Starting phenix.real_space_refine on Sat Jun 21 19:31:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asw_15623/06_2025/8asw_15623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asw_15623/06_2025/8asw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8asw_15623/06_2025/8asw_15623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asw_15623/06_2025/8asw_15623.map" model { file = "/net/cci-nas-00/data/ceres_data/8asw_15623/06_2025/8asw_15623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asw_15623/06_2025/8asw_15623.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: 13.74, per 1000 atoms: 0.55 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: 6.04 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 8.80 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: 13.13 Time building geometry restraints manager: 7.27 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: 34219 2.47 - 4.93: 497 4.93 - 7.40: 41 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=" CB MET C 184 " pdb=" CG MET C 184 " pdb=" SD MET C 184 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ASP A 773 " pdb=" N ILE A 774 " pdb=" CA ILE A 774 " ideal model delta sigma weight residual 121.97 115.00 6.97 1.80e+00 3.09e-01 1.50e+01 ... (remaining 34763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 14642 33.29 - 66.58: 767 66.58 - 99.86: 110 99.86 - 133.15: 4 133.15 - 166.44: 4 Dihedral angle restraints: 15527 sinusoidal: 7031 harmonic: 8496 Sorted by residual: dihedral pdb=" C4' A X 7 " pdb=" C3' A X 7 " pdb=" C2' A X 7 " pdb=" C1' A X 7 " ideal model delta sinusoidal sigma weight residual -35.00 32.54 -67.54 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" C5' A X 7 " pdb=" C4' A X 7 " pdb=" C3' A X 7 " pdb=" O3' A X 7 " ideal model delta sinusoidal sigma weight residual 147.00 85.63 61.37 1 8.00e+00 1.56e-02 7.81e+01 dihedral pdb=" O4' A X 7 " pdb=" C2' A X 7 " pdb=" C1' A X 7 " pdb=" C3' A X 7 " ideal model delta sinusoidal sigma weight residual -35.00 22.82 -57.82 1 8.00e+00 1.56e-02 7.01e+01 ... (remaining 15524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3228 0.056 - 0.112: 631 0.112 - 0.169: 75 0.169 - 0.225: 4 0.225 - 0.281: 3 Chirality restraints: 3941 Sorted by residual: chirality pdb=" C3' A X 7 " pdb=" C4' A X 7 " pdb=" O3' A X 7 " pdb=" C2' A X 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A1197 " pdb=" CA VAL A1197 " pdb=" CG1 VAL A1197 " pdb=" CG2 VAL A1197 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C3' U X 65 " pdb=" C4' U X 65 " pdb=" O3' U X 65 " pdb=" C2' U X 65 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.41e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 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: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 72.770 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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= 0.247 Angle : 0.828 47.763 34777 Z= 0.423 Chirality : 0.044 0.281 3941 Planarity : 0.004 0.057 4195 Dihedral : 19.806 166.439 10045 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 PHE 0.016 0.002 PHE C 319 TYR 0.025 0.002 TYR C 216 ARG 0.005 0.001 ARG C 360 Details of bonding type rmsd hydrogen bonds : bond 0.14678 ( 956) hydrogen bonds : angle 6.51793 ( 2637) metal coordination : bond 0.06425 ( 4) metal coordination : angle 21.63959 ( 9) covalent geometry : bond 0.00514 (25428) covalent geometry : angle 0.75160 (34768) *********************** 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 : 2.964 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: 0.3581 time to fit residues: 71.4759 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 : 2.905 ------------------------------------------------------------------------------- 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 249 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 650 ASN A1031 HIS ** 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** B 584 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1021 GLN D1164 GLN D1166 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.085411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066571 restraints weight = 109026.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066588 restraints weight = 75682.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066913 restraints weight = 57501.640| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25432 Z= 0.141 Angle : 0.702 50.789 34777 Z= 0.326 Chirality : 0.043 0.306 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.963 162.833 4378 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 2.86 % Allowed : 25.73 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 2883 helix: 0.08 (0.18), residues: 803 sheet: -1.28 (0.20), residues: 670 loop : -2.25 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 PHE 0.014 0.001 PHE A 285 TYR 0.025 0.001 TYR C 216 ARG 0.006 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 956) hydrogen bonds : angle 5.42668 ( 2637) metal coordination : bond 0.03343 ( 4) metal coordination : angle 20.10679 ( 9) covalent geometry : bond 0.00297 (25428) covalent geometry : angle 0.62265 (34768) *********************** 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 194 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 121 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7560 (p0) cc_final: 0.7069 (p0) REVERT: A 675 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8556 (mm) REVERT: A 842 TYR cc_start: 0.6771 (t80) cc_final: 0.6568 (t80) REVERT: A 1031 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.7067 (t70) REVERT: B 781 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7481 (mtt90) REVERT: D 1328 TYR cc_start: 0.1430 (OUTLIER) cc_final: 0.0779 (t80) outliers start: 73 outliers final: 34 residues processed: 187 average time/residue: 0.3259 time to fit residues: 102.9918 Evaluate side-chains 142 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 2.651 ------------------------------------------------------------------------------- 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 675 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1031 HIS 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 178 LEU 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 C residue 384 THR Chi-restraints excluded: chain D residue 1143 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 158 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 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** D1164 GLN 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 = 0.084691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065980 restraints weight = 109124.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065819 restraints weight = 79408.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066329 restraints weight = 59447.231| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25432 Z= 0.175 Angle : 0.696 52.737 34777 Z= 0.324 Chirality : 0.043 0.263 3941 Planarity : 0.004 0.048 4195 Dihedral : 15.780 169.227 4369 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.09 % Favored : 90.74 % Rotamer: Outliers : 4.27 % Allowed : 25.53 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2883 helix: 0.06 (0.18), residues: 811 sheet: -1.28 (0.20), residues: 676 loop : -2.24 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 308 HIS 0.008 0.001 HIS A1031 PHE 0.018 0.001 PHE A 954 TYR 0.027 0.001 TYR A1007 ARG 0.003 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 956) hydrogen bonds : angle 5.31577 ( 2637) metal coordination : bond 0.04244 ( 4) metal coordination : angle 19.87166 ( 9) covalent geometry : bond 0.00382 (25428) covalent geometry : angle 0.61831 (34768) *********************** 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 218 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 109 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7594 (p0) cc_final: 0.7085 (p0) REVERT: A 169 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8295 (pp) REVERT: A 408 ASP cc_start: 0.6906 (p0) cc_final: 0.6450 (p0) REVERT: A 842 TYR cc_start: 0.6930 (t80) cc_final: 0.6711 (t80) REVERT: A 1031 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7165 (t70) REVERT: B 713 MET cc_start: 0.4657 (tpp) cc_final: 0.3251 (ttp) REVERT: B 781 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7484 (mtt90) REVERT: D 1285 MET cc_start: 0.7948 (tpp) cc_final: 0.7219 (mtm) REVERT: D 1328 TYR cc_start: 0.1526 (OUTLIER) cc_final: 0.0907 (t80) outliers start: 109 outliers final: 66 residues processed: 209 average time/residue: 0.3361 time to fit residues: 116.6802 Evaluate side-chains 172 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 102 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 349 THR Chi-restraints excluded: chain A residue 360 VAL 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 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 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 716 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 1031 HIS 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 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU 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 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 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 37 LEU Chi-restraints excluded: chain C residue 41 THR 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 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 259 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 223 optimal weight: 0.0970 chunk 83 optimal weight: 0.3980 chunk 181 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 HIS ** A1059 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.085560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066953 restraints weight = 109726.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067460 restraints weight = 72507.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067641 restraints weight = 56744.683| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25432 Z= 0.126 Angle : 0.651 47.761 34777 Z= 0.306 Chirality : 0.042 0.230 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.618 171.940 4369 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.91 % Favored : 91.92 % Rotamer: Outliers : 4.08 % Allowed : 25.45 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.16), residues: 2883 helix: 0.24 (0.18), residues: 800 sheet: -1.16 (0.20), residues: 677 loop : -2.17 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 308 HIS 0.008 0.001 HIS A1290 PHE 0.028 0.001 PHE D1296 TYR 0.017 0.001 TYR C 136 ARG 0.004 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 956) hydrogen bonds : angle 5.09558 ( 2637) metal coordination : bond 0.03259 ( 4) metal coordination : angle 17.61772 ( 9) covalent geometry : bond 0.00268 (25428) covalent geometry : angle 0.58604 (34768) *********************** 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 221 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 117 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7558 (p0) cc_final: 0.7028 (p0) REVERT: A 408 ASP cc_start: 0.6699 (p0) cc_final: 0.6255 (p0) REVERT: A 1031 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.7010 (t70) REVERT: A 1037 MET cc_start: 0.7296 (tpt) cc_final: 0.6452 (tpt) REVERT: B 713 MET cc_start: 0.4498 (tpp) cc_final: 0.3086 (ttp) REVERT: B 781 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7172 (mtt-85) REVERT: D 1328 TYR cc_start: 0.1462 (OUTLIER) cc_final: 0.0599 (t80) outliers start: 104 outliers final: 61 residues processed: 207 average time/residue: 0.3192 time to fit residues: 110.9705 Evaluate side-chains 170 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 106 time to evaluate : 2.884 ------------------------------------------------------------------------------- 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 267 VAL 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 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 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 720 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 1008 LYS Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 1031 HIS 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 20 VAL Chi-restraints excluded: chain B residue 110 LEU 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 530 LEU Chi-restraints excluded: chain B residue 592 THR 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 37 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 12 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 254 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 116 optimal weight: 0.0670 chunk 253 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.085592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066829 restraints weight = 109012.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066695 restraints weight = 78869.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067117 restraints weight = 57610.573| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1528 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 : 0.648 47.486 34777 Z= 0.302 Chirality : 0.042 0.227 3941 Planarity : 0.003 0.050 4195 Dihedral : 15.531 171.223 4369 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.26 % Favored : 91.57 % Rotamer: Outliers : 4.16 % Allowed : 25.88 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2883 helix: 0.28 (0.19), residues: 795 sheet: -1.05 (0.20), residues: 669 loop : -2.12 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.009 0.001 HIS A1031 PHE 0.019 0.001 PHE C 205 TYR 0.016 0.001 TYR A1007 ARG 0.004 0.000 ARG A1065 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 956) hydrogen bonds : angle 4.99515 ( 2637) metal coordination : bond 0.03426 ( 4) metal coordination : angle 17.39238 ( 9) covalent geometry : bond 0.00266 (25428) covalent geometry : angle 0.58404 (34768) *********************** 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 218 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 112 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7635 (p0) cc_final: 0.7119 (p0) REVERT: A 408 ASP cc_start: 0.6666 (p0) cc_final: 0.6285 (p0) REVERT: B 713 MET cc_start: 0.4413 (tpp) cc_final: 0.2967 (ttp) REVERT: C 152 ASP cc_start: 0.7749 (t0) cc_final: 0.7396 (t0) REVERT: C 225 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8787 (t) REVERT: C 338 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6596 (t80) REVERT: D 1285 MET cc_start: 0.7947 (tpp) cc_final: 0.7151 (mtm) REVERT: D 1328 TYR cc_start: 0.1493 (OUTLIER) cc_final: 0.0583 (t80) outliers start: 106 outliers final: 75 residues processed: 207 average time/residue: 0.3121 time to fit residues: 109.6225 Evaluate side-chains 183 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 105 time to evaluate : 2.641 ------------------------------------------------------------------------------- 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 110 VAL Chi-restraints excluded: chain A residue 111 PHE 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 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 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 720 VAL 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 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 1166 ASN 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 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 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 679 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 LEU 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 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL 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 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS ** A1059 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.085384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066703 restraints weight = 108760.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066474 restraints weight = 78476.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066795 restraints weight = 59843.636| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25432 Z= 0.139 Angle : 0.657 48.815 34777 Z= 0.306 Chirality : 0.042 0.225 3941 Planarity : 0.003 0.051 4195 Dihedral : 15.499 170.359 4369 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 4.43 % Allowed : 25.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2883 helix: 0.28 (0.19), residues: 797 sheet: -1.03 (0.20), residues: 666 loop : -2.11 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 308 HIS 0.007 0.001 HIS A1290 PHE 0.021 0.001 PHE D1296 TYR 0.016 0.001 TYR C 136 ARG 0.004 0.000 ARG B 781 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 956) hydrogen bonds : angle 4.98081 ( 2637) metal coordination : bond 0.03820 ( 4) metal coordination : angle 17.78278 ( 9) covalent geometry : bond 0.00303 (25428) covalent geometry : angle 0.59161 (34768) *********************** 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 222 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 109 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7721 (p0) cc_final: 0.7217 (p0) REVERT: A 408 ASP cc_start: 0.6885 (p0) cc_final: 0.6537 (p0) REVERT: B 713 MET cc_start: 0.4445 (tpp) cc_final: 0.2992 (ttp) REVERT: C 225 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8821 (t) REVERT: C 338 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6587 (t80) REVERT: D 1328 TYR cc_start: 0.1628 (OUTLIER) cc_final: 0.0443 (t80) outliers start: 113 outliers final: 88 residues processed: 210 average time/residue: 0.3237 time to fit residues: 114.4113 Evaluate side-chains 195 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 104 time to evaluate : 3.041 ------------------------------------------------------------------------------- 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 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 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 360 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER 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 606 LEU Chi-restraints excluded: chain A residue 653 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 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 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 1166 ASN 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 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 221 LEU Chi-restraints excluded: chain B residue 287 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 592 THR 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 742 ILE 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 94 SER Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 LEU 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 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL 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 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE 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 13 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 208 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.083164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064356 restraints weight = 109417.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064070 restraints weight = 75883.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064679 restraints weight = 58196.326| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 25432 Z= 0.272 Angle : 0.783 59.988 34777 Z= 0.363 Chirality : 0.045 0.229 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.748 169.703 4369 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.58 % Favored : 89.25 % Rotamer: Outliers : 4.90 % Allowed : 26.27 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 2883 helix: -0.03 (0.18), residues: 798 sheet: -1.26 (0.20), residues: 673 loop : -2.30 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 682 HIS 0.009 0.001 HIS C 110 PHE 0.023 0.002 PHE D1296 TYR 0.024 0.002 TYR C 131 ARG 0.006 0.001 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 956) hydrogen bonds : angle 5.33924 ( 2637) metal coordination : bond 0.06602 ( 4) metal coordination : angle 21.68377 ( 9) covalent geometry : bond 0.00605 (25428) covalent geometry : angle 0.70106 (34768) *********************** 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 218 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 93 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.9331 (mmt) cc_final: 0.9073 (mmm) REVERT: A 105 ASP cc_start: 0.7611 (p0) cc_final: 0.7128 (p0) REVERT: A 252 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 588 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 1280 LEU cc_start: 0.7443 (tt) cc_final: 0.6885 (tp) REVERT: B 713 MET cc_start: 0.4525 (tpp) cc_final: 0.3026 (ttp) REVERT: C 225 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8921 (t) REVERT: C 338 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6741 (t80) REVERT: D 1285 MET cc_start: 0.8080 (tpp) cc_final: 0.7014 (mtm) REVERT: D 1288 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7790 (tp40) REVERT: D 1328 TYR cc_start: 0.1714 (OUTLIER) cc_final: 0.0634 (t80) outliers start: 125 outliers final: 96 residues processed: 211 average time/residue: 0.3053 time to fit residues: 110.1285 Evaluate side-chains 193 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 91 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 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 252 THR 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 360 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 494 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 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 711 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 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 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 1097 VAL 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 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 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 THR 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 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 742 ILE 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 94 SER 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 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 537 VAL 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 1224 THR Chi-restraints excluded: chain D residue 1288 GLN 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 144 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.085157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066335 restraints weight = 108440.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066287 restraints weight = 78471.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066638 restraints weight = 58339.225| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25432 Z= 0.125 Angle : 0.675 51.956 34777 Z= 0.311 Chirality : 0.043 0.223 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.574 169.618 4369 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.94 % Favored : 91.88 % Rotamer: Outliers : 3.76 % Allowed : 27.33 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2883 helix: 0.14 (0.18), residues: 795 sheet: -1.17 (0.20), residues: 667 loop : -2.13 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.006 0.001 HIS A1290 PHE 0.024 0.001 PHE D1296 TYR 0.019 0.001 TYR C 113 ARG 0.004 0.000 ARG B 781 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 956) hydrogen bonds : angle 5.07277 ( 2637) metal coordination : bond 0.03632 ( 4) metal coordination : angle 18.72627 ( 9) covalent geometry : bond 0.00263 (25428) covalent geometry : angle 0.60357 (34768) *********************** 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 203 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 107 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7614 (p0) cc_final: 0.7138 (p0) REVERT: A 588 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 1280 LEU cc_start: 0.7388 (tt) cc_final: 0.6880 (tp) REVERT: B 306 MET cc_start: 0.7217 (ptm) cc_final: 0.6970 (ptm) REVERT: B 713 MET cc_start: 0.4475 (tpp) cc_final: 0.2957 (ttp) REVERT: C 184 MET cc_start: 0.8114 (mmm) cc_final: 0.7839 (mmm) REVERT: C 225 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8810 (t) REVERT: C 338 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6648 (t80) REVERT: D 1328 TYR cc_start: 0.1722 (OUTLIER) cc_final: 0.0385 (t80) outliers start: 96 outliers final: 75 residues processed: 191 average time/residue: 0.3077 time to fit residues: 100.3438 Evaluate side-chains 180 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 101 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 423 ASP Chi-restraints excluded: chain A residue 494 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 579 LEU Chi-restraints excluded: chain A residue 588 LEU 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 720 VAL 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 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 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 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 530 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 742 ILE 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 94 SER Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 178 LEU 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 294 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** 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 = 0.3794 r_free = 0.3794 target = 0.083931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065140 restraints weight = 109431.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065057 restraints weight = 76423.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065361 restraints weight = 60341.585| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 25432 Z= 0.207 Angle : 0.723 56.467 34777 Z= 0.334 Chirality : 0.044 0.228 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.628 168.320 4369 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.82 % Favored : 90.01 % Rotamer: Outliers : 4.04 % Allowed : 27.02 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2883 helix: 0.02 (0.18), residues: 807 sheet: -1.26 (0.20), residues: 698 loop : -2.23 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 682 HIS 0.008 0.001 HIS C 110 PHE 0.026 0.002 PHE D1296 TYR 0.018 0.002 TYR C 136 ARG 0.005 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 956) hydrogen bonds : angle 5.15860 ( 2637) metal coordination : bond 0.05359 ( 4) metal coordination : angle 20.29352 ( 9) covalent geometry : bond 0.00458 (25428) covalent geometry : angle 0.64573 (34768) *********************** 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 203 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 100 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.9336 (mmt) cc_final: 0.9078 (mmm) REVERT: A 105 ASP cc_start: 0.7635 (p0) cc_final: 0.7153 (p0) REVERT: A 252 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 588 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 1021 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: A 1280 LEU cc_start: 0.7457 (tt) cc_final: 0.7007 (tp) REVERT: B 650 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7595 (ttpt) REVERT: B 713 MET cc_start: 0.4452 (tpp) cc_final: 0.2865 (ttp) REVERT: C 225 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8929 (t) REVERT: C 338 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6682 (t80) REVERT: D 1285 MET cc_start: 0.8016 (tpp) cc_final: 0.6745 (mtp) REVERT: D 1328 TYR cc_start: 0.1730 (OUTLIER) cc_final: 0.0402 (t80) outliers start: 103 outliers final: 86 residues processed: 195 average time/residue: 0.3249 time to fit residues: 107.9085 Evaluate side-chains 191 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 98 time to evaluate : 2.835 ------------------------------------------------------------------------------- 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 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 252 THR 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 360 VAL Chi-restraints excluded: chain A residue 366 SER 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 527 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 681 HIS 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 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 1021 GLN Chi-restraints excluded: chain A residue 1097 VAL 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 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 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 672 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 742 ILE 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 94 SER 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 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 429 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 69 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN ** 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 = 0.3818 r_free = 0.3818 target = 0.085018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066112 restraints weight = 108219.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065878 restraints weight = 72634.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066296 restraints weight = 54464.092| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25432 Z= 0.135 Angle : 0.680 52.298 34777 Z= 0.314 Chirality : 0.043 0.227 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.496 167.342 4367 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.15 % Favored : 91.68 % Rotamer: Outliers : 3.45 % Allowed : 27.73 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2883 helix: 0.17 (0.18), residues: 798 sheet: -1.11 (0.20), residues: 670 loop : -2.13 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 362 HIS 0.006 0.001 HIS A1290 PHE 0.024 0.001 PHE D1296 TYR 0.014 0.001 TYR C 136 ARG 0.003 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 956) hydrogen bonds : angle 5.03746 ( 2637) metal coordination : bond 0.04051 ( 4) metal coordination : angle 18.82489 ( 9) covalent geometry : bond 0.00292 (25428) covalent geometry : angle 0.60876 (34768) ********************** 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 192 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 104 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7692 (p0) cc_final: 0.7230 (p0) REVERT: A 252 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 588 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8510 (tt) REVERT: A 1280 LEU cc_start: 0.7507 (tt) cc_final: 0.7129 (tp) REVERT: B 278 MET cc_start: 0.7146 (mmm) cc_final: 0.6935 (mmt) REVERT: B 713 MET cc_start: 0.4488 (tpp) cc_final: 0.2968 (ttp) REVERT: C 225 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8776 (t) REVERT: C 338 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6612 (t80) REVERT: D 1285 MET cc_start: 0.8047 (tpp) cc_final: 0.6944 (mtp) REVERT: D 1328 TYR cc_start: 0.1798 (OUTLIER) cc_final: 0.0473 (t80) outliers start: 88 outliers final: 80 residues processed: 182 average time/residue: 0.3258 time to fit residues: 100.6423 Evaluate side-chains 187 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 102 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 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 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 423 ASP Chi-restraints excluded: chain A residue 494 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 579 LEU Chi-restraints excluded: chain A residue 588 LEU 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 681 HIS 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 749 VAL 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 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 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 390 ASP 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 672 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 742 ILE 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 94 SER 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 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 531 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.084424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065771 restraints weight = 108451.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065454 restraints weight = 74208.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065928 restraints weight = 58179.507| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 25432 Z= 0.176 Angle : 0.705 54.760 34777 Z= 0.324 Chirality : 0.043 0.230 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.505 165.855 4367 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.33 % Favored : 90.50 % Rotamer: Outliers : 3.80 % Allowed : 27.45 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2883 helix: 0.15 (0.18), residues: 800 sheet: -1.22 (0.20), residues: 699 loop : -2.16 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 PHE 0.028 0.002 PHE A 954 TYR 0.028 0.001 TYR A 973 ARG 0.004 0.000 ARG C 360 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 956) hydrogen bonds : angle 5.08421 ( 2637) metal coordination : bond 0.04812 ( 4) metal coordination : angle 19.69299 ( 9) covalent geometry : bond 0.00388 (25428) covalent geometry : angle 0.63033 (34768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6755.28 seconds wall clock time: 119 minutes 1.62 seconds (7141.62 seconds total)