0.7054 (ttp) REVERT: C 107 PHE cc_start: 0.8651 (m-80) cc_final: 0.8329 (m-80) REVERT: C 208 ARG cc_start: 0.8537 (tmm-80) cc_final: 0.8229 (tmm-80) REVERT: C 404 MET cc_start: 0.8569 (ttt) cc_final: 0.8109 (ptm) REVERT: C 519 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 926 MET cc_start: 0.8985 (mmm) cc_final: 0.8540 (tpp) REVERT: D 541 MET cc_start: 0.8425 (mmm) cc_final: 0.8204 (mtp) REVERT: D 858 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8114 (tptp) REVERT: D 895 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (mtp180) REVERT: F 341 TYR cc_start: 0.8393 (m-80) cc_final: 0.7942 (m-80) REVERT: F 349 TRP cc_start: 0.8366 (m100) cc_final: 0.7762 (m100) REVERT: E 105 GLU cc_start: 0.8288 (pp20) cc_final: 0.7824 (pp20) outliers start: 48 outliers final: 38 residues processed: 237 average time/residue: 0.1584 time to fit residues: 60.6137 Evaluate side-chains 222 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 895 ARG Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain E residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 96 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 317 optimal weight: 30.0000 chunk 245 optimal weight: 0.3980 chunk 137 optimal weight: 8.9990 chunk 170 optimal weight: 0.9990 chunk 281 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070870 restraints weight = 69955.965| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.97 r_work: 0.2965 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27891 Z= 0.208 Angle : 0.600 10.676 38221 Z= 0.317 Chirality : 0.044 0.276 4364 Planarity : 0.004 0.053 4661 Dihedral : 18.159 178.026 4664 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.93 % Allowed : 23.45 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.15 (0.15), residues: 3230 helix: 1.72 (0.15), residues: 1280 sheet: -0.71 (0.29), residues: 334 loop : -1.08 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 18 TYR 0.061 0.002 TYR E 56 PHE 0.012 0.001 PHE D 7 TRP 0.007 0.001 TRP C 938 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (27885) covalent geometry : angle 0.59939 / 0.32 (38215) hydrogen bonds : bond 0.03881 / 2.62 ( 1174) hydrogen bonds : angle 4.49726 / 3.25 ( 3285) metal coordination : bond 0.01292 / 0.71 ( 6) metal coordination : angle 1.77325 / 0.92 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8558 (ttp) cc_final: 0.8330 (ttp) REVERT: C 103 MET cc_start: 0.7496 (ttp) cc_final: 0.7123 (ttp) REVERT: C 107 PHE cc_start: 0.8701 (m-80) cc_final: 0.8375 (m-80) REVERT: C 208 ARG cc_start: 0.8559 (tmm-80) cc_final: 0.8246 (tmm-80) REVERT: C 404 MET cc_start: 0.8633 (ttt) cc_final: 0.8344 (ptm) REVERT: C 630 MET cc_start: 0.8577 (tpp) cc_final: 0.8202 (tpp) REVERT: C 926 MET cc_start: 0.9094 (mmm) cc_final: 0.8704 (tpp) REVERT: D 242 ARG cc_start: 0.8892 (tmm-80) cc_final: 0.8373 (tmm-80) REVERT: D 858 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8136 (tptp) REVERT: D 866 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8382 (mtm110) REVERT: F 341 TYR cc_start: 0.8450 (m-80) cc_final: 0.7996 (m-80) REVERT: F 349 TRP cc_start: 0.8393 (m100) cc_final: 0.7753 (m100) REVERT: E 105 GLU cc_start: 0.8237 (pp20) cc_final: 0.7898 (pp20) outliers start: 52 outliers final: 45 residues processed: 228 average time/residue: 0.1612 time to fit residues: 59.6781 Evaluate side-chains 227 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain E residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 226 optimal weight: 0.1980 chunk 204 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 1 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 321 optimal weight: 30.0000 chunk 251 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072149 restraints weight = 69263.171| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.94 r_work: 0.3008 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27891 Z= 0.118 Angle : 0.559 10.402 38221 Z= 0.296 Chirality : 0.042 0.270 4364 Planarity : 0.004 0.048 4661 Dihedral : 18.093 178.250 4664 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.78 % Allowed : 23.75 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.25 (0.15), residues: 3230 helix: 1.78 (0.15), residues: 1280 sheet: -0.57 (0.29), residues: 321 loop : -1.03 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 18 TYR 0.057 0.001 TYR E 56 PHE 0.014 0.001 PHE D1186 TRP 0.012 0.001 TRP C 938 HIS 0.009 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (27885) covalent geometry : angle 0.55839 / 0.30 (38215) hydrogen bonds : bond 0.03523 / 2.35 ( 1174) hydrogen bonds : angle 4.35410 / 3.16 ( 3285) metal coordination : bond 0.00332 / 0.17 ( 6) metal coordination : angle 1.61045 / 0.90 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5362.18 seconds wall clock time: 92 minutes 46.35 seconds (5566.35 seconds total)