Starting phenix.real_space_refine on Sat Aug 8 01:40:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.cif" model { file = "/net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asw_15623/08_2026/8asw_15623.map" } resolution = 3.96 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= 0.001 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 73 5.49 5 S 100 5.16 5 C 15403 2.51 5 N 4219 2.21 5 O 4982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24781 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1255, 10014 Classifications: {'peptide': 1255} Link IDs: {'PTRANS': 41, 'TRANS': 1213} Chain breaks: 1 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6177 Classifications: {'peptide': 772} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 746} Chain breaks: 1 Chain: "C" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4236 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2769 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "X" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1559 Classifications: {'RNAv2': 73} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 27, 'rna3p_pyr': 27} Link IDs: {'rna2p': 19, 'rna3p': 53} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'5AD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17020 SG CYS C 121 101.938 65.799 107.346 1.00 54.66 S ATOM 16995 SG CYS C 118 106.716 63.440 108.105 1.00 58.89 S ATOM 16920 SG CYS C 108 101.260 59.927 108.980 1.00 47.95 S Time building chain proxies: 5.12, per 1000 atoms: 0.21 Number of scatterers: 24781 At special positions: 0 Unit cell: (174.96, 150.66, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 100 16.00 P 73 15.00 O 4982 8.00 N 4219 7.00 C 15403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 978.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE2 SF4 C 601 " - pdb=" NE2 HIS C 110 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 121 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 108 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 118 " Number of angles added : 9 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 31 sheets defined 30.9% alpha, 22.5% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.576A pdb=" N TRP A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 756 removed outlier: 3.566A pdb=" N VAL A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.614A pdb=" N ASP A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 786 through 794 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.652A pdb=" N LEU A 800 " --> pdb=" O ARG A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.705A pdb=" N TYR A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 843 " --> pdb=" O MET A 839 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 868 removed outlier: 3.638A pdb=" N SER A 868 " --> pdb=" O ASN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 876 through 887 removed outlier: 3.534A pdb=" N ILE A 880 " --> pdb=" O TYR A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 902 removed outlier: 3.565A pdb=" N ALA A 895 " --> pdb=" O ASN A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 919 Processing helix chain 'A' and resid 920 through 931 Processing helix chain 'A' and resid 934 through 942 Processing helix chain 'A' and resid 947 through 960 removed outlier: 3.593A pdb=" N TYR A 951 " --> pdb=" O ASP A 947 " (cutoff:3.500A) Proline residue: A 953 - end of helix Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 976 through 985 Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 995 through 1005 Processing helix chain 'A' and resid 1006 through 1014 Processing helix chain 'A' and resid 1017 through 1036 Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 4.329A pdb=" N MET A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1061 Processing helix chain 'A' and resid 1063 through 1075 Processing helix chain 'A' and resid 1078 through 1094 removed outlier: 3.526A pdb=" N VAL A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1106 Processing helix chain 'A' and resid 1109 through 1120 Processing helix chain 'A' and resid 1123 through 1133 Processing helix chain 'A' and resid 1136 through 1142 removed outlier: 4.493A pdb=" N GLU A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1172 Processing helix chain 'A' and resid 1259 through 1283 removed outlier: 4.562A pdb=" N ARG A1265 " --> pdb=" O ARG A1261 " (cutoff:3.500A) Proline residue: A1271 - end of helix Processing helix chain 'A' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ALA A1289 " --> pdb=" O MET A1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.916A pdb=" N THR B 750 " --> pdb=" O GLU B 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 39 removed outlier: 4.232A pdb=" N SER C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.661A pdb=" N TYR C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 74 through 82 removed outlier: 4.168A pdb=" N TYR C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.491A pdb=" N TYR C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.844A pdb=" N LEU C 186 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 204 Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.939A pdb=" N GLN C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 301 through 314 removed outlier: 3.955A pdb=" N ARG C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 350 through 364 removed outlier: 3.597A pdb=" N LEU C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.921A pdb=" N GLN C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 522 removed outlier: 3.539A pdb=" N LEU C 511 " --> pdb=" O GLY C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 538 removed outlier: 3.624A pdb=" N ARG C 538 " --> pdb=" O VAL C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'D' and resid 1019 through 1034 removed outlier: 3.860A pdb=" N VAL D1023 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1045 Processing helix chain 'D' and resid 1051 through 1062 removed outlier: 4.051A pdb=" N SER D1060 " --> pdb=" O GLY D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1075 removed outlier: 3.572A pdb=" N ALA D1067 " --> pdb=" O ARG D1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1093 removed outlier: 3.536A pdb=" N SER D1089 " --> pdb=" O GLU D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1106 removed outlier: 3.616A pdb=" N ALA D1099 " --> pdb=" O ARG D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1119 Processing helix chain 'D' and resid 1122 through 1132 Processing helix chain 'D' and resid 1136 through 1143 removed outlier: 4.284A pdb=" N GLU D1140 " --> pdb=" O ASP D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1169 Processing helix chain 'D' and resid 1214 through 1218 removed outlier: 3.882A pdb=" N LYS D1217 " --> pdb=" O TYR D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1227 through 1231 removed outlier: 4.103A pdb=" N THR D1230 " --> pdb=" O SER D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1283 Proline residue: D1271 - end of helix Processing helix chain 'D' and resid 1285 through 1305 removed outlier: 3.602A pdb=" N ALA D1289 " --> pdb=" O MET D1285 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D1305 " --> pdb=" O ASP D1301 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.529A pdb=" N ILE A 22 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 425 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP A 423 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.529A pdb=" N ILE A 22 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 425 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP A 423 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR A 400 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 49 removed outlier: 7.199A pdb=" N VAL A 62 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 71 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 87 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 73 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 83 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.950A pdb=" N VAL A 160 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A 148 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 158 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP A 150 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 156 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A 170 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 255 removed outlier: 6.001A pdb=" N SER A 289 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 294 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 310 removed outlier: 4.900A pdb=" N GLY A 345 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362 removed outlier: 3.756A pdb=" N SER A 359 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 391 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR A 381 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 389 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 441 through 446 Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 480 removed outlier: 6.559A pdb=" N LEU A 495 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 517 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 497 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 529 through 536 removed outlier: 3.715A pdb=" N SER A 529 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 544 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 533 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 542 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE A 535 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 540 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A 551 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU A 571 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A 553 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 569 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 555 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 565 " --> pdb=" O ASP A 557 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 576 through 581 removed outlier: 3.978A pdb=" N THR A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN A 599 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 608 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 624 removed outlier: 4.213A pdb=" N ALA A 661 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA A 655 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AB6, first strand: chain 'A' and resid 716 through 721 removed outlier: 5.568A pdb=" N LEU A 717 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLN A 730 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TRP C 442 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG C 463 " --> pdb=" O TRP C 442 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 444 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG C 461 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU C 446 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C 459 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR C 448 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 485 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG C 463 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL C 483 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER C 481 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 532 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 483 " --> pdb=" O ILE C 532 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 5 through 12 removed outlier: 6.509A pdb=" N ILE B 5 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA B 786 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER B 784 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AB9, first strand: chain 'B' and resid 62 through 68 removed outlier: 3.704A pdb=" N CYS B 64 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE B 73 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 98 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS B 87 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N CYS B 96 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 107 through 113 removed outlier: 3.589A pdb=" N ALA B 109 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG B 130 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU B 140 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 153 through 162 removed outlier: 6.968A pdb=" N GLY B 171 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 156 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 169 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU B 158 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 167 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 160 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 165 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY B 172 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER B 181 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 194 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ILE B 183 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS B 192 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.541A pdb=" N ILE B 230 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 276 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 232 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG B 236 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 288 removed outlier: 6.663A pdb=" N GLU B 309 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N CYS B 319 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.700A pdb=" N THR B 369 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 393 removed outlier: 6.295A pdb=" N THR B 409 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG B 434 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 411 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 428 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR B 417 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N ILE B 426 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 444 through 447 removed outlier: 6.608A pdb=" N SER B 464 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 561 through 566 removed outlier: 6.774A pdb=" N ALA B 576 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 564 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 574 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE B 566 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU B 572 " --> pdb=" O ILE B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 609 through 614 removed outlier: 5.412A pdb=" N GLU B 634 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 656 through 661 removed outlier: 6.904A pdb=" N ALA B 673 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 659 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 671 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TRP B 661 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL B 669 " --> pdb=" O TRP B 661 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 679 " --> pdb=" O SER B 697 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 697 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 681 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 704 through 709 removed outlier: 7.141A pdb=" N ILE B 729 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN B 744 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 731 " --> pdb=" O ILE B 742 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.702A pdb=" N VAL C 174 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY C 226 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 230 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 251 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 253 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 255 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER C 292 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU C 324 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 331 through 332 removed outlier: 3.671A pdb=" N SER C 385 " --> pdb=" O VAL C 331 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 10913 1.43 - 1.64: 14354 1.64 - 1.85: 149 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 25428 Sorted by residual: bond pdb=" N ILE A 770 " pdb=" CA ILE A 770 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.27e+00 bond pdb=" N ARG A 769 " pdb=" CA ARG A 769 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.93e+00 bond pdb=" N ASN A 771 " pdb=" CA ASN A 771 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.66e+00 bond pdb=" N LEU A 772 " pdb=" CA LEU A 772 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.82e+00 bond pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.06e-02 8.90e+03 4.82e+00 ... (remaining 25423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 34059 2.47 - 4.93: 647 4.93 - 7.40: 51 7.40 - 9.87: 6 9.87 - 12.34: 5 Bond angle restraints: 34768 Sorted by residual: angle pdb=" C ARG A 350 " pdb=" N LEU A 351 " pdb=" CA LEU A 351 " ideal model delta sigma weight residual 120.68 128.70 -8.02 1.52e+00 4.33e-01 2.78e+01 angle pdb=" N ILE A 804 " pdb=" CA ILE A 804 " pdb=" C ILE A 804 " ideal model delta sigma weight residual 111.91 107.24 4.67 8.90e-01 1.26e+00 2.75e+01 angle pdb=" C ASN A1306 " pdb=" CA ASN A1306 " pdb=" CB ASN A1306 " ideal model delta sigma weight residual 115.79 110.61 5.18 1.19e+00 7.06e-01 1.90e+01 angle pdb=" C3' G X 15 " pdb=" O3' G X 15 " pdb=" P U X 16 " ideal model delta sigma weight residual 119.70 124.70 -5.00 1.20e+00 6.94e-01 1.74e+01 angle pdb=" C3' U X 65 " pdb=" O3' U X 65 " pdb=" P U X 66 " ideal model delta sigma weight residual 119.70 124.69 -4.99 1.20e+00 6.94e-01 1.73e+01 ... (remaining 34763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 14388 33.29 - 66.58: 728 66.58 - 99.86: 91 99.86 - 133.15: 2 133.15 - 166.44: 4 Dihedral angle restraints: 15213 sinusoidal: 6717 harmonic: 8496 Sorted by residual: dihedral pdb=" C4' U X 17 " pdb=" C3' U X 17 " pdb=" C2' U X 17 " pdb=" C1' U X 17 " ideal model delta sinusoidal sigma weight residual 36.34 -37.50 73.84 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' G X 46 " pdb=" C3' G X 46 " pdb=" C2' G X 46 " pdb=" C1' G X 46 " ideal model delta sinusoidal sigma weight residual 36.35 -36.86 73.21 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' U X 20 " pdb=" C3' U X 20 " pdb=" C2' U X 20 " pdb=" C1' U X 20 " ideal model delta sinusoidal sigma weight residual 36.34 -36.79 73.14 1 3.10e+00 1.04e-01 7.09e+02 ... (remaining 15210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3380 0.070 - 0.140: 436 0.140 - 0.211: 24 0.211 - 0.281: 87 0.281 - 0.351: 14 Chirality restraints: 3941 Sorted by residual: chirality pdb=" P U X 16 " pdb=" OP1 U X 16 " pdb=" OP2 U X 16 " pdb=" O5' U X 16 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" P C X 48 " pdb=" OP1 C X 48 " pdb=" OP2 C X 48 " pdb=" O5' C X 48 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" P U X 66 " pdb=" OP1 U X 66 " pdb=" OP2 U X 66 " pdb=" O5' U X 66 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 3938 not shown) Planarity restraints: 4195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 768 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C HIS A 768 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS A 768 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 769 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D1285 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C MET D1285 " -0.039 2.00e-02 2.50e+03 pdb=" O MET D1285 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG D1286 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 488 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C VAL C 488 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL C 488 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 489 " 0.013 2.00e-02 2.50e+03 ... (remaining 4192 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 570 2.63 - 3.20: 23711 3.20 - 3.76: 40259 3.76 - 4.33: 55270 4.33 - 4.90: 88941 Nonbonded interactions: 208751 Sorted by model distance: nonbonded pdb=" O2' U X 65 " pdb=" OP1 U X 66 " model vdw 2.061 3.040 nonbonded pdb=" OG1 THR A 665 " pdb=" OG1 THR A 677 " model vdw 2.100 3.040 nonbonded pdb=" OD1 ASP A1005 " pdb=" OH TYR A1007 " model vdw 2.111 3.040 nonbonded pdb=" OE2 GLU A1181 " pdb=" OG SER A1202 " model vdw 2.112 3.040 nonbonded pdb=" OG SER C 292 " pdb=" OH TYR C 313 " model vdw 2.116 3.040 ... (remaining 208746 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 31.540 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.005 0.121 25432 Z= 0.249 Angle : 0.871 47.763 34777 Z= 0.432 Chirality : 0.060 0.351 3941 Planarity : 0.004 0.057 4195 Dihedral : 19.302 166.439 9731 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.51 % Favored : 89.25 % Rotamer: Outliers : 0.71 % Allowed : 28.59 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.15), residues: 2883 helix: 0.02 (0.18), residues: 789 sheet: -1.33 (0.20), residues: 683 loop : -2.36 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 360 TYR 0.025 0.002 TYR C 216 PHE 0.016 0.002 PHE C 319 TRP 0.021 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.25 (25428) covalent geometry : angle 0.79882 / 0.43 (34768) hydrogen bonds : bond 0.14678 / 9.67 ( 956) hydrogen bonds : angle 6.51793 / 4.44 ( 2637) metal coordination : bond 0.06425 / 3.08 ( 4) metal coordination : angle 21.63959 / 10.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1328 TYR cc_start: 0.0718 (OUTLIER) cc_final: 0.0394 (t80) outliers start: 18 outliers final: 8 residues processed: 119 average time/residue: 0.1592 time to fit residues: 31.8107 Evaluate side-chains 110 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1328 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 650 ASN ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 142 HIS ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.084979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066266 restraints weight = 109287.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066201 restraints weight = 73503.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066533 restraints weight = 57038.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066653 restraints weight = 48792.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066736 restraints weight = 44240.982| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25432 Z= 0.174 Angle : 0.912 52.962 34777 Z= 0.389 Chirality : 0.074 1.380 3941 Planarity : 0.004 0.048 4195 Dihedral : 13.369 169.203 4064 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.78 % Favored : 91.05 % Rotamer: Outliers : 3.02 % Allowed : 25.96 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.15), residues: 2883 helix: 0.00 (0.18), residues: 809 sheet: -1.30 (0.20), residues: 664 loop : -2.29 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1286 TYR 0.026 0.001 TYR C 216 PHE 0.014 0.001 PHE A 285 TRP 0.012 0.001 TRP B 308 HIS 0.006 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (25428) covalent geometry : angle 0.84613 / 0.39 (34768) hydrogen bonds : bond 0.04881 / 3.31 ( 956) hydrogen bonds : angle 5.53945 / 3.74 ( 2637) metal coordination : bond 0.04140 / 1.99 ( 4) metal coordination : angle 21.15556 / 10.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 112 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7630 (p0) cc_final: 0.7157 (p0) REVERT: A 675 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 842 TYR cc_start: 0.6815 (t80) cc_final: 0.6596 (t80) REVERT: B 781 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7501 (mtt90) REVERT: C 553 MET cc_start: 0.8456 (mmm) cc_final: 0.8239 (mmt) REVERT: D 1328 TYR cc_start: 0.1366 (OUTLIER) cc_final: 0.0805 (t80) outliers start: 77 outliers final: 31 residues processed: 182 average time/residue: 0.1556 time to fit residues: 47.5721 Evaluate side-chains 137 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 6 optimal weight: 8.9990 chunk 215 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.083672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064817 restraints weight = 109924.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064675 restraints weight = 67142.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064950 restraints weight = 58586.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065076 restraints weight = 51248.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065398 restraints weight = 43298.303| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 25432 Z= 0.235 Angle : 0.866 58.982 34777 Z= 0.378 Chirality : 0.063 1.302 3941 Planarity : 0.004 0.046 4195 Dihedral : 13.303 161.472 4055 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.20 % Favored : 89.63 % Rotamer: Outliers : 5.06 % Allowed : 25.29 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.19 (0.15), residues: 2883 helix: -0.09 (0.18), residues: 811 sheet: -1.33 (0.20), residues: 660 loop : -2.36 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1213 TYR 0.023 0.002 TYR C 136 PHE 0.021 0.002 PHE D1296 TRP 0.013 0.001 TRP B 308 HIS 0.009 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (25428) covalent geometry : angle 0.79245 / 0.38 (34768) hydrogen bonds : bond 0.04550 / 3.07 ( 956) hydrogen bonds : angle 5.47986 / 3.70 ( 2637) metal coordination : bond 0.05357 / 2.59 ( 4) metal coordination : angle 21.77348 / 10.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 106 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7602 (p0) cc_final: 0.7107 (p0) REVERT: A 169 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (pp) REVERT: B 713 MET cc_start: 0.4672 (tpp) cc_final: 0.3298 (ttp) REVERT: B 781 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7561 (mtt90) REVERT: C 338 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6722 (t80) REVERT: D 1253 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5842 (tp30) REVERT: D 1328 TYR cc_start: 0.1608 (OUTLIER) cc_final: 0.0942 (t80) outliers start: 129 outliers final: 76 residues processed: 227 average time/residue: 0.1403 time to fit residues: 53.2535 Evaluate side-chains 181 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 100 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1253 GLU Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 111 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 GLN ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.082989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064136 restraints weight = 109426.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064062 restraints weight = 68543.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064447 restraints weight = 57696.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064493 restraints weight = 50036.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064662 restraints weight = 43241.016| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 25432 Z= 0.272 Angle : 0.879 60.652 34777 Z= 0.388 Chirality : 0.062 1.310 3941 Planarity : 0.005 0.043 4195 Dihedral : 13.146 160.263 4055 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.44 % Favored : 89.39 % Rotamer: Outliers : 6.35 % Allowed : 25.37 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.36 (0.15), residues: 2883 helix: -0.25 (0.18), residues: 812 sheet: -1.50 (0.20), residues: 677 loop : -2.43 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 21 TYR 0.022 0.002 TYR C 136 PHE 0.017 0.002 PHE A 413 TRP 0.014 0.001 TRP B 682 HIS 0.010 0.001 HIS A1290 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 (25428) covalent geometry : angle 0.80564 / 0.39 (34768) hydrogen bonds : bond 0.04688 / 3.18 ( 956) hydrogen bonds : angle 5.55119 / 3.74 ( 2637) metal coordination : bond 0.06414 / 3.10 ( 4) metal coordination : angle 21.94371 / 11.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 98 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7597 (p0) cc_final: 0.7116 (p0) REVERT: A 169 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (pp) REVERT: A 252 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 355 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6785 (mm-30) REVERT: A 439 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8526 (p0) REVERT: A 588 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 1125 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5293 (mm) REVERT: B 713 MET cc_start: 0.4772 (tpp) cc_final: 0.3133 (ttp) REVERT: B 781 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7698 (mtt90) REVERT: C 131 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6384 (p90) REVERT: C 225 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8850 (t) REVERT: C 338 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6744 (t80) REVERT: D 1253 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5882 (tp30) REVERT: D 1328 TYR cc_start: 0.1667 (OUTLIER) cc_final: 0.0580 (t80) outliers start: 162 outliers final: 115 residues processed: 251 average time/residue: 0.1389 time to fit residues: 58.5405 Evaluate side-chains 220 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 93 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1021 GLN Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1218 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1253 GLU Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 178 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 240 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 102 optimal weight: 0.0370 chunk 229 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 236 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 484 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 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 = 0.3828 r_free = 0.3828 target = 0.085406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066609 restraints weight = 108498.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066805 restraints weight = 68276.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066908 restraints weight = 54777.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067086 restraints weight = 50755.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067359 restraints weight = 42098.427| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25432 Z= 0.125 Angle : 0.764 50.608 34777 Z= 0.337 Chirality : 0.057 1.245 3941 Planarity : 0.004 0.046 4195 Dihedral : 12.903 160.138 4055 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.91 % Favored : 91.92 % Rotamer: Outliers : 3.29 % Allowed : 27.61 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.15), residues: 2883 helix: 0.04 (0.18), residues: 805 sheet: -1.27 (0.20), residues: 670 loop : -2.22 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 282 TYR 0.015 0.001 TYR C 136 PHE 0.027 0.001 PHE D1296 TRP 0.009 0.001 TRP A 255 HIS 0.007 0.001 HIS A1290 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (25428) covalent geometry : angle 0.70551 / 0.34 (34768) hydrogen bonds : bond 0.03822 / 2.53 ( 956) hydrogen bonds : angle 5.18290 / 3.48 ( 2637) metal coordination : bond 0.03269 / 1.57 ( 4) metal coordination : angle 18.31676 / 9.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 118 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7624 (p0) cc_final: 0.7151 (p0) REVERT: A 169 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 408 ASP cc_start: 0.6930 (p0) cc_final: 0.6535 (p0) REVERT: A 1037 MET cc_start: 0.7111 (tpt) cc_final: 0.6884 (tpt) REVERT: B 650 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7570 (ttpt) REVERT: B 713 MET cc_start: 0.4474 (tpp) cc_final: 0.2891 (ttp) REVERT: B 781 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7489 (mtt90) REVERT: C 152 ASP cc_start: 0.7617 (t0) cc_final: 0.7337 (t0) REVERT: D 1068 MET cc_start: 0.6986 (mtp) cc_final: 0.6369 (ptp) REVERT: D 1253 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5728 (tp30) REVERT: D 1285 MET cc_start: 0.7831 (tpp) cc_final: 0.7031 (mtp) REVERT: D 1328 TYR cc_start: 0.1727 (OUTLIER) cc_final: 0.0846 (t80) outliers start: 84 outliers final: 49 residues processed: 193 average time/residue: 0.1372 time to fit residues: 44.6796 Evaluate side-chains 157 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1253 GLU Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 185 optimal weight: 4.9990 chunk 112 optimal weight: 0.0670 chunk 156 optimal weight: 9.9990 chunk 275 optimal weight: 40.0000 chunk 263 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 161 optimal weight: 0.0770 chunk 121 optimal weight: 1.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 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 = 0.3815 r_free = 0.3815 target = 0.084788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066064 restraints weight = 108786.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065905 restraints weight = 74819.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066327 restraints weight = 57079.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066505 restraints weight = 47936.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066531 restraints weight = 43414.323| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25432 Z= 0.156 Angle : 0.766 52.087 34777 Z= 0.338 Chirality : 0.056 1.218 3941 Planarity : 0.004 0.047 4195 Dihedral : 12.813 159.715 4055 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 4.43 % Allowed : 26.98 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.15), residues: 2883 helix: 0.12 (0.18), residues: 801 sheet: -1.21 (0.20), residues: 670 loop : -2.18 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.018 0.001 TYR C 113 PHE 0.021 0.001 PHE C 205 TRP 0.008 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (25428) covalent geometry : angle 0.70406 / 0.34 (34768) hydrogen bonds : bond 0.03875 / 2.57 ( 956) hydrogen bonds : angle 5.12115 / 3.45 ( 2637) metal coordination : bond 0.04295 / 2.07 ( 4) metal coordination : angle 18.80903 / 9.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 106 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7662 (p0) cc_final: 0.7165 (p0) REVERT: A 169 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8268 (pp) REVERT: A 252 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 588 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8499 (tt) REVERT: A 1147 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7092 (tp) REVERT: B 650 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7539 (ttpt) REVERT: B 713 MET cc_start: 0.4506 (tpp) cc_final: 0.2871 (ttp) REVERT: B 781 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7174 (mtt-85) REVERT: C 225 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8767 (t) REVERT: D 1068 MET cc_start: 0.7005 (mtp) cc_final: 0.6373 (ptp) REVERT: D 1328 TYR cc_start: 0.1737 (OUTLIER) cc_final: 0.0759 (t80) outliers start: 113 outliers final: 78 residues processed: 209 average time/residue: 0.1400 time to fit residues: 49.0964 Evaluate side-chains 185 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 99 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 112 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 247 optimal weight: 0.5980 chunk 199 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 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 = 0.3773 r_free = 0.3773 target = 0.082976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064095 restraints weight = 108870.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064172 restraints weight = 69139.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064370 restraints weight = 58283.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064516 restraints weight = 49734.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064843 restraints weight = 42850.616| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 25432 Z= 0.272 Angle : 0.867 60.783 34777 Z= 0.386 Chirality : 0.058 1.197 3941 Planarity : 0.005 0.052 4195 Dihedral : 12.953 159.593 4055 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.58 % Favored : 89.25 % Rotamer: Outliers : 5.37 % Allowed : 26.24 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.15), residues: 2883 helix: -0.14 (0.18), residues: 805 sheet: -1.39 (0.20), residues: 679 loop : -2.35 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 282 TYR 0.018 0.002 TYR C 136 PHE 0.028 0.002 PHE D1296 TRP 0.013 0.001 TRP B 682 HIS 0.009 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (25428) covalent geometry : angle 0.79222 / 0.38 (34768) hydrogen bonds : bond 0.04504 / 2.99 ( 956) hydrogen bonds : angle 5.40736 / 3.66 ( 2637) metal coordination : bond 0.06398 / 3.09 ( 4) metal coordination : angle 21.93821 / 11.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 93 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7633 (p0) cc_final: 0.7147 (p0) REVERT: A 169 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8199 (pp) REVERT: A 252 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 588 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8519 (tt) REVERT: A 1147 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7108 (tp) REVERT: B 650 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7738 (ttpt) REVERT: B 713 MET cc_start: 0.4616 (tpp) cc_final: 0.3025 (ttp) REVERT: B 781 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7751 (mtt90) REVERT: C 131 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.6388 (p90) REVERT: C 225 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8850 (t) REVERT: C 338 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6622 (t80) REVERT: D 1125 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6819 (mp) REVERT: D 1328 TYR cc_start: 0.1894 (OUTLIER) cc_final: 0.0931 (t80) outliers start: 137 outliers final: 103 residues processed: 224 average time/residue: 0.1349 time to fit residues: 51.3932 Evaluate side-chains 206 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 92 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1125 ILE Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 222 optimal weight: 0.8980 chunk 223 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 HIS ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.085451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066843 restraints weight = 108076.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066604 restraints weight = 75528.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067056 restraints weight = 57390.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067253 restraints weight = 49000.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067337 restraints weight = 43183.855| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25432 Z= 0.124 Angle : 0.757 50.788 34777 Z= 0.335 Chirality : 0.055 1.130 3941 Planarity : 0.004 0.048 4195 Dihedral : 12.729 160.624 4053 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.60 % Favored : 92.23 % Rotamer: Outliers : 3.53 % Allowed : 28.20 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.95 (0.15), residues: 2883 helix: 0.07 (0.18), residues: 801 sheet: -1.15 (0.20), residues: 654 loop : -2.20 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 282 TYR 0.012 0.001 TYR C 136 PHE 0.026 0.001 PHE D1296 TRP 0.012 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25428) covalent geometry : angle 0.69692 / 0.33 (34768) hydrogen bonds : bond 0.03714 / 2.42 ( 956) hydrogen bonds : angle 5.10334 / 3.44 ( 2637) metal coordination : bond 0.03528 / 1.70 ( 4) metal coordination : angle 18.35267 / 9.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 114 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7606 (p0) cc_final: 0.7125 (p0) REVERT: A 169 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8238 (pp) REVERT: A 252 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 1021 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: A 1037 MET cc_start: 0.6764 (tpt) cc_final: 0.6541 (tpt) REVERT: A 1147 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7085 (tp) REVERT: B 650 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7546 (ttpt) REVERT: B 713 MET cc_start: 0.4448 (tpp) cc_final: 0.2821 (ttp) REVERT: B 781 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7606 (mtt90) REVERT: C 225 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8772 (t) REVERT: D 1285 MET cc_start: 0.7987 (tpp) cc_final: 0.6843 (mtp) REVERT: D 1328 TYR cc_start: 0.1627 (OUTLIER) cc_final: 0.0412 (t80) outliers start: 90 outliers final: 68 residues processed: 196 average time/residue: 0.1455 time to fit residues: 47.7494 Evaluate side-chains 180 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 104 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1021 GLN Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 132 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 198 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 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 = 0.3807 r_free = 0.3807 target = 0.084456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065703 restraints weight = 108960.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065815 restraints weight = 74497.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065960 restraints weight = 57297.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066128 restraints weight = 51046.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066220 restraints weight = 45306.740| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25432 Z= 0.158 Angle : 0.771 52.499 34777 Z= 0.341 Chirality : 0.054 1.111 3941 Planarity : 0.004 0.047 4195 Dihedral : 12.705 160.485 4053 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.16 % Favored : 90.67 % Rotamer: Outliers : 3.73 % Allowed : 28.00 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.15), residues: 2883 helix: 0.09 (0.18), residues: 800 sheet: -1.24 (0.20), residues: 692 loop : -2.17 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.014 0.001 TYR C 136 PHE 0.021 0.001 PHE D1296 TRP 0.008 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (25428) covalent geometry : angle 0.70861 / 0.34 (34768) hydrogen bonds : bond 0.03807 / 2.50 ( 956) hydrogen bonds : angle 5.10604 / 3.46 ( 2637) metal coordination : bond 0.04398 / 2.12 ( 4) metal coordination : angle 18.92787 / 9.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 103 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7578 (p0) cc_final: 0.7092 (p0) REVERT: A 169 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 252 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 588 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 1147 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7093 (tp) REVERT: B 306 MET cc_start: 0.7336 (ptm) cc_final: 0.7074 (ptm) REVERT: B 650 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7519 (ttpt) REVERT: B 713 MET cc_start: 0.4460 (tpp) cc_final: 0.2904 (ttp) REVERT: B 781 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7633 (mtt90) REVERT: C 225 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8761 (t) REVERT: C 338 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6603 (t80) REVERT: D 1285 MET cc_start: 0.7876 (tpp) cc_final: 0.6958 (ptt) REVERT: D 1328 TYR cc_start: 0.1659 (OUTLIER) cc_final: 0.0331 (t80) outliers start: 95 outliers final: 75 residues processed: 191 average time/residue: 0.1421 time to fit residues: 46.0590 Evaluate side-chains 186 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 102 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 76 optimal weight: 0.9990 chunk 238 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 246 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 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 = 0.3811 r_free = 0.3811 target = 0.084671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.065917 restraints weight = 109238.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065991 restraints weight = 77662.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066146 restraints weight = 61186.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066420 restraints weight = 52551.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066518 restraints weight = 45862.291| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25432 Z= 0.153 Angle : 0.769 52.679 34777 Z= 0.339 Chirality : 0.054 1.063 3941 Planarity : 0.004 0.048 4195 Dihedral : 12.666 160.929 4053 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.60 % Favored : 91.22 % Rotamer: Outliers : 3.73 % Allowed : 28.08 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.15), residues: 2883 helix: 0.11 (0.18), residues: 801 sheet: -1.24 (0.20), residues: 693 loop : -2.15 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.014 0.001 TYR C 136 PHE 0.021 0.001 PHE D1296 TRP 0.009 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (25428) covalent geometry : angle 0.70638 / 0.34 (34768) hydrogen bonds : bond 0.03730 / 2.43 ( 956) hydrogen bonds : angle 5.08145 / 3.45 ( 2637) metal coordination : bond 0.04201 / 2.02 ( 4) metal coordination : angle 18.97448 / 9.71 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 104 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7602 (p0) cc_final: 0.7105 (p0) REVERT: A 252 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 588 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (tt) REVERT: A 1147 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7132 (tp) REVERT: B 306 MET cc_start: 0.7312 (ptm) cc_final: 0.7029 (ptm) REVERT: B 650 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7501 (ttpt) REVERT: B 781 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7665 (mtt90) REVERT: C 338 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6554 (t80) REVERT: D 1285 MET cc_start: 0.7948 (tpp) cc_final: 0.6853 (mtp) REVERT: D 1328 TYR cc_start: 0.1714 (OUTLIER) cc_final: 0.0265 (t80) outliers start: 95 outliers final: 79 residues processed: 191 average time/residue: 0.1455 time to fit residues: 46.0496 Evaluate side-chains 187 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 101 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 170 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 254 optimal weight: 0.1980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 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 = 0.3802 r_free = 0.3802 target = 0.084237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065571 restraints weight = 108905.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065447 restraints weight = 76878.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065751 restraints weight = 59768.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065944 restraints weight = 52566.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066055 restraints weight = 46187.929| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 25432 Z= 0.175 Angle : 0.784 54.270 34777 Z= 0.346 Chirality : 0.054 1.033 3941 Planarity : 0.004 0.049 4195 Dihedral : 12.676 160.528 4053 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.19 % Favored : 90.63 % Rotamer: Outliers : 4.00 % Allowed : 27.73 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.15), residues: 2883 helix: 0.14 (0.18), residues: 798 sheet: -1.29 (0.20), residues: 699 loop : -2.16 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.014 0.001 TYR C 136 PHE 0.021 0.001 PHE D1296 TRP 0.008 0.001 TRP A 362 HIS 0.008 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (25428) covalent geometry : angle 0.71843 / 0.35 (34768) hydrogen bonds : bond 0.03822 / 2.50 ( 956) hydrogen bonds : angle 5.11112 / 3.47 ( 2637) metal coordination : bond 0.04737 / 2.28 ( 4) metal coordination : angle 19.51946 / 9.95 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.49 seconds wall clock time: 60 minutes 6.02 seconds (3606.02 seconds total)