Starting phenix.real_space_refine on Sat Sep 12 23:46:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t8h_10401/09_2026/6t8h_10401_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8h_10401/09_2026/6t8h_10401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t8h_10401/09_2026/6t8h_10401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8h_10401/09_2026/6t8h_10401.map" model { file = "/net/cci-nas-00/data/ceres_data/6t8h_10401/09_2026/6t8h_10401_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8h_10401/09_2026/6t8h_10401_neut.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 4 6.06 5 P 34 5.49 5 S 75 5.16 5 C 12297 2.51 5 N 3244 2.21 5 O 3710 1.98 5 H 33 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19398 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1950 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3345 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 390} Chain breaks: 1 Chain: "B" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9501 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1121} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1950 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "D" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1950 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "P" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "T" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 347 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10706 SG CYS B 706 102.750 43.270 74.558 1.00 99.36 S ATOM 10728 SG CYS B 709 101.852 42.311 76.372 1.00104.89 S ATOM 10793 SG CYS B 718 101.528 45.234 76.055 1.00 95.92 S ATOM 10814 SG CYS B 721 105.014 45.227 75.754 1.00 97.36 S ATOM 10897 SG CYS B 731 89.968 28.756 58.650 1.00106.91 S ATOM 10921 SG CYS B 734 91.346 27.074 60.823 1.00111.08 S ATOM 11049 SG CYS B 750 93.383 26.785 58.444 1.00114.17 S ATOM 11071 SG CYS B 753 90.050 25.063 58.121 1.00118.66 S ATOM 14062 SG CYS B1123 57.561 45.023 65.105 1.00118.28 S ATOM 14084 SG CYS B1126 58.252 41.730 63.166 1.00120.23 S ATOM 14190 SG CYS B1139 54.932 41.922 65.603 1.00110.09 S ATOM 14210 SG CYS B1142 59.188 42.029 66.786 1.00110.26 S Time building chain proxies: 3.66, per 1000 atoms: 0.19 Number of scatterers: 19398 At special positions: 0 Unit cell: (119.52, 135.29, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Fe 1 26.01 S 75 16.00 P 34 15.00 O 3710 8.00 N 3244 7.00 C 12297 6.00 H 33 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 866.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" ND1 HIS A 560 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 497 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 734 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1126 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1142 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1123 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1139 " Number of angles added : 18 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4376 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 21 sheets defined 35.0% alpha, 20.6% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'E' and resid 9 through 22 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 73 through 82 Processing helix chain 'E' and resid 138 through 152 removed outlier: 3.922A pdb=" N LEU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 209 Processing helix chain 'A' and resid 219 through 244 removed outlier: 4.194A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 464 through 473 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.895A pdb=" N MET A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'B' and resid 5 through 31 removed outlier: 3.692A pdb=" N GLN B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 59 through 72 removed outlier: 3.931A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.719A pdb=" N ALA B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 150 through 169 removed outlier: 4.154A pdb=" N ALA B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.509A pdb=" N MET B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 459 through 476 removed outlier: 4.120A pdb=" N LEU B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.738A pdb=" N VAL B 543 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.500A pdb=" N VAL B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 584 through 592 removed outlier: 3.930A pdb=" N THR B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 removed outlier: 3.650A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 631 through 640 Processing helix chain 'B' and resid 677 through 682 removed outlier: 4.249A pdb=" N GLY B 681 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 693 removed outlier: 3.551A pdb=" N ALA B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 Processing helix chain 'B' and resid 766 through 779 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.831A pdb=" N GLY B 805 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.935A pdb=" N ILE B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 Processing helix chain 'B' and resid 877 through 897 removed outlier: 4.213A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 944 through 951 Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 973 through 977 Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.736A pdb=" N ASN B1006 " --> pdb=" O GLU B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1022 removed outlier: 3.571A pdb=" N TYR B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.596A pdb=" N VAL B1031 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1041 removed outlier: 3.735A pdb=" N LEU B1041 " --> pdb=" O GLU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1085 removed outlier: 4.006A pdb=" N ARG B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B1085 " --> pdb=" O GLN B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1117 Proline residue: B1107 - end of helix removed outlier: 3.999A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1156 removed outlier: 3.669A pdb=" N ILE B1155 " --> pdb=" O SER B1151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B1156 " --> pdb=" O LYS B1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1151 through 1156' Processing helix chain 'B' and resid 1158 through 1169 Processing helix chain 'B' and resid 1172 through 1190 removed outlier: 3.717A pdb=" N PHE B1190 " --> pdb=" O ILE B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1214 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.922A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'D' and resid 9 through 22 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 73 through 82 Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.922A pdb=" N LEU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 209 Processing sheet with id=AA1, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.652A pdb=" N THR E 108 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS C 178 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU C 169 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 154 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.647A pdb=" N ALA E 27 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU E 26 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET E 41 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA E 28 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG E 39 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 52 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 238 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR E 232 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 216 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 195 through 200 removed outlier: 6.557A pdb=" N SER E 154 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU E 169 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS E 178 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 108 " --> pdb=" O LYS E 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 201 removed outlier: 5.344A pdb=" N VAL A 199 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 487 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 565 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 278 removed outlier: 5.462A pdb=" N VAL A 273 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 288 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 275 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N PHE A 329 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 295 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA A 331 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 297 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS A 333 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N TYR A 335 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE A 329 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER A 324 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA A 331 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 322 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.137A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A 354 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU A 399 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 356 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE A 401 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE A 358 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A 599 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 612 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 601 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 608 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.640A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 875 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 935 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.640A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 826 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA B 943 " --> pdb=" O THR B 826 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 828 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 129 removed outlier: 9.164A pdb=" N GLU B 217 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 139 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 219 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 141 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.033A pdb=" N ALA B 654 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.022A pdb=" N ARG B 353 " --> pdb=" O ILE B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 414 through 416 removed outlier: 6.427A pdb=" N ILE B 406 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 560 through 562 removed outlier: 3.677A pdb=" N LYS B 574 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AB6, first strand: chain 'B' and resid 697 through 701 Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AB8, first strand: chain 'B' and resid 832 through 833 Processing sheet with id=AB9, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AC1, first strand: chain 'C' and resid 60 through 62 removed outlier: 4.451A pdb=" N THR C 108 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS D 178 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU D 169 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 154 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.647A pdb=" N ALA C 27 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU C 26 " --> pdb=" O MET C 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET C 41 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA C 28 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG C 39 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 52 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 238 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR C 232 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 216 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.647A pdb=" N ALA D 27 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU D 26 " --> pdb=" O MET D 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET D 41 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA D 28 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG D 39 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 52 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 238 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR D 232 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU D 216 " --> pdb=" O TYR D 232 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 33 1.04 - 1.24: 2164 1.24 - 1.43: 5982 1.43 - 1.62: 11524 1.62 - 1.82: 132 Bond restraints: 19835 Sorted by residual: bond pdb=" C GLN A 345 " pdb=" N LYS A 346 " ideal model delta sigma weight residual 1.327 1.167 0.159 1.39e-02 5.18e+03 1.32e+02 bond pdb=" CA ASN B 541 " pdb=" C ASN B 541 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.41e-02 5.03e+03 2.75e+01 bond pdb=" C TRP B 365 " pdb=" N GLY B 366 " ideal model delta sigma weight residual 1.333 1.289 0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" C ARG B 338 " pdb=" N PRO B 339 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.22e-02 6.72e+03 1.57e+01 bond pdb=" C VAL B 514 " pdb=" N LYS B 515 " ideal model delta sigma weight residual 1.331 1.283 0.047 1.24e-02 6.50e+03 1.45e+01 ... (remaining 19830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.71: 26872 5.71 - 11.41: 72 11.41 - 17.12: 6 17.12 - 22.82: 1 22.82 - 28.53: 1 Bond angle restraints: 26952 Sorted by residual: angle pdb=" O3' DA T 10 " pdb=" P DC T 11 " pdb=" OP1 DC T 11 " ideal model delta sigma weight residual 108.00 79.47 28.53 3.00e+00 1.11e-01 9.04e+01 angle pdb=" O3' DA T 10 " pdb=" P DC T 11 " pdb=" OP2 DC T 11 " ideal model delta sigma weight residual 108.00 86.19 21.81 3.00e+00 1.11e-01 5.28e+01 angle pdb=" C TRP B 540 " pdb=" N ASN B 541 " pdb=" CA ASN B 541 " ideal model delta sigma weight residual 122.38 110.02 12.36 1.81e+00 3.05e-01 4.66e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 123.49 -3.59 6.00e-01 2.78e+00 3.57e+01 angle pdb=" O4 DT P 16 " pdb=" C4 DT P 16 " pdb=" C5 DT P 16 " ideal model delta sigma weight residual 124.90 121.15 3.75 7.00e-01 2.04e+00 2.87e+01 ... (remaining 26947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 11318 15.01 - 30.01: 473 30.01 - 45.02: 156 45.02 - 60.02: 98 60.02 - 75.03: 6 Dihedral angle restraints: 12051 sinusoidal: 5253 harmonic: 6798 Sorted by residual: dihedral pdb=" CA GLY B 437 " pdb=" C GLY B 437 " pdb=" N ASP B 438 " pdb=" CA ASP B 438 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LYS B 668 " pdb=" C LYS B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLU B1093 " pdb=" C GLU B1093 " pdb=" N HIS B1094 " pdb=" CA HIS B1094 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 12048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 3012 0.384 - 0.768: 1 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 1 Chirality restraints: 3014 Sorted by residual: chirality pdb=" P DC T 11 " pdb=" OP1 DC T 11 " pdb=" OP2 DC T 11 " pdb=" O5' DC T 11 " both_signs ideal model delta sigma weight residual True 2.34 0.41 1.92 2.00e-01 2.50e+01 9.22e+01 chirality pdb=" CB VAL B1141 " pdb=" CA VAL B1141 " pdb=" CG1 VAL B1141 " pdb=" CG2 VAL B1141 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE B 830 " pdb=" CA ILE B 830 " pdb=" CG1 ILE B 830 " pdb=" CG2 ILE B 830 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 3011 not shown) Planarity restraints: 3378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 462 " -0.027 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP B 462 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 462 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP B 462 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 462 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 462 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 462 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 462 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 462 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 462 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1093 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C GLU B1093 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU B1093 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B1094 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 435 " -0.007 2.00e-02 2.50e+03 2.17e-02 9.42e+00 pdb=" CG TYR B 435 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 435 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR B 435 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 435 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 435 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 435 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 435 " 0.004 2.00e-02 2.50e+03 ... (remaining 3375 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 64 2.28 - 2.86: 7020 2.86 - 3.44: 23165 3.44 - 4.02: 36905 4.02 - 4.60: 53699 Nonbonded interactions: 120853 Sorted by model distance: nonbonded pdb=" O SER B1103 " pdb=" CD PRO B1107 " model vdw 1.696 3.100 nonbonded pdb=" O PHE B1121 " pdb=" CB LYS B1129 " model vdw 1.704 3.100 nonbonded pdb=" CB PHE B 443 " pdb=" OD2 ASP B1008 " model vdw 1.745 3.100 nonbonded pdb=" CD1 ILE B1106 " pdb=" CD1 ILE B1179 " model vdw 1.819 3.400 nonbonded pdb=" NE2 HIS A 562 " pdb="FE FE A 701 " model vdw 1.875 2.290 ... (remaining 120848 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 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.200 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 23.000 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.013 0.423 19816 Z= 0.608 Angle : 1.224 49.151 26904 Z= 0.640 Chirality : 0.065 1.920 3014 Planarity : 0.006 0.074 3345 Dihedral : 11.304 75.030 7642 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 39.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.62 % Favored : 91.25 % Rotamer: Outliers : 0.94 % Allowed : 2.61 % Favored : 96.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.15), residues: 2332 helix: -2.74 (0.15), residues: 690 sheet: -1.95 (0.21), residues: 514 loop : -2.56 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 931 TYR 0.046 0.004 TYR B 435 PHE 0.034 0.004 PHE B 524 TRP 0.080 0.006 TRP B 462 HIS 0.023 0.003 HIS B1005 Details of bonding type rmsd/Z covalent geometry : bond 0.01184 / 0.57 (19802) covalent geometry : angle 1.10152 / 0.63 (26886) hydrogen bonds : bond 0.15517 / 10.26 ( 886) hydrogen bonds : angle 10.36870 / 6.98 ( 2390) metal coordination : bond 0.23905 / 15.47 ( 14) metal coordination : angle 20.63037 / 13.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 613 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 594 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 ILE cc_start: 0.8266 (pt) cc_final: 0.8001 (tt) REVERT: E 109 ARG cc_start: 0.7218 (mtm180) cc_final: 0.6459 (mtm-85) REVERT: E 181 LEU cc_start: 0.7589 (mt) cc_final: 0.7220 (tp) REVERT: A 212 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.4505 (tptt) REVERT: A 262 SER cc_start: 0.6350 (m) cc_final: 0.6078 (t) REVERT: A 418 ASP cc_start: 0.7675 (t70) cc_final: 0.7459 (t0) REVERT: B 111 THR cc_start: 0.8698 (p) cc_final: 0.8305 (t) REVERT: B 149 SER cc_start: 0.7570 (m) cc_final: 0.7212 (p) REVERT: B 332 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8305 (tppt) REVERT: B 552 TRP cc_start: 0.9098 (t60) cc_final: 0.8878 (t60) REVERT: B 705 LYS cc_start: 0.8718 (tttt) cc_final: 0.8359 (tmtt) REVERT: B 772 ASN cc_start: 0.8433 (t160) cc_final: 0.8203 (t0) REVERT: B 776 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 1099 LYS cc_start: 0.8063 (tptp) cc_final: 0.7178 (tptt) REVERT: B 1103 SER cc_start: 0.3333 (OUTLIER) cc_final: 0.2871 (t) REVERT: B 1145 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5065 (mmtt) REVERT: C 36 ILE cc_start: 0.7466 (mt) cc_final: 0.7186 (mm) REVERT: C 90 ILE cc_start: 0.8629 (mp) cc_final: 0.7845 (mt) REVERT: C 147 ASP cc_start: 0.7891 (m-30) cc_final: 0.6836 (m-30) REVERT: D 22 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8196 (mpp80) REVERT: D 45 ARG cc_start: 0.8201 (mpt180) cc_final: 0.7970 (mmt180) REVERT: D 167 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7130 (ttm170) REVERT: D 238 ARG cc_start: 0.7604 (pmt-80) cc_final: 0.7285 (pmt-80) REVERT: D 240 ILE cc_start: 0.7935 (mt) cc_final: 0.6882 (mt) outliers start: 19 outliers final: 4 residues processed: 609 average time/residue: 0.1768 time to fit residues: 152.2194 Evaluate side-chains 310 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 302 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain D residue 167 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 514 HIS A 587 GLN B 180 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN B 602 ASN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 ASN B 811 ASN ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 ASN B1094 HIS B1102 ASN B1104 HIS C 75 HIS C 223 ASN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 75 HIS D 97 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.139720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104704 restraints weight = 36173.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102424 restraints weight = 23921.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103827 restraints weight = 23658.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103925 restraints weight = 16855.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105559 restraints weight = 14908.640| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19816 Z= 0.144 Angle : 0.737 39.265 26904 Z= 0.345 Chirality : 0.058 1.967 3014 Planarity : 0.005 0.083 3345 Dihedral : 13.150 76.685 2913 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 44.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.96 % Allowed : 11.10 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.16), residues: 2332 helix: -1.00 (0.17), residues: 709 sheet: -1.43 (0.21), residues: 541 loop : -2.00 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 763 TYR 0.021 0.001 TYR B 138 PHE 0.015 0.001 PHE A 586 TRP 0.024 0.002 TRP B 274 HIS 0.004 0.001 HIS A 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (19802) covalent geometry : angle 0.65122 / 0.34 (26886) hydrogen bonds : bond 0.04924 / 3.27 ( 886) hydrogen bonds : angle 7.25027 / 4.89 ( 2390) metal coordination : bond 0.01936 / 1.03 ( 14) metal coordination : angle 13.39465 / 8.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 363 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7302 (mtm180) REVERT: E 181 LEU cc_start: 0.7567 (mt) cc_final: 0.7346 (tp) REVERT: A 212 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.4664 (tptt) REVERT: A 418 ASP cc_start: 0.7853 (t70) cc_final: 0.7537 (t0) REVERT: A 525 LYS cc_start: 0.7350 (mttt) cc_final: 0.6235 (mmtt) REVERT: B 34 ASP cc_start: 0.6815 (m-30) cc_final: 0.6302 (m-30) REVERT: B 149 SER cc_start: 0.7451 (m) cc_final: 0.7023 (p) REVERT: B 256 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7036 (ttmt) REVERT: B 332 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8260 (tppt) REVERT: B 388 GLU cc_start: 0.8386 (pp20) cc_final: 0.8089 (pt0) REVERT: B 552 TRP cc_start: 0.8993 (t60) cc_final: 0.8756 (t60) REVERT: B 772 ASN cc_start: 0.8409 (t0) cc_final: 0.8072 (t0) REVERT: B 776 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 814 TYR cc_start: 0.8541 (m-10) cc_final: 0.8271 (m-10) REVERT: B 911 ASP cc_start: 0.7912 (m-30) cc_final: 0.7711 (m-30) REVERT: B 1099 LYS cc_start: 0.8330 (tptp) cc_final: 0.7689 (tptp) REVERT: B 1103 SER cc_start: 0.6191 (OUTLIER) cc_final: 0.5538 (t) REVERT: C 15 GLN cc_start: 0.8412 (mt0) cc_final: 0.7987 (mm-40) REVERT: C 36 ILE cc_start: 0.7574 (mt) cc_final: 0.7226 (mm) REVERT: C 38 MET cc_start: 0.8068 (tpt) cc_final: 0.7641 (tpt) REVERT: C 177 VAL cc_start: 0.9215 (t) cc_final: 0.8838 (m) REVERT: D 167 ARG cc_start: 0.7312 (ptm160) cc_final: 0.7063 (ptm160) REVERT: D 238 ARG cc_start: 0.7744 (pmt-80) cc_final: 0.7474 (pmt-80) outliers start: 60 outliers final: 35 residues processed: 403 average time/residue: 0.1593 time to fit residues: 94.0342 Evaluate side-chains 318 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 8 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN A 205 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 HIS ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104098 restraints weight = 36186.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102614 restraints weight = 24287.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103947 restraints weight = 23657.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103975 restraints weight = 16690.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104911 restraints weight = 14868.161| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19816 Z= 0.115 Angle : 0.596 25.674 26904 Z= 0.293 Chirality : 0.055 1.947 3014 Planarity : 0.004 0.051 3345 Dihedral : 12.918 79.106 2903 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 43.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.52 % Allowed : 14.50 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2332 helix: -0.09 (0.18), residues: 722 sheet: -1.01 (0.22), residues: 546 loop : -1.67 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.017 0.001 TYR C 231 PHE 0.011 0.001 PHE E 7 TRP 0.026 0.001 TRP B 274 HIS 0.002 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19802) covalent geometry : angle 0.57156 / 0.29 (26886) hydrogen bonds : bond 0.04112 / 2.70 ( 886) hydrogen bonds : angle 6.42263 / 4.33 ( 2390) metal coordination : bond 0.00878 / 0.47 ( 14) metal coordination : angle 6.57491 / 4.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 143 GLU cc_start: 0.6249 (tp30) cc_final: 0.5655 (tp30) REVERT: E 228 GLN cc_start: 0.8234 (tt0) cc_final: 0.7773 (tm-30) REVERT: E 238 ARG cc_start: 0.7792 (pmt-80) cc_final: 0.7556 (pmt-80) REVERT: A 212 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.4829 (tptt) REVERT: B 7 MET cc_start: 0.8261 (tpp) cc_final: 0.7843 (mmm) REVERT: B 34 ASP cc_start: 0.6752 (m-30) cc_final: 0.6312 (m-30) REVERT: B 63 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7853 (tpt170) REVERT: B 310 MET cc_start: 0.7904 (ttp) cc_final: 0.7629 (ttp) REVERT: B 332 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8311 (tppt) REVERT: B 392 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7656 (mttt) REVERT: B 552 TRP cc_start: 0.9031 (t60) cc_final: 0.8568 (t60) REVERT: B 553 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7580 (mtm180) REVERT: B 772 ASN cc_start: 0.8337 (t0) cc_final: 0.8044 (t0) REVERT: B 776 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 818 ASP cc_start: 0.8224 (p0) cc_final: 0.7881 (p0) REVERT: B 1099 LYS cc_start: 0.8347 (tptp) cc_final: 0.8013 (tptp) REVERT: C 15 GLN cc_start: 0.8373 (mt0) cc_final: 0.8073 (mm-40) REVERT: C 22 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8430 (ttm-80) REVERT: C 36 ILE cc_start: 0.7460 (mt) cc_final: 0.7088 (mm) REVERT: C 177 VAL cc_start: 0.9154 (t) cc_final: 0.8866 (m) REVERT: D 167 ARG cc_start: 0.7283 (ptm160) cc_final: 0.6981 (ptm160) outliers start: 51 outliers final: 40 residues processed: 334 average time/residue: 0.1549 time to fit residues: 76.6940 Evaluate side-chains 304 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 141 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 184 optimal weight: 10.0000 chunk 213 optimal weight: 0.2980 chunk 203 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 0.0670 chunk 113 optimal weight: 0.0010 chunk 47 optimal weight: 5.9990 overall best weight: 1.0728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 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 = 0.3882 r_free = 0.3882 target = 0.139370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103698 restraints weight = 36101.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101689 restraints weight = 24894.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102835 restraints weight = 25910.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103303 restraints weight = 17483.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104339 restraints weight = 15642.442| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19816 Z= 0.117 Angle : 0.562 25.665 26904 Z= 0.276 Chirality : 0.055 1.935 3014 Planarity : 0.003 0.045 3345 Dihedral : 12.812 78.310 2900 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 43.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 15.19 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2332 helix: 0.38 (0.19), residues: 721 sheet: -0.91 (0.22), residues: 544 loop : -1.38 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 39 TYR 0.016 0.001 TYR B1169 PHE 0.015 0.001 PHE C 58 TRP 0.014 0.001 TRP A 379 HIS 0.003 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (19802) covalent geometry : angle 0.54587 / 0.28 (26886) hydrogen bonds : bond 0.03732 / 2.43 ( 886) hydrogen bonds : angle 6.05442 / 4.08 ( 2390) metal coordination : bond 0.00776 / 0.43 ( 14) metal coordination : angle 5.14595 / 3.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 GLN cc_start: 0.8684 (mt0) cc_final: 0.8463 (mp10) REVERT: E 143 GLU cc_start: 0.6509 (tp30) cc_final: 0.6126 (tp30) REVERT: E 228 GLN cc_start: 0.8298 (tt0) cc_final: 0.7957 (tt0) REVERT: E 238 ARG cc_start: 0.7766 (pmt-80) cc_final: 0.7522 (pmt-80) REVERT: A 212 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.4838 (tptt) REVERT: A 525 LYS cc_start: 0.7397 (mttt) cc_final: 0.6611 (mttt) REVERT: B 310 MET cc_start: 0.7965 (ttp) cc_final: 0.7647 (ttp) REVERT: B 332 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8299 (tppt) REVERT: B 392 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7630 (mttt) REVERT: B 448 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7929 (tt0) REVERT: B 552 TRP cc_start: 0.9027 (t60) cc_final: 0.8627 (t60) REVERT: B 772 ASN cc_start: 0.8324 (t0) cc_final: 0.8055 (t0) REVERT: B 776 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7293 (mt-10) REVERT: B 818 ASP cc_start: 0.8177 (p0) cc_final: 0.7838 (p0) REVERT: B 1191 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6525 (tm-30) REVERT: C 15 GLN cc_start: 0.8411 (mt0) cc_final: 0.8086 (mm-40) REVERT: C 110 THR cc_start: 0.7921 (m) cc_final: 0.7655 (t) REVERT: C 177 VAL cc_start: 0.9183 (t) cc_final: 0.8867 (m) REVERT: D 167 ARG cc_start: 0.7259 (ptm160) cc_final: 0.6948 (ptm160) outliers start: 59 outliers final: 47 residues processed: 303 average time/residue: 0.1532 time to fit residues: 69.4415 Evaluate side-chains 302 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1211 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 228 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 114 optimal weight: 0.0050 chunk 196 optimal weight: 0.0060 chunk 229 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 153 optimal weight: 0.0060 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 overall best weight: 0.5828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS C 75 HIS ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.140913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106008 restraints weight = 36175.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103648 restraints weight = 26423.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104738 restraints weight = 27454.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105161 restraints weight = 18880.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105758 restraints weight = 16599.065| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19816 Z= 0.094 Angle : 0.536 25.530 26904 Z= 0.262 Chirality : 0.055 1.924 3014 Planarity : 0.003 0.046 3345 Dihedral : 12.722 77.417 2900 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 43.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.86 % Allowed : 15.29 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2332 helix: 0.81 (0.19), residues: 719 sheet: -0.74 (0.22), residues: 546 loop : -1.15 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 22 TYR 0.023 0.001 TYR C 231 PHE 0.012 0.001 PHE A 329 TRP 0.016 0.001 TRP A 379 HIS 0.003 0.000 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (19802) covalent geometry : angle 0.52394 / 0.26 (26886) hydrogen bonds : bond 0.03402 / 2.22 ( 886) hydrogen bonds : angle 5.71479 / 3.85 ( 2390) metal coordination : bond 0.00581 / 0.33 ( 14) metal coordination : angle 4.45778 / 2.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ARG cc_start: 0.7411 (mtm110) cc_final: 0.7173 (mtm-85) REVERT: E 143 GLU cc_start: 0.6639 (tp30) cc_final: 0.6308 (tp30) REVERT: E 242 LEU cc_start: 0.8678 (tp) cc_final: 0.8429 (tt) REVERT: A 212 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.4970 (tptt) REVERT: A 525 LYS cc_start: 0.7390 (mttt) cc_final: 0.6099 (mmtt) REVERT: B 310 MET cc_start: 0.7921 (ttp) cc_final: 0.7574 (ttp) REVERT: B 332 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8342 (tppt) REVERT: B 392 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7553 (mttt) REVERT: B 552 TRP cc_start: 0.8965 (t60) cc_final: 0.8679 (t60) REVERT: B 772 ASN cc_start: 0.8231 (t0) cc_final: 0.8030 (t0) REVERT: B 776 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 1099 LYS cc_start: 0.8327 (tptp) cc_final: 0.7859 (tptp) REVERT: B 1191 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6519 (tm-30) REVERT: C 15 GLN cc_start: 0.8324 (mt0) cc_final: 0.7998 (mm-40) REVERT: C 110 THR cc_start: 0.7777 (m) cc_final: 0.7521 (t) REVERT: C 162 ASN cc_start: 0.7603 (m-40) cc_final: 0.7311 (m-40) REVERT: C 177 VAL cc_start: 0.9111 (t) cc_final: 0.8831 (m) outliers start: 58 outliers final: 44 residues processed: 309 average time/residue: 0.1516 time to fit residues: 70.5495 Evaluate side-chains 293 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1186 ILE Chi-restraints excluded: chain B residue 1211 ARG Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 141 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 75 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN B1005 HIS C 52 ASN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100448 restraints weight = 36283.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099057 restraints weight = 28210.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099390 restraints weight = 33031.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100079 restraints weight = 20755.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100449 restraints weight = 17931.784| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 19816 Z= 0.246 Angle : 0.676 25.753 26904 Z= 0.330 Chirality : 0.057 1.929 3014 Planarity : 0.004 0.050 3345 Dihedral : 12.800 74.821 2900 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 48.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.80 % Allowed : 15.89 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2332 helix: 0.44 (0.19), residues: 725 sheet: -0.79 (0.21), residues: 577 loop : -1.36 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 63 TYR 0.025 0.002 TYR B 354 PHE 0.023 0.002 PHE B 947 TRP 0.015 0.002 TRP B 796 HIS 0.008 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (19802) covalent geometry : angle 0.66295 / 0.33 (26886) hydrogen bonds : bond 0.04102 / 2.69 ( 886) hydrogen bonds : angle 5.76504 / 3.88 ( 2390) metal coordination : bond 0.00915 / 0.49 ( 14) metal coordination : angle 5.12981 / 3.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 244 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: E 109 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7294 (mtm-85) REVERT: E 143 GLU cc_start: 0.6760 (tp30) cc_final: 0.6555 (tp30) REVERT: A 212 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.5072 (tptt) REVERT: A 525 LYS cc_start: 0.7420 (mttt) cc_final: 0.6172 (mmtt) REVERT: B 34 ASP cc_start: 0.7508 (m-30) cc_final: 0.6862 (m-30) REVERT: B 310 MET cc_start: 0.7970 (ttp) cc_final: 0.7622 (ttp) REVERT: B 332 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8385 (tppt) REVERT: B 392 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7659 (mttt) REVERT: B 552 TRP cc_start: 0.9047 (t60) cc_final: 0.8683 (t60) REVERT: B 772 ASN cc_start: 0.8284 (t0) cc_final: 0.8045 (t0) REVERT: B 776 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 15 GLN cc_start: 0.8347 (mt0) cc_final: 0.8032 (mm-40) REVERT: C 110 THR cc_start: 0.7846 (m) cc_final: 0.7611 (t) outliers start: 77 outliers final: 56 residues processed: 287 average time/residue: 0.1473 time to fit residues: 64.0793 Evaluate side-chains 292 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1211 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 233 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 130 optimal weight: 0.0010 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN ** C 228 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 = 0.3859 r_free = 0.3859 target = 0.137647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101796 restraints weight = 36058.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099658 restraints weight = 26229.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100505 restraints weight = 25487.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101281 restraints weight = 17838.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101533 restraints weight = 15937.659| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19816 Z= 0.097 Angle : 0.543 25.490 26904 Z= 0.265 Chirality : 0.055 1.926 3014 Planarity : 0.003 0.043 3345 Dihedral : 12.685 74.371 2900 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 44.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.42 % Allowed : 17.41 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2332 helix: 0.81 (0.19), residues: 738 sheet: -0.72 (0.21), residues: 577 loop : -1.07 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 109 TYR 0.022 0.001 TYR C 231 PHE 0.012 0.001 PHE B 947 TRP 0.018 0.001 TRP A 379 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (19802) covalent geometry : angle 0.53004 / 0.26 (26886) hydrogen bonds : bond 0.03399 / 2.21 ( 886) hydrogen bonds : angle 5.47264 / 3.68 ( 2390) metal coordination : bond 0.00591 / 0.34 ( 14) metal coordination : angle 4.52710 / 2.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: E 109 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7212 (mtm-85) REVERT: E 143 GLU cc_start: 0.6821 (tp30) cc_final: 0.6560 (tp30) REVERT: A 212 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.5073 (tptt) REVERT: A 525 LYS cc_start: 0.7412 (mttt) cc_final: 0.6131 (mmtt) REVERT: B 7 MET cc_start: 0.8417 (tpp) cc_final: 0.7879 (mmm) REVERT: B 34 ASP cc_start: 0.7428 (m-30) cc_final: 0.6762 (m-30) REVERT: B 310 MET cc_start: 0.8014 (ttp) cc_final: 0.7705 (ttp) REVERT: B 332 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8360 (tppt) REVERT: B 552 TRP cc_start: 0.9045 (t60) cc_final: 0.8528 (t60) REVERT: B 772 ASN cc_start: 0.8315 (t0) cc_final: 0.7995 (t0) REVERT: B 776 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 1145 LYS cc_start: 0.5525 (OUTLIER) cc_final: 0.5116 (pptt) REVERT: C 15 GLN cc_start: 0.8420 (mt0) cc_final: 0.8098 (mm-40) REVERT: C 22 ARG cc_start: 0.8742 (ttm110) cc_final: 0.8385 (ttm-80) REVERT: C 110 THR cc_start: 0.7927 (m) cc_final: 0.7670 (t) REVERT: C 177 VAL cc_start: 0.9124 (t) cc_final: 0.8912 (m) outliers start: 49 outliers final: 38 residues processed: 283 average time/residue: 0.1417 time to fit residues: 60.7486 Evaluate side-chains 283 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 155 optimal weight: 5.9990 chunk 188 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 176 optimal weight: 0.0010 chunk 228 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN C 52 ASN ** C 228 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 = 0.3820 r_free = 0.3820 target = 0.134770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099185 restraints weight = 36303.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097090 restraints weight = 25464.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097945 restraints weight = 27529.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098394 restraints weight = 18817.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098863 restraints weight = 16428.957| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19816 Z= 0.191 Angle : 0.612 25.637 26904 Z= 0.298 Chirality : 0.055 1.907 3014 Planarity : 0.004 0.047 3345 Dihedral : 12.701 74.038 2900 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 48.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.96 % Allowed : 17.51 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2332 helix: 0.71 (0.19), residues: 738 sheet: -0.57 (0.22), residues: 571 loop : -1.21 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 109 TYR 0.022 0.001 TYR C 231 PHE 0.018 0.001 PHE B 947 TRP 0.016 0.002 TRP B 274 HIS 0.006 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (19802) covalent geometry : angle 0.59895 / 0.30 (26886) hydrogen bonds : bond 0.03664 / 2.40 ( 886) hydrogen bonds : angle 5.48121 / 3.69 ( 2390) metal coordination : bond 0.00821 / 0.44 ( 14) metal coordination : angle 4.96201 / 3.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7354 (mtm-85) REVERT: E 143 GLU cc_start: 0.6936 (tp30) cc_final: 0.6406 (tp30) REVERT: A 212 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.5182 (tptt) REVERT: A 525 LYS cc_start: 0.7438 (mttt) cc_final: 0.6158 (mmtt) REVERT: B 7 MET cc_start: 0.8499 (tpp) cc_final: 0.7951 (mmm) REVERT: B 310 MET cc_start: 0.8095 (ttp) cc_final: 0.7807 (ttp) REVERT: B 332 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8369 (tppt) REVERT: B 392 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7599 (mttt) REVERT: B 663 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8559 (mtmm) REVERT: B 772 ASN cc_start: 0.8306 (t0) cc_final: 0.8027 (t0) REVERT: B 776 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7504 (mt-10) REVERT: B 1145 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5408 (pptt) REVERT: C 15 GLN cc_start: 0.8394 (mt0) cc_final: 0.8074 (mm-40) REVERT: C 22 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8414 (ttm-80) REVERT: C 110 THR cc_start: 0.7982 (m) cc_final: 0.7709 (t) REVERT: C 177 VAL cc_start: 0.9131 (t) cc_final: 0.8911 (m) outliers start: 60 outliers final: 49 residues processed: 278 average time/residue: 0.1516 time to fit residues: 63.3785 Evaluate side-chains 288 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 147 optimal weight: 0.8980 chunk 229 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 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 = 0.3838 r_free = 0.3838 target = 0.135606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100154 restraints weight = 36625.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099035 restraints weight = 31529.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099502 restraints weight = 34589.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100147 restraints weight = 23044.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100474 restraints weight = 20191.867| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19816 Z= 0.193 Angle : 0.609 25.301 26904 Z= 0.297 Chirality : 0.055 1.903 3014 Planarity : 0.004 0.043 3345 Dihedral : 12.716 72.486 2900 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 48.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.11 % Allowed : 17.76 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2332 helix: 0.65 (0.19), residues: 743 sheet: -0.58 (0.21), residues: 580 loop : -1.21 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 981 TYR 0.020 0.001 TYR C 231 PHE 0.018 0.001 PHE B 947 TRP 0.018 0.002 TRP B 274 HIS 0.006 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (19802) covalent geometry : angle 0.59359 / 0.30 (26886) hydrogen bonds : bond 0.03593 / 2.34 ( 886) hydrogen bonds : angle 5.43274 / 3.66 ( 2390) metal coordination : bond 0.00814 / 0.45 ( 14) metal coordination : angle 5.24765 / 3.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 143 GLU cc_start: 0.7231 (tp30) cc_final: 0.6980 (tp30) REVERT: E 238 ARG cc_start: 0.7994 (pmt-80) cc_final: 0.7367 (ppt170) REVERT: A 212 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.5194 (tptt) REVERT: B 7 MET cc_start: 0.8539 (tpp) cc_final: 0.8092 (mmm) REVERT: B 63 ARG cc_start: 0.8674 (tmt-80) cc_final: 0.8271 (tpm170) REVERT: B 310 MET cc_start: 0.7969 (ttp) cc_final: 0.7667 (ttp) REVERT: B 332 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8434 (tppt) REVERT: B 392 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7586 (mttt) REVERT: B 663 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8541 (mtmm) REVERT: B 772 ASN cc_start: 0.8219 (t0) cc_final: 0.7996 (t0) REVERT: B 776 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 1099 LYS cc_start: 0.8207 (tptp) cc_final: 0.7893 (tptp) REVERT: C 15 GLN cc_start: 0.8279 (mt0) cc_final: 0.7982 (mm-40) REVERT: C 22 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8481 (ttm-80) REVERT: C 110 THR cc_start: 0.7816 (m) cc_final: 0.7577 (t) outliers start: 63 outliers final: 50 residues processed: 275 average time/residue: 0.1525 time to fit residues: 62.9030 Evaluate side-chains 283 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 151 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 chunk 153 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 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 = 0.3842 r_free = 0.3842 target = 0.135801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100330 restraints weight = 36757.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099413 restraints weight = 32314.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100036 restraints weight = 33335.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100437 restraints weight = 22805.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101623 restraints weight = 19788.883| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 19816 Z= 0.189 Angle : 0.775 59.200 26904 Z= 0.424 Chirality : 0.055 1.905 3014 Planarity : 0.004 0.041 3345 Dihedral : 12.723 72.488 2900 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 50.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.61 % Allowed : 18.45 % Favored : 78.93 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2332 helix: 0.65 (0.19), residues: 743 sheet: -0.62 (0.21), residues: 580 loop : -1.22 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 356 TYR 0.020 0.001 TYR C 231 PHE 0.017 0.001 PHE B 947 TRP 0.016 0.002 TRP B 274 HIS 0.005 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (19802) covalent geometry : angle 0.76344 / 0.42 (26886) hydrogen bonds : bond 0.03636 / 2.38 ( 886) hydrogen bonds : angle 5.42975 / 3.66 ( 2390) metal coordination : bond 0.00753 / 0.41 ( 14) metal coordination : angle 5.25028 / 3.24 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 143 GLU cc_start: 0.7280 (tp30) cc_final: 0.6956 (tp30) REVERT: E 238 ARG cc_start: 0.7969 (pmt-80) cc_final: 0.7361 (ppt170) REVERT: A 212 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.5182 (tptt) REVERT: B 7 MET cc_start: 0.8535 (tpp) cc_final: 0.8093 (mmm) REVERT: B 63 ARG cc_start: 0.8674 (tmt-80) cc_final: 0.8280 (tpm170) REVERT: B 310 MET cc_start: 0.7927 (ttp) cc_final: 0.7636 (ttp) REVERT: B 332 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8426 (tppt) REVERT: B 392 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7564 (mttt) REVERT: B 772 ASN cc_start: 0.8208 (t0) cc_final: 0.7988 (t0) REVERT: B 776 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7509 (mt-10) REVERT: B 1099 LYS cc_start: 0.8183 (tptp) cc_final: 0.7870 (tptp) REVERT: B 1145 LYS cc_start: 0.5050 (OUTLIER) cc_final: 0.4380 (mmmt) REVERT: C 15 GLN cc_start: 0.8295 (mt0) cc_final: 0.7992 (mm-40) REVERT: C 22 ARG cc_start: 0.8770 (ttm110) cc_final: 0.8496 (ttm-80) REVERT: C 110 THR cc_start: 0.7825 (m) cc_final: 0.7589 (t) outliers start: 53 outliers final: 50 residues processed: 264 average time/residue: 0.1561 time to fit residues: 62.1248 Evaluate side-chains 285 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 223 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 106 optimal weight: 0.0670 chunk 213 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 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 = 0.3843 r_free = 0.3843 target = 0.135811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100752 restraints weight = 36900.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099406 restraints weight = 32516.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100337 restraints weight = 32940.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100596 restraints weight = 23183.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101563 restraints weight = 20067.139| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 19816 Z= 0.189 Angle : 0.775 59.200 26904 Z= 0.424 Chirality : 0.055 1.905 3014 Planarity : 0.004 0.041 3345 Dihedral : 12.723 72.488 2900 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 50.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.61 % Allowed : 18.50 % Favored : 78.89 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2332 helix: 0.65 (0.19), residues: 743 sheet: -0.62 (0.21), residues: 580 loop : -1.22 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 356 TYR 0.020 0.001 TYR C 231 PHE 0.017 0.001 PHE B 947 TRP 0.016 0.002 TRP B 274 HIS 0.005 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (19802) covalent geometry : angle 0.76344 / 0.42 (26886) hydrogen bonds : bond 0.03636 / 2.38 ( 886) hydrogen bonds : angle 5.42975 / 3.66 ( 2390) metal coordination : bond 0.00753 / 0.41 ( 14) metal coordination : angle 5.25028 / 3.24 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.42 seconds wall clock time: 52 minutes 50.43 seconds (3170.43 seconds total)