Starting phenix.real_space_refine on Mon Jun 23 11:19:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji2_61492/06_2025/9ji2_61492.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji2_61492/06_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_61492/06_2025/9ji2_61492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji2_61492/06_2025/9ji2_61492.map" model { file = "/net/cci-nas-00/data/ceres_data/9ji2_61492/06_2025/9ji2_61492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji2_61492/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.34, per 1000 atoms: 0.53 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: 6.44 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 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: 8.77 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: 11.68 Time building geometry restraints manager: 7.65 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: 1.170 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: 1.020 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 69.010 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.060 ------------------------------------------------------------------------------- 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 : 2.899 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: 0.3989 time to fit residues: 131.6839 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 : 2.761 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.103166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074626 restraints weight = 69702.334| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.08 r_work: 0.3050 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 3.095 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: 0.9327 (mtmm) cc_final: 0.8973 (mtmm) REVERT: B 27 GLU cc_start: 0.8532 (pm20) cc_final: 0.8147 (pm20) REVERT: B 30 PHE cc_start: 0.8248 (m-80) cc_final: 0.7992 (m-80) REVERT: B 95 MET cc_start: 0.8695 (mmt) cc_final: 0.8461 (mmm) REVERT: B 133 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8309 (tppp) REVERT: B 191 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8325 (ptpt) REVERT: C 107 PHE cc_start: 0.8427 (m-80) cc_final: 0.8121 (m-80) REVERT: C 404 MET cc_start: 0.8653 (ttt) cc_final: 0.8219 (ptm) REVERT: D 541 MET cc_start: 0.8474 (mmm) cc_final: 0.8189 (ttt) REVERT: D 858 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7682 (ttpt) REVERT: F 315 MET cc_start: 0.8838 (mtt) cc_final: 0.8633 (mmm) REVERT: F 349 TRP cc_start: 0.8354 (m100) cc_final: 0.7793 (m100) REVERT: F 507 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8790 (tm-30) REVERT: E 70 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7585 (mm-40) REVERT: E 105 GLU cc_start: 0.8242 (pp20) cc_final: 0.7991 (pp20) outliers start: 60 outliers final: 23 residues processed: 275 average time/residue: 0.4216 time to fit residues: 181.1337 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 : 3.027 ------------------------------------------------------------------------------- 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: 0.6980 chunk 192 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 295 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071503 restraints weight = 69166.849| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.94 r_work: 0.2989 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27891 Z= 0.188 Angle : 0.558 7.456 38221 Z= 0.298 Chirality : 0.042 0.160 4364 Planarity : 0.004 0.052 4661 Dihedral : 17.922 175.956 4664 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.23 % Allowed : 21.26 % 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: 0.11 (0.15), residues: 3230 helix: 1.71 (0.15), residues: 1264 sheet: -0.77 (0.28), residues: 362 loop : -1.09 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.010 0.001 HIS C 841 PHE 0.011 0.001 PHE D1186 TYR 0.011 0.001 TYR C1083 ARG 0.005 0.000 ARG C 465 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 1174) hydrogen bonds : angle 4.57761 ( 3285) metal coordination : bond 0.01045 ( 6) metal coordination : angle 1.46038 ( 6) covalent geometry : bond 0.00432 (27885) covalent geometry : angle 0.55822 (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: 60 poor density : 200 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: C 107 PHE cc_start: 0.8538 (m-80) cc_final: 0.8257 (m-80) REVERT: C 160 MET cc_start: 0.8598 (tmm) cc_final: 0.8389 (tmm) REVERT: C 219 ARG cc_start: 0.7160 (mpp-170) cc_final: 0.6898 (mpp-170) REVERT: C 404 MET cc_start: 0.8677 (ttt) cc_final: 0.8279 (ptm) REVERT: C 713 MET cc_start: 0.8991 (tpp) cc_final: 0.8770 (tpp) REVERT: C 841 HIS cc_start: 0.7975 (t-170) cc_final: 0.7755 (t-170) REVERT: C 926 MET cc_start: 0.8986 (tpp) cc_final: 0.8585 (tpp) REVERT: D 554 GLU cc_start: 0.8411 (tp30) cc_final: 0.8034 (tt0) REVERT: D 858 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7817 (ttpt) REVERT: F 507 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8761 (tm-30) outliers start: 60 outliers final: 36 residues processed: 253 average time/residue: 0.3744 time to fit residues: 152.9942 Evaluate side-chains 222 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 186 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 289 optimal weight: 20.0000 chunk 119 optimal weight: 0.0470 chunk 293 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 599 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.101607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073168 restraints weight = 69852.697| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.97 r_work: 0.3027 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1206 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= 0.120 Angle : 0.518 10.095 38221 Z= 0.275 Chirality : 0.041 0.174 4364 Planarity : 0.004 0.050 4661 Dihedral : 17.901 178.417 4664 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.42 % Allowed : 21.29 % Favored : 76.29 % 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: 1.77 (0.15), residues: 1278 sheet: -0.63 (0.28), residues: 352 loop : -1.00 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.004 0.001 HIS D 748 PHE 0.013 0.001 PHE C 99 TYR 0.009 0.001 TYR C 344 ARG 0.003 0.000 ARG D 770 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 1174) hydrogen bonds : angle 4.37844 ( 3285) metal coordination : bond 0.00491 ( 6) metal coordination : angle 1.13339 ( 6) covalent geometry : bond 0.00269 (27885) covalent geometry : angle 0.51809 (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 271 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8516 (m-80) cc_final: 0.8257 (m-80) REVERT: C 355 MET cc_start: 0.8323 (ttm) cc_final: 0.8063 (ttm) REVERT: C 404 MET cc_start: 0.8667 (ttt) cc_final: 0.8175 (ptm) REVERT: C 519 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 713 MET cc_start: 0.9014 (tpp) cc_final: 0.8789 (tpp) REVERT: C 815 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8863 (t) REVERT: D 373 MET cc_start: 0.9031 (tpp) cc_final: 0.8789 (mmm) REVERT: D 858 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8105 (tptp) REVERT: F 349 TRP cc_start: 0.8316 (m100) cc_final: 0.7696 (m100) REVERT: F 507 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8768 (tm-30) REVERT: E 105 GLU cc_start: 0.8222 (pp20) cc_final: 0.7903 (pp20) outliers start: 65 outliers final: 39 residues processed: 262 average time/residue: 0.4312 time to fit residues: 185.2765 Evaluate side-chains 229 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 187 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 171 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 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 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 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 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 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: 0.1980 chunk 126 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 160 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.2564 ------------------------------------------------------------------------------- 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** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.099839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071333 restraints weight = 69918.821| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.96 r_work: 0.2988 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27891 Z= 0.168 Angle : 0.552 8.594 38221 Z= 0.292 Chirality : 0.042 0.161 4364 Planarity : 0.004 0.052 4661 Dihedral : 17.931 178.887 4664 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.08 % Allowed : 21.11 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.15), residues: 3230 helix: 1.76 (0.15), residues: 1272 sheet: -0.67 (0.28), residues: 362 loop : -1.04 (0.16), residues: 1596 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 0.011 0.001 PHE D1186 TYR 0.011 0.001 TYR C1083 ARG 0.005 0.000 ARG B 6 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1174) hydrogen bonds : angle 4.43797 ( 3285) metal coordination : bond 0.00855 ( 6) metal coordination : angle 1.73153 ( 6) covalent geometry : bond 0.00384 (27885) covalent geometry : angle 0.55164 (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 271 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 188 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8635 (m-80) cc_final: 0.8341 (m-80) REVERT: C 219 ARG cc_start: 0.7332 (mpp-170) cc_final: 0.7109 (mpp-170) REVERT: C 230 ARG cc_start: 0.4221 (tpt90) cc_final: 0.3823 (tpt90) REVERT: C 404 MET cc_start: 0.8724 (ttt) cc_final: 0.8347 (ptm) REVERT: C 713 MET cc_start: 0.9044 (tpp) cc_final: 0.8791 (tpp) REVERT: C 841 HIS cc_start: 0.7923 (t-170) cc_final: 0.7663 (t-170) REVERT: C 875 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: C 926 MET cc_start: 0.9020 (mmm) cc_final: 0.8688 (tpp) REVERT: D 89 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8056 (mtp180) REVERT: D 541 MET cc_start: 0.8501 (mmm) cc_final: 0.8296 (mtp) REVERT: D 858 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8121 (tptp) REVERT: F 341 TYR cc_start: 0.8425 (m-80) cc_final: 0.8062 (m-80) REVERT: F 349 TRP cc_start: 0.8364 (m100) cc_final: 0.7734 (m100) REVERT: F 507 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8766 (tm-30) REVERT: E 56 TYR cc_start: 0.8294 (t80) cc_final: 0.8066 (t80) REVERT: E 105 GLU cc_start: 0.8157 (pp20) cc_final: 0.7649 (pp20) outliers start: 83 outliers final: 57 residues processed: 261 average time/residue: 0.4589 time to fit residues: 198.2461 Evaluate side-chains 242 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 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 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 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU 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 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 Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.097712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069090 restraints weight = 69819.774| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.94 r_work: 0.2941 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27891 Z= 0.245 Angle : 0.618 8.990 38221 Z= 0.326 Chirality : 0.043 0.163 4364 Planarity : 0.004 0.057 4661 Dihedral : 18.073 177.670 4664 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.27 % Allowed : 21.66 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.15), residues: 3230 helix: 1.58 (0.15), residues: 1271 sheet: -0.79 (0.28), residues: 365 loop : -1.12 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 938 HIS 0.005 0.001 HIS D 505 PHE 0.013 0.002 PHE D 7 TYR 0.013 0.002 TYR C1083 ARG 0.005 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1174) hydrogen bonds : angle 4.61432 ( 3285) metal coordination : bond 0.01420 ( 6) metal coordination : angle 2.63141 ( 6) covalent geometry : bond 0.00563 (27885) covalent geometry : angle 0.61747 (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: 88 poor density : 184 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9233 (pp) REVERT: C 107 PHE cc_start: 0.8740 (m-80) cc_final: 0.8423 (m-80) REVERT: C 219 ARG cc_start: 0.7276 (mpp-170) cc_final: 0.6984 (mpp-170) REVERT: C 230 ARG cc_start: 0.4543 (tpt90) cc_final: 0.4310 (tpt90) REVERT: C 404 MET cc_start: 0.8959 (ttt) cc_final: 0.8381 (ptm) REVERT: C 713 MET cc_start: 0.9151 (tpp) cc_final: 0.8940 (tpp) REVERT: C 835 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8626 (p) REVERT: C 841 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7799 (t-170) REVERT: C 875 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: C 926 MET cc_start: 0.8994 (mmm) cc_final: 0.8457 (tpp) REVERT: D 89 ARG cc_start: 0.9000 (ttm-80) cc_final: 0.8312 (mtp180) REVERT: D 541 MET cc_start: 0.8537 (mmm) cc_final: 0.8291 (mtp) REVERT: D 858 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8171 (tptp) REVERT: D 895 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8527 (mtp180) REVERT: F 349 TRP cc_start: 0.8408 (m100) cc_final: 0.7761 (m100) REVERT: F 507 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8749 (tm-30) REVERT: E 105 GLU cc_start: 0.8290 (pp20) cc_final: 0.7850 (pp20) outliers start: 88 outliers final: 62 residues processed: 262 average time/residue: 0.3945 time to fit residues: 171.1446 Evaluate side-chains 245 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 178 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 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 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 356 THR 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 573 SER Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 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 841 HIS 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 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 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: 6.9990 chunk 159 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 274 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072214 restraints weight = 69990.394| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.98 r_work: 0.3006 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1711 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= 0.114 Angle : 0.537 9.047 38221 Z= 0.283 Chirality : 0.041 0.157 4364 Planarity : 0.004 0.047 4661 Dihedral : 17.975 178.131 4664 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.34 % Allowed : 23.26 % Favored : 74.40 % 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: 1.77 (0.15), residues: 1280 sheet: -0.59 (0.29), residues: 332 loop : -1.01 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 938 HIS 0.017 0.001 HIS C 841 PHE 0.014 0.001 PHE D1186 TYR 0.035 0.001 TYR E 56 ARG 0.003 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 1174) hydrogen bonds : angle 4.34088 ( 3285) metal coordination : bond 0.00368 ( 6) metal coordination : angle 1.62515 ( 6) covalent geometry : bond 0.00253 (27885) covalent geometry : angle 0.53634 (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 268 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8671 (m-80) cc_final: 0.8367 (m-80) REVERT: C 230 ARG cc_start: 0.4514 (tpt90) cc_final: 0.4123 (tpt90) REVERT: C 404 MET cc_start: 0.8943 (ttt) cc_final: 0.8456 (ptm) REVERT: C 519 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8178 (p) REVERT: C 926 MET cc_start: 0.8842 (mmm) cc_final: 0.8510 (tpp) REVERT: D 242 ARG cc_start: 0.8919 (tmm-80) cc_final: 0.8355 (tmm-80) REVERT: D 541 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: D 759 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8927 (tm-30) REVERT: D 858 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8105 (tptp) REVERT: F 349 TRP cc_start: 0.8304 (m100) cc_final: 0.7717 (m100) REVERT: F 507 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8724 (tm-30) outliers start: 63 outliers final: 46 residues processed: 257 average time/residue: 0.5033 time to fit residues: 212.8589 Evaluate side-chains 235 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 187 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 C residue 80 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 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 560 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 653 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 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 541 MET 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 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 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 423 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 281 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 296 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3674 r_free = 0.3674 target = 0.099757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.071509 restraints weight = 69832.498| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.96 r_work: 0.2989 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1826 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= 0.145 Angle : 0.548 9.484 38221 Z= 0.287 Chirality : 0.041 0.178 4364 Planarity : 0.004 0.049 4661 Dihedral : 17.924 177.699 4664 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.64 % Allowed : 23.37 % Favored : 73.99 % 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: 1.80 (0.15), residues: 1280 sheet: -0.59 (0.29), residues: 333 loop : -1.01 (0.16), residues: 1617 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 0.012 0.001 PHE D1186 TYR 0.037 0.001 TYR E 56 ARG 0.007 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 1174) hydrogen bonds : angle 4.34085 ( 3285) metal coordination : bond 0.00694 ( 6) metal coordination : angle 1.61691 ( 6) covalent geometry : bond 0.00330 (27885) covalent geometry : angle 0.54794 (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 258 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.8671 (m-80) cc_final: 0.8373 (m-80) REVERT: C 219 ARG cc_start: 0.7321 (mpp-170) cc_final: 0.7090 (mpp-170) REVERT: C 404 MET cc_start: 0.8950 (ttt) cc_final: 0.8342 (ptm) REVERT: C 519 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8265 (p) REVERT: C 926 MET cc_start: 0.8858 (mmm) cc_final: 0.8551 (tpp) REVERT: D 183 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5738 (pm20) REVERT: D 242 ARG cc_start: 0.8932 (tmm-80) cc_final: 0.8402 (tmm-80) REVERT: D 541 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8246 (mtp) REVERT: D 759 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8949 (tm-30) REVERT: D 858 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8099 (tptp) REVERT: D 895 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8530 (mtp180) REVERT: F 349 TRP cc_start: 0.8418 (m100) cc_final: 0.7902 (m100) REVERT: F 507 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8677 (tm-30) REVERT: E 105 GLU cc_start: 0.8262 (pp20) cc_final: 0.8011 (pp20) outliers start: 71 outliers final: 54 residues processed: 248 average time/residue: 0.5427 time to fit residues: 224.9931 Evaluate side-chains 243 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 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 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 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 560 LEU 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 D residue 28 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 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 718 ASP Chi-restraints excluded: chain D residue 759 GLN 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 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 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: 0.0030 chunk 290 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 overall best weight: 3.3396 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.097969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069631 restraints weight = 69694.166| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.92 r_work: 0.2954 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1995 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 : 0.596 9.971 38221 Z= 0.313 Chirality : 0.043 0.245 4364 Planarity : 0.004 0.054 4661 Dihedral : 18.026 176.606 4664 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.75 % Allowed : 23.49 % 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: 0.14 (0.15), residues: 3230 helix: 1.69 (0.15), residues: 1279 sheet: -0.83 (0.28), residues: 348 loop : -1.04 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 938 HIS 0.007 0.001 HIS B 124 PHE 0.013 0.001 PHE C 906 TYR 0.047 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 1174) hydrogen bonds : angle 4.48804 ( 3285) metal coordination : bond 0.01226 ( 6) metal coordination : angle 2.49958 ( 6) covalent geometry : bond 0.00499 (27885) covalent geometry : angle 0.59535 (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 257 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.8594 (mmt) cc_final: 0.8318 (mmm) REVERT: C 44 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9227 (pp) REVERT: C 107 PHE cc_start: 0.8725 (m-80) cc_final: 0.8425 (m-80) REVERT: C 219 ARG cc_start: 0.7404 (mpp-170) cc_final: 0.7145 (mpp-170) REVERT: C 404 MET cc_start: 0.8954 (ttt) cc_final: 0.8357 (ptm) REVERT: C 630 MET cc_start: 0.8710 (tpp) cc_final: 0.8313 (tpp) REVERT: C 835 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 926 MET cc_start: 0.8882 (mmm) cc_final: 0.8596 (tpp) REVERT: D 183 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5861 (pm20) REVERT: D 242 ARG cc_start: 0.8961 (tmm-80) cc_final: 0.8499 (tmm-80) REVERT: D 541 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8281 (mtp) REVERT: D 759 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8850 (tm-30) REVERT: D 858 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8144 (tptp) REVERT: D 895 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8492 (mtp180) REVERT: F 507 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8718 (tm-30) REVERT: E 105 GLU cc_start: 0.8184 (pp20) cc_final: 0.7926 (pp20) outliers start: 74 outliers final: 60 residues processed: 250 average time/residue: 0.3897 time to fit residues: 158.4824 Evaluate side-chains 239 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 A residue 183 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 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 44 LEU 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 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 560 LEU 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 835 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 475 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 718 ASP Chi-restraints excluded: chain D residue 759 GLN 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 1033 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1229 THR Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain E residue 104 LEU 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: 0.9990 chunk 149 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.099824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071687 restraints weight = 69701.922| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.95 r_work: 0.2998 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2018 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= 0.124 Angle : 0.550 10.318 38221 Z= 0.288 Chirality : 0.041 0.215 4364 Planarity : 0.004 0.048 4661 Dihedral : 17.996 178.721 4664 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.19 % Allowed : 24.12 % Favored : 73.69 % 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: 0.26 (0.15), residues: 3230 helix: 1.78 (0.15), residues: 1280 sheet: -0.54 (0.29), residues: 324 loop : -1.02 (0.16), residues: 1626 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 0.013 0.001 PHE D1186 TYR 0.042 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 1174) hydrogen bonds : angle 4.33859 ( 3285) metal coordination : bond 0.00501 ( 6) metal coordination : angle 1.74312 ( 6) covalent geometry : bond 0.00279 (27885) covalent geometry : angle 0.54987 (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 246 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8591 (pm20) cc_final: 0.8381 (pm20) REVERT: B 80 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9357 (mp) REVERT: B 95 MET cc_start: 0.8677 (mmt) cc_final: 0.8369 (mmm) REVERT: C 107 PHE cc_start: 0.8682 (m-80) cc_final: 0.8387 (m-80) REVERT: C 219 ARG cc_start: 0.7382 (mpp-170) cc_final: 0.7100 (mpp-170) REVERT: C 404 MET cc_start: 0.8927 (ttt) cc_final: 0.8320 (ptm) REVERT: C 630 MET cc_start: 0.8660 (tpp) cc_final: 0.8157 (tpp) REVERT: C 926 MET cc_start: 0.8778 (mmm) cc_final: 0.8471 (tpp) REVERT: D 183 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: D 242 ARG cc_start: 0.8949 (tmm-80) cc_final: 0.8477 (tmm-80) REVERT: D 541 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: D 759 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8884 (tm-30) REVERT: D 858 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8090 (tptp) REVERT: F 349 TRP cc_start: 0.8513 (m100) cc_final: 0.8035 (m100) REVERT: F 507 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8716 (tm-30) REVERT: E 41 ASP cc_start: 0.8000 (m-30) cc_final: 0.7698 (t0) outliers start: 59 outliers final: 51 residues processed: 235 average time/residue: 0.3810 time to fit residues: 145.9785 Evaluate side-chains 237 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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 A residue 183 VAL 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 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 560 LEU 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 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 718 ASP Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 825 THR 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 423 LEU Chi-restraints excluded: chain E residue 104 LEU 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: 0.0010 chunk 248 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 89 optimal weight: 0.1980 chunk 146 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.101886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.073882 restraints weight = 68823.837| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.93 r_work: 0.3042 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27891 Z= 0.108 Angle : 0.529 10.103 38221 Z= 0.277 Chirality : 0.041 0.180 4364 Planarity : 0.004 0.045 4661 Dihedral : 17.894 179.093 4664 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.16 % Allowed : 24.08 % 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: 0.40 (0.15), residues: 3230 helix: 1.87 (0.15), residues: 1281 sheet: -0.41 (0.29), residues: 321 loop : -0.93 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 938 HIS 0.003 0.001 HIS D 748 PHE 0.013 0.001 PHE D1186 TYR 0.031 0.001 TYR E 56 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 1174) hydrogen bonds : angle 4.19629 ( 3285) metal coordination : bond 0.00236 ( 6) metal coordination : angle 1.26053 ( 6) covalent geometry : bond 0.00238 (27885) covalent geometry : angle 0.52863 (38215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14220.69 seconds wall clock time: 251 minutes 43.90 seconds (15103.90 seconds total)