Starting phenix.real_space_refine on Sun May 25 17:19:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji2_61492/05_2025/9ji2_61492.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji2_61492/05_2025/9ji2_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_61492/05_2025/9ji2_61492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji2_61492/05_2025/9ji2_61492.map" model { file = "/net/cci-nas-00/data/ceres_data/9ji2_61492/05_2025/9ji2_61492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji2_61492/05_2025/9ji2_61492.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} 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: 16.23, per 1000 atoms: 0.60 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: 8.07 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 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: 10.70 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: 12.86 Time building geometry restraints manager: 9.25 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=" N VAL F 463 " pdb=" CA VAL F 463 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.58e+00 bond pdb=" N VAL D 880 " pdb=" CA VAL D 880 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.26e-02 6.30e+03 6.99e+00 bond pdb=" N VAL D 878 " pdb=" CA VAL D 878 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.85e+00 bond pdb=" N ASP C 474 " pdb=" CA ASP C 474 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 6.77e+00 bond pdb=" N LEU F 464 " pdb=" CA LEU F 464 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.97e+00 ... (remaining 27880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 37634 2.02 - 4.03: 518 4.03 - 6.05: 51 6.05 - 8.06: 7 8.06 - 10.08: 5 Bond angle restraints: 38215 Sorted by residual: angle pdb=" N ILE D 916 " pdb=" CA ILE D 916 " pdb=" C ILE D 916 " ideal model delta sigma weight residual 113.53 109.73 3.80 9.80e-01 1.04e+00 1.50e+01 angle pdb=" CB MET D1112 " pdb=" CG MET D1112 " pdb=" SD MET D1112 " ideal model delta sigma weight residual 112.70 122.78 -10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET C1076 " pdb=" CG MET C1076 " pdb=" SD MET C1076 " ideal model delta sigma weight residual 112.70 122.66 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA GLU F 507 " pdb=" CB GLU F 507 " pdb=" CG GLU F 507 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C TRP D 656 " pdb=" N GLN D 657 " pdb=" CA GLN D 657 " ideal model delta sigma weight residual 120.06 123.75 -3.69 1.19e+00 7.06e-01 9.63e+00 ... (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: 2884 0.032 - 0.065: 955 0.065 - 0.097: 347 0.097 - 0.130: 164 0.130 - 0.162: 14 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: 0.700 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: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 78.240 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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= 0.135 Angle : 0.566 10.081 38221 Z= 0.309 Chirality : 0.041 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP C 938 HIS 0.003 0.001 HIS D 854 PHE 0.014 0.001 PHE D 512 TYR 0.016 0.001 TYR B 176 ARG 0.014 0.000 ARG C 465 Details of bonding type rmsd hydrogen bonds : bond 0.13608 ( 1174) hydrogen bonds : angle 5.73111 ( 3285) metal coordination : bond 0.00265 ( 6) metal coordination : angle 1.53938 ( 6) covalent geometry : bond 0.00279 (27885) covalent geometry : angle 0.56572 (38215) *********************** 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 : 2.888 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: 0.3963 time to fit residues: 130.0749 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 : 3.158 ------------------------------------------------------------------------------- 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 280 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 134 optimal weight: 0.0470 chunk 260 optimal weight: 30.0000 chunk 100 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 301 optimal weight: 0.0070 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN C 442 GLN C 679 ASN C 841 HIS ** C1055 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074619 restraints weight = 68639.469| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.06 r_work: 0.3048 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27891 Z= 0.112 Angle : 0.526 7.186 38221 Z= 0.281 Chirality : 0.041 0.155 4364 Planarity : 0.004 0.055 4661 Dihedral : 17.882 175.261 4664 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.23 % Allowed : 19.88 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3230 helix: 1.74 (0.15), residues: 1271 sheet: -0.67 (0.28), residues: 348 loop : -1.14 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.004 0.001 HIS C1042 PHE 0.013 0.001 PHE D1186 TYR 0.015 0.001 TYR B 176 ARG 0.009 0.000 ARG C 465 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1174) hydrogen bonds : angle 4.60404 ( 3285) metal coordination : bond 0.00320 ( 6) metal coordination : angle 0.94460 ( 6) covalent geometry : bond 0.00243 (27885) covalent geometry : angle 0.52579 (38215) *********************** 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 284 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.9336 (mtmm) cc_final: 0.8981 (mtmm) REVERT: B 27 GLU cc_start: 0.8536 (pm20) cc_final: 0.8146 (pm20) REVERT: B 30 PHE cc_start: 0.8247 (m-80) cc_final: 0.7988 (m-80) REVERT: B 95 MET cc_start: 0.8705 (mmt) cc_final: 0.8465 (mmm) REVERT: B 133 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8306 (tppp) REVERT: B 191 LYS cc_start: 0.8680 (ptmm) cc_final: 0.8325 (ptpt) REVERT: C 107 PHE cc_start: 0.8427 (m-80) cc_final: 0.8120 (m-80) REVERT: C 404 MET cc_start: 0.8661 (ttt) cc_final: 0.8223 (ptm) REVERT: D 541 MET cc_start: 0.8478 (mmm) cc_final: 0.8193 (ttt) REVERT: D 858 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7676 (ttpt) REVERT: F 315 MET cc_start: 0.8830 (mtt) cc_final: 0.8626 (mmm) REVERT: F 349 TRP cc_start: 0.8351 (m100) cc_final: 0.7786 (m100) REVERT: F 507 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8790 (tm-30) REVERT: E 70 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7584 (mm-40) REVERT: E 105 GLU cc_start: 0.8244 (pp20) cc_final: 0.7993 (pp20) outliers start: 60 outliers final: 23 residues processed: 275 average time/residue: 0.4087 time to fit residues: 175.9778 Evaluate side-chains 220 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 34 LEU 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 174 VAL Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 841 HIS 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 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 1075 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 464 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 45 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 GLN ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070760 restraints weight = 70187.625| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.96 r_work: 0.2971 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27891 Z= 0.217 Angle : 0.581 7.744 38221 Z= 0.310 Chirality : 0.042 0.165 4364 Planarity : 0.004 0.053 4661 Dihedral : 17.950 176.010 4664 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.45 % Allowed : 21.03 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3230 helix: 1.67 (0.15), residues: 1264 sheet: -0.72 (0.28), residues: 357 loop : -1.12 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.021 0.001 HIS F 516 PHE 0.013 0.001 PHE C 439 TYR 0.012 0.001 TYR C1083 ARG 0.004 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 1174) hydrogen bonds : angle 4.63496 ( 3285) metal coordination : bond 0.01143 ( 6) metal coordination : angle 1.64200 ( 6) covalent geometry : bond 0.00494 (27885) covalent geometry : angle 0.58096 (38215) *********************** 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 260 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: B 12 ASP cc_start: 0.8633 (t0) cc_final: 0.8417 (t0) REVERT: C 160 MET cc_start: 0.8618 (tmm) cc_final: 0.8406 (tmm) REVERT: C 219 ARG cc_start: 0.7157 (mpp-170) cc_final: 0.6925 (mpp-170) REVERT: C 404 MET cc_start: 0.8687 (ttt) cc_final: 0.8284 (ptm) REVERT: C 713 MET cc_start: 0.9042 (tpp) cc_final: 0.8806 (tpp) REVERT: C 841 HIS cc_start: 0.7914 (t-170) cc_final: 0.7712 (t-170) REVERT: C 926 MET cc_start: 0.9007 (tpp) cc_final: 0.8611 (tpp) REVERT: D 554 GLU cc_start: 0.8466 (tp30) cc_final: 0.7960 (tt0) REVERT: D 858 LYS cc_start: 0.8415 (ttpt) cc_final: 0.7826 (ttpt) REVERT: E 105 GLU cc_start: 0.8221 (pp20) cc_final: 0.7786 (pp20) outliers start: 66 outliers final: 39 residues processed: 253 average time/residue: 0.3718 time to fit residues: 151.2548 Evaluate side-chains 220 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 C residue 80 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 475 VAL 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 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 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 68 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 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 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 1181 ILE Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 423 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 138 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 289 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 293 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** 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 = 0.3687 r_free = 0.3687 target = 0.100592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072048 restraints weight = 70102.300| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.98 r_work: 0.3003 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1225 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= 0.139 Angle : 0.536 10.882 38221 Z= 0.284 Chirality : 0.041 0.168 4364 Planarity : 0.004 0.050 4661 Dihedral : 17.946 177.719 4664 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.90 % Allowed : 20.74 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3230 helix: 1.73 (0.15), residues: 1276 sheet: -0.75 (0.28), residues: 363 loop : -1.04 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.004 0.001 HIS D 854 PHE 0.013 0.001 PHE C 99 TYR 0.022 0.001 TYR E 56 ARG 0.003 0.000 ARG C 465 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1174) hydrogen bonds : angle 4.45479 ( 3285) metal coordination : bond 0.00684 ( 6) metal coordination : angle 1.41007 ( 6) covalent geometry : bond 0.00313 (27885) covalent geometry : angle 0.53579 (38215) *********************** 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 277 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 199 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8549 (m-80) cc_final: 0.8282 (m-80) REVERT: C 230 ARG cc_start: 0.4146 (tpt90) cc_final: 0.3941 (tpt90) REVERT: C 404 MET cc_start: 0.8670 (ttt) cc_final: 0.8212 (ptm) REVERT: C 713 MET cc_start: 0.9014 (tpp) cc_final: 0.8762 (tpp) REVERT: C 815 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8865 (t) REVERT: D 373 MET cc_start: 0.9040 (tpp) cc_final: 0.8800 (mmm) REVERT: D 541 MET cc_start: 0.8467 (mmm) cc_final: 0.8237 (mtp) REVERT: D 858 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8126 (tptp) REVERT: F 349 TRP cc_start: 0.8356 (m100) cc_final: 0.7731 (m100) REVERT: E 105 GLU cc_start: 0.8190 (pp20) cc_final: 0.7946 (pp20) outliers start: 78 outliers final: 50 residues processed: 268 average time/residue: 0.3627 time to fit residues: 159.1075 Evaluate side-chains 234 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 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 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 447 SER 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 732 GLU 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 815 THR 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 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 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 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 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 1252 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 255 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** F 388 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.098383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070107 restraints weight = 68736.153| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.88 r_work: 0.2965 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27891 Z= 0.225 Angle : 0.598 8.612 38221 Z= 0.316 Chirality : 0.043 0.166 4364 Planarity : 0.004 0.056 4661 Dihedral : 18.035 177.442 4664 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.20 % Allowed : 21.11 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3230 helix: 1.61 (0.15), residues: 1270 sheet: -0.81 (0.28), residues: 352 loop : -1.12 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.005 0.001 HIS E 100 PHE 0.014 0.002 PHE C 99 TYR 0.027 0.002 TYR E 56 ARG 0.004 0.000 ARG C 562 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 1174) hydrogen bonds : angle 4.61500 ( 3285) metal coordination : bond 0.01275 ( 6) metal coordination : angle 2.39975 ( 6) covalent geometry : bond 0.00518 (27885) covalent geometry : angle 0.59743 (38215) *********************** 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 267 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 181 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: C 107 PHE cc_start: 0.8696 (m-80) cc_final: 0.8389 (m-80) REVERT: C 404 MET cc_start: 0.8710 (ttt) cc_final: 0.8353 (ptm) REVERT: C 713 MET cc_start: 0.9111 (tpp) cc_final: 0.8855 (tpp) REVERT: C 875 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: C 926 MET cc_start: 0.9058 (mmm) cc_final: 0.8536 (tpp) REVERT: D 541 MET cc_start: 0.8521 (mmm) cc_final: 0.8292 (mtp) REVERT: D 858 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8198 (tptp) REVERT: F 349 TRP cc_start: 0.8400 (m100) cc_final: 0.7765 (m100) REVERT: E 105 GLU cc_start: 0.8174 (pp20) cc_final: 0.7818 (pp20) outliers start: 86 outliers final: 61 residues processed: 257 average time/residue: 0.3590 time to fit residues: 152.7539 Evaluate side-chains 235 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 VAL 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 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 174 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 442 GLN 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 514 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 560 LEU 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 732 GLU 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 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 261 ILE 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 696 ILE Chi-restraints excluded: chain D residue 718 ASP 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 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 422 SER Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 320 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** 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 = 0.3644 r_free = 0.3644 target = 0.097866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069691 restraints weight = 69101.954| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.88 r_work: 0.2956 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 27891 Z= 0.233 Angle : 0.603 8.460 38221 Z= 0.319 Chirality : 0.043 0.165 4364 Planarity : 0.004 0.057 4661 Dihedral : 18.099 176.740 4664 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.42 % Allowed : 21.37 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3230 helix: 1.58 (0.15), residues: 1271 sheet: -0.88 (0.28), residues: 360 loop : -1.16 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.005 0.001 HIS D 854 PHE 0.013 0.001 PHE D1186 TYR 0.051 0.002 TYR E 56 ARG 0.005 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 1174) hydrogen bonds : angle 4.62535 ( 3285) metal coordination : bond 0.01305 ( 6) metal coordination : angle 2.53313 ( 6) covalent geometry : bond 0.00537 (27885) covalent geometry : angle 0.60232 (38215) *********************** 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 272 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 180 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: A 123 MET cc_start: 0.8602 (ttp) cc_final: 0.8209 (ttp) REVERT: A 185 GLN cc_start: 0.7620 (mp10) cc_final: 0.7175 (mp10) REVERT: C 44 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9220 (pp) REVERT: C 107 PHE cc_start: 0.8729 (m-80) cc_final: 0.8422 (m-80) REVERT: C 404 MET cc_start: 0.9001 (ttt) cc_final: 0.8392 (ptm) REVERT: C 656 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: C 835 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8633 (p) REVERT: C 875 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: C 926 MET cc_start: 0.9008 (mmm) cc_final: 0.8459 (tpp) REVERT: D 183 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5800 (pm20) REVERT: D 541 MET cc_start: 0.8525 (mmm) cc_final: 0.8279 (mtp) REVERT: D 858 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8201 (tptp) REVERT: D 895 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8496 (mtp180) REVERT: F 349 TRP cc_start: 0.8403 (m100) cc_final: 0.7767 (m100) REVERT: E 56 TYR cc_start: 0.8633 (t80) cc_final: 0.8343 (t80) REVERT: E 105 GLU cc_start: 0.8191 (pp20) cc_final: 0.7883 (pp20) outliers start: 92 outliers final: 66 residues processed: 262 average time/residue: 0.3737 time to fit residues: 160.2123 Evaluate side-chains 247 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE 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 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 B residue 227 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 373 PHE 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 502 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 732 GLU 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 815 THR Chi-restraints excluded: chain C residue 835 THR 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 997 ASP 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 157 VAL Chi-restraints excluded: chain D residue 183 GLU 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 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 718 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 895 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 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 422 SER Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 261 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 274 optimal weight: 0.1980 chunk 194 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 286 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.099894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071722 restraints weight = 70135.847| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.96 r_work: 0.2996 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27891 Z= 0.126 Angle : 0.538 8.964 38221 Z= 0.284 Chirality : 0.041 0.190 4364 Planarity : 0.004 0.048 4661 Dihedral : 17.994 177.585 4664 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.79 % Allowed : 22.89 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3230 helix: 1.75 (0.15), residues: 1280 sheet: -0.73 (0.29), residues: 339 loop : -1.05 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.005 0.001 HIS F 516 PHE 0.014 0.001 PHE D1186 TYR 0.036 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1174) hydrogen bonds : angle 4.37410 ( 3285) metal coordination : bond 0.00517 ( 6) metal coordination : angle 1.68530 ( 6) covalent geometry : bond 0.00284 (27885) covalent geometry : angle 0.53746 (38215) *********************** 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 264 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 189 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7630 (mp10) cc_final: 0.7406 (mp10) REVERT: C 107 PHE cc_start: 0.8679 (m-80) cc_final: 0.8370 (m-80) REVERT: C 404 MET cc_start: 0.8965 (ttt) cc_final: 0.8343 (ptm) REVERT: C 519 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8198 (p) REVERT: C 926 MET cc_start: 0.8903 (mmm) cc_final: 0.8575 (tpp) REVERT: D 242 ARG cc_start: 0.8982 (tmm-80) cc_final: 0.8479 (tmm-80) REVERT: D 541 MET cc_start: 0.8443 (mmm) cc_final: 0.8182 (ttm) REVERT: D 759 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8918 (tm-30) REVERT: D 858 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8103 (tptp) REVERT: F 246 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8094 (mp0) REVERT: F 349 TRP cc_start: 0.8350 (m100) cc_final: 0.7748 (m100) REVERT: E 41 ASP cc_start: 0.7952 (m-30) cc_final: 0.7750 (t0) REVERT: E 56 TYR cc_start: 0.8364 (t80) cc_final: 0.7996 (t80) REVERT: E 105 GLU cc_start: 0.8219 (pp20) cc_final: 0.7890 (pp20) outliers start: 75 outliers final: 52 residues processed: 255 average time/residue: 0.3830 time to fit residues: 158.3515 Evaluate side-chains 232 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE 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 174 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 442 GLN 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 519 VAL Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 732 GLU 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 815 THR 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 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 759 GLN 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 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 1240 CYS Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 281 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 1 optimal weight: 0.0020 chunk 101 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 156 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 1.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 443 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072173 restraints weight = 68885.918| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.93 r_work: 0.3005 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1818 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= 0.125 Angle : 0.540 9.154 38221 Z= 0.284 Chirality : 0.041 0.265 4364 Planarity : 0.004 0.048 4661 Dihedral : 17.919 177.547 4664 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.68 % Allowed : 23.30 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3230 helix: 1.81 (0.15), residues: 1280 sheet: -0.68 (0.28), residues: 340 loop : -1.00 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.003 0.001 HIS D 854 PHE 0.013 0.001 PHE D1186 TYR 0.030 0.001 TYR E 56 ARG 0.007 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1174) hydrogen bonds : angle 4.31847 ( 3285) metal coordination : bond 0.00483 ( 6) metal coordination : angle 1.52840 ( 6) covalent geometry : bond 0.00281 (27885) covalent geometry : angle 0.53944 (38215) *********************** 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 265 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8661 (m-80) cc_final: 0.8366 (m-80) REVERT: C 219 ARG cc_start: 0.7327 (mpp-170) cc_final: 0.7106 (mpp-170) REVERT: C 404 MET cc_start: 0.8941 (ttt) cc_final: 0.8325 (ptm) REVERT: C 519 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8233 (p) REVERT: C 926 MET cc_start: 0.8855 (mmm) cc_final: 0.8528 (tpp) REVERT: D 183 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5752 (pm20) REVERT: D 242 ARG cc_start: 0.8973 (tmm-80) cc_final: 0.8485 (tmm-80) REVERT: D 541 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8201 (ttm) REVERT: D 759 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8928 (tm-30) REVERT: D 858 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8084 (tptp) REVERT: F 246 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8135 (mp0) REVERT: F 349 TRP cc_start: 0.8305 (m100) cc_final: 0.7711 (m100) REVERT: E 41 ASP cc_start: 0.7965 (m-30) cc_final: 0.7738 (t0) REVERT: E 56 TYR cc_start: 0.8356 (t80) cc_final: 0.7848 (t80) REVERT: E 105 GLU cc_start: 0.8197 (pp20) cc_final: 0.7857 (pp20) outliers start: 72 outliers final: 57 residues processed: 254 average time/residue: 0.3609 time to fit residues: 149.7161 Evaluate side-chains 245 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE 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 80 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 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 373 PHE Chi-restraints excluded: chain C residue 442 GLN 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 519 VAL Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 MET 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 815 THR 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 102 THR Chi-restraints excluded: chain D residue 183 GLU 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 541 MET 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 696 ILE Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 759 GLN 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 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 1240 CYS 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 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 97 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071054 restraints weight = 70453.089| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.01 r_work: 0.2981 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27891 Z= 0.158 Angle : 0.560 10.229 38221 Z= 0.294 Chirality : 0.042 0.285 4364 Planarity : 0.004 0.050 4661 Dihedral : 17.946 177.306 4664 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.45 % Allowed : 23.52 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3230 helix: 1.79 (0.15), residues: 1280 sheet: -0.68 (0.28), residues: 339 loop : -1.01 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.004 0.001 HIS D 854 PHE 0.013 0.001 PHE D1186 TYR 0.029 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1174) hydrogen bonds : angle 4.35740 ( 3285) metal coordination : bond 0.00754 ( 6) metal coordination : angle 1.78941 ( 6) covalent geometry : bond 0.00363 (27885) covalent geometry : angle 0.56006 (38215) *********************** 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 248 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7981 (mp10) cc_final: 0.7662 (mp10) REVERT: B 27 GLU cc_start: 0.8627 (pm20) cc_final: 0.8343 (pm20) REVERT: B 80 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9416 (mp) REVERT: C 103 MET cc_start: 0.7710 (ttp) cc_final: 0.7378 (ttp) REVERT: C 107 PHE cc_start: 0.8684 (m-80) cc_final: 0.8392 (m-80) REVERT: C 219 ARG cc_start: 0.7355 (mpp-170) cc_final: 0.7099 (mpp-170) REVERT: C 404 MET cc_start: 0.8991 (ttt) cc_final: 0.8364 (ptm) REVERT: C 519 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8267 (p) REVERT: C 630 MET cc_start: 0.8730 (tpp) cc_final: 0.8257 (tpp) REVERT: C 926 MET cc_start: 0.8871 (mmm) cc_final: 0.8548 (tpp) REVERT: D 183 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5859 (pm20) REVERT: D 242 ARG cc_start: 0.8981 (tmm-80) cc_final: 0.8476 (tmm-80) REVERT: D 759 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8918 (tm-30) REVERT: D 858 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8103 (tptp) REVERT: F 246 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8190 (mp0) REVERT: F 349 TRP cc_start: 0.8312 (m100) cc_final: 0.7716 (m100) REVERT: E 41 ASP cc_start: 0.8065 (m-30) cc_final: 0.7864 (t0) REVERT: E 56 TYR cc_start: 0.8422 (t80) cc_final: 0.8112 (t80) REVERT: E 105 GLU cc_start: 0.8226 (pp20) cc_final: 0.7873 (pp20) outliers start: 66 outliers final: 57 residues processed: 239 average time/residue: 0.3688 time to fit residues: 144.2919 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 : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE 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 80 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 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 174 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 442 GLN 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 519 VAL Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 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 815 THR 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 102 THR Chi-restraints excluded: chain D residue 183 GLU 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 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 759 GLN Chi-restraints excluded: chain D residue 800 ILE 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 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1240 CYS 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 F residue 445 VAL Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 186 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.100600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072480 restraints weight = 69484.799| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.96 r_work: 0.3013 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27891 Z= 0.117 Angle : 0.540 10.672 38221 Z= 0.283 Chirality : 0.041 0.280 4364 Planarity : 0.004 0.047 4661 Dihedral : 17.929 178.410 4664 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.16 % Allowed : 23.67 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3230 helix: 1.86 (0.15), residues: 1281 sheet: -0.51 (0.29), residues: 326 loop : -0.95 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 938 HIS 0.003 0.001 HIS D 748 PHE 0.014 0.001 PHE D1186 TYR 0.027 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1174) hydrogen bonds : angle 4.26238 ( 3285) metal coordination : bond 0.00374 ( 6) metal coordination : angle 1.48212 ( 6) covalent geometry : bond 0.00263 (27885) covalent geometry : angle 0.54012 (38215) ********************** 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 249 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7988 (mp10) cc_final: 0.7661 (mp10) REVERT: B 80 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9297 (mp) REVERT: C 103 MET cc_start: 0.7921 (ttp) cc_final: 0.7649 (ttp) REVERT: C 107 PHE cc_start: 0.8656 (m-80) cc_final: 0.8368 (m-80) REVERT: C 219 ARG cc_start: 0.7330 (mpp-170) cc_final: 0.6960 (mpp-170) REVERT: C 404 MET cc_start: 0.8907 (ttt) cc_final: 0.8420 (ptm) REVERT: C 519 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8188 (p) REVERT: C 926 MET cc_start: 0.8820 (mmm) cc_final: 0.8489 (tpp) REVERT: D 183 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5817 (pm20) REVERT: D 242 ARG cc_start: 0.8973 (tmm-80) cc_final: 0.8460 (tmm-80) REVERT: D 759 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8933 (tm-30) REVERT: D 858 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8076 (tptp) REVERT: F 246 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8177 (mp0) REVERT: F 349 TRP cc_start: 0.8275 (m100) cc_final: 0.7721 (m100) REVERT: E 41 ASP cc_start: 0.7913 (m-30) cc_final: 0.7615 (t0) REVERT: E 56 TYR cc_start: 0.8319 (t80) cc_final: 0.8029 (t80) REVERT: E 99 ILE cc_start: 0.9135 (mm) cc_final: 0.8755 (mt) outliers start: 58 outliers final: 51 residues processed: 239 average time/residue: 0.3757 time to fit residues: 146.7531 Evaluate side-chains 243 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 2.922 ------------------------------------------------------------------------------- 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 80 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 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 442 GLN 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 519 VAL Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 653 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 815 THR 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 102 THR Chi-restraints excluded: chain D residue 183 GLU 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 447 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 759 GLN Chi-restraints excluded: chain D residue 800 ILE 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 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1240 CYS 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 F residue 445 VAL Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 58 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3669 r_free = 0.3669 target = 0.099432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071273 restraints weight = 69877.253| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.96 r_work: 0.2986 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27891 Z= 0.161 Angle : 0.568 14.398 38221 Z= 0.295 Chirality : 0.042 0.278 4364 Planarity : 0.004 0.050 4661 Dihedral : 17.962 178.027 4664 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.38 % Allowed : 23.86 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3230 helix: 1.80 (0.15), residues: 1280 sheet: -0.58 (0.29), residues: 331 loop : -0.95 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.005 0.001 HIS D 854 PHE 0.012 0.001 PHE D1186 TYR 0.027 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1174) hydrogen bonds : angle 4.31694 ( 3285) metal coordination : bond 0.00805 ( 6) metal coordination : angle 1.73749 ( 6) covalent geometry : bond 0.00370 (27885) covalent geometry : angle 0.56724 (38215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13053.61 seconds wall clock time: 226 minutes 20.31 seconds (13580.31 seconds total)