Starting phenix.real_space_refine on Mon Sep 30 10:59:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/09_2024/8asw_15623.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/09_2024/8asw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/09_2024/8asw_15623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/09_2024/8asw_15623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/09_2024/8asw_15623.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/09_2024/8asw_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 13.56, 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: 5.44 Conformation dependent library (CDL) restraints added in 2.7 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: 7.53 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: 10.18 Time building geometry restraints manager: 6.43 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 60.990 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.910 ------------------------------------------------------------------------------- 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 0.042 25428 Z= 0.336 Angle : 0.752 12.336 34768 Z= 0.422 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 *********************** 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 fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 2.759 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: 0.3290 time to fit residues: 65.4605 Evaluate side-chains 110 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 0.032 25428 Z= 0.193 Angle : 0.623 9.526 34768 Z= 0.325 Chirality : 0.043 0.306 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.963 162.832 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 *********************** 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 fitting. rotamer outliers: 73 poor density : 121 time to evaluate : 2.907 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7667 (p0) cc_final: 0.7193 (p0) REVERT: A 842 TYR cc_start: 0.6873 (t80) cc_final: 0.6642 (t80) REVERT: A 1031 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.7165 (t70) REVERT: B 781 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7451 (mtt90) REVERT: D 1328 TYR cc_start: 0.0953 (OUTLIER) cc_final: 0.0479 (t80) outliers start: 73 outliers final: 34 residues processed: 187 average time/residue: 0.3267 time to fit residues: 102.9735 Evaluate side-chains 141 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 2.725 ------------------------------------------------------------------------------- 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 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 148 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** A 983 HIS ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25428 Z= 0.337 Angle : 0.664 9.676 34768 Z= 0.346 Chirality : 0.044 0.263 3941 Planarity : 0.004 0.046 4195 Dihedral : 15.868 169.383 4369 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.92 % Favored : 89.91 % Rotamer: Outliers : 4.82 % Allowed : 25.69 % Favored : 69.49 % 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: -2.14 (0.15), residues: 2883 helix: -0.05 (0.18), residues: 811 sheet: -1.32 (0.20), residues: 663 loop : -2.32 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 308 HIS 0.009 0.001 HIS C 110 PHE 0.017 0.002 PHE A 954 TYR 0.026 0.002 TYR A1007 ARG 0.004 0.001 ARG C 21 *********************** 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 227 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 104 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7708 (p0) cc_final: 0.7222 (p0) REVERT: A 169 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8242 (pp) REVERT: A 842 TYR cc_start: 0.7141 (t80) cc_final: 0.6920 (t80) REVERT: A 1031 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7257 (t70) REVERT: B 713 MET cc_start: 0.4698 (tpp) cc_final: 0.3245 (ttp) REVERT: B 781 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7533 (mtt90) REVERT: C 338 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6773 (t80) REVERT: D 1328 TYR cc_start: 0.1125 (OUTLIER) cc_final: 0.0668 (t80) outliers start: 123 outliers final: 72 residues processed: 219 average time/residue: 0.3246 time to fit residues: 119.9918 Evaluate side-chains 178 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 101 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 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 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 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 10 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 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 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 265 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 285 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25428 Z= 0.292 Angle : 0.647 9.599 34768 Z= 0.336 Chirality : 0.044 0.237 3941 Planarity : 0.004 0.045 4195 Dihedral : 15.814 171.782 4369 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.26 % Favored : 90.57 % Rotamer: Outliers : 5.41 % Allowed : 25.06 % Favored : 69.53 % 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: -0.06 (0.18), residues: 812 sheet: -1.33 (0.20), residues: 668 loop : -2.34 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.008 0.001 HIS A1290 PHE 0.015 0.002 PHE A 285 TYR 0.020 0.002 TYR C 136 ARG 0.006 0.000 ARG C 43 *********************** 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 242 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 104 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7724 (p0) cc_final: 0.7237 (p0) REVERT: A 169 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 252 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 588 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8504 (tt) REVERT: B 713 MET cc_start: 0.4670 (tpp) cc_final: 0.3063 (ttp) REVERT: B 781 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7570 (mtt90) REVERT: C 225 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8895 (t) REVERT: C 338 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6793 (t80) REVERT: D 1328 TYR cc_start: 0.1315 (OUTLIER) cc_final: 0.0740 (t80) outliers start: 138 outliers final: 91 residues processed: 233 average time/residue: 0.3051 time to fit residues: 119.6662 Evaluate side-chains 197 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 99 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR 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 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 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 749 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 1018 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 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 281 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 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 67 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 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 1143 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 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25428 Z= 0.264 Angle : 0.635 9.413 34768 Z= 0.329 Chirality : 0.043 0.231 3941 Planarity : 0.004 0.046 4195 Dihedral : 15.749 171.799 4369 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.92 % Favored : 89.91 % Rotamer: Outliers : 5.61 % Allowed : 25.37 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.18), residues: 810 sheet: -1.28 (0.20), residues: 662 loop : -2.30 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 PHE 0.015 0.002 PHE D1296 TYR 0.018 0.001 TYR C 136 ARG 0.005 0.000 ARG C 43 *********************** 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 248 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 105 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7735 (p0) cc_final: 0.7251 (p0) REVERT: A 169 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 252 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 355 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: A 588 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 1037 MET cc_start: 0.7656 (tpt) cc_final: 0.7173 (tpt) REVERT: A 1125 ILE cc_start: 0.5292 (OUTLIER) cc_final: 0.4815 (mm) REVERT: B 713 MET cc_start: 0.4568 (tpp) cc_final: 0.2980 (ttp) REVERT: B 781 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7574 (mtt90) REVERT: C 225 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8900 (t) REVERT: C 338 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6768 (t80) REVERT: D 1328 TYR cc_start: 0.1372 (OUTLIER) cc_final: 0.0841 (t80) outliers start: 143 outliers final: 100 residues processed: 239 average time/residue: 0.3295 time to fit residues: 131.2947 Evaluate side-chains 206 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 97 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 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 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 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 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 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 1125 ILE 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 26 VAL Chi-restraints excluded: chain B residue 72 ASP 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 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 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 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 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 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 95 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 236 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 0.0020 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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** ** A1059 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25428 Z= 0.164 Angle : 0.595 10.735 34768 Z= 0.307 Chirality : 0.043 0.225 3941 Planarity : 0.004 0.048 4195 Dihedral : 15.574 170.815 4369 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.67 % Favored : 92.16 % Rotamer: Outliers : 3.45 % Allowed : 27.57 % Favored : 68.98 % 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: 0.20 (0.18), residues: 801 sheet: -1.13 (0.20), residues: 681 loop : -2.13 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 308 HIS 0.007 0.001 HIS A1290 PHE 0.033 0.001 PHE D1296 TYR 0.015 0.001 TYR C 136 ARG 0.007 0.000 ARG A 282 *********************** 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 206 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 118 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7777 (p0) cc_final: 0.7291 (p0) REVERT: A 408 ASP cc_start: 0.6915 (p0) cc_final: 0.6431 (p0) REVERT: B 713 MET cc_start: 0.4408 (tpp) cc_final: 0.2815 (ttp) REVERT: B 781 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7015 (mtt-85) REVERT: D 1328 TYR cc_start: 0.1380 (OUTLIER) cc_final: 0.0591 (t80) outliers start: 88 outliers final: 59 residues processed: 197 average time/residue: 0.3225 time to fit residues: 106.6172 Evaluate side-chains 164 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 103 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 369 LEU 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 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU 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 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 1014 TYR 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 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 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 545 HIS 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 85 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR 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 1224 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1299 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 173 optimal weight: 0.2980 chunk 131 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 650 ASN A1031 HIS A1035 ASN ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25428 Z= 0.171 Angle : 0.591 10.507 34768 Z= 0.304 Chirality : 0.043 0.228 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.500 169.153 4369 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.50 % Favored : 91.33 % Rotamer: Outliers : 3.80 % Allowed : 27.37 % 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: -1.78 (0.16), residues: 2883 helix: 0.27 (0.18), residues: 796 sheet: -1.04 (0.20), residues: 668 loop : -2.13 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 308 HIS 0.008 0.001 HIS A1290 PHE 0.021 0.001 PHE C 205 TYR 0.019 0.001 TYR C 113 ARG 0.006 0.000 ARG A 282 *********************** 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 208 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 111 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7794 (p0) cc_final: 0.7299 (p0) REVERT: A 408 ASP cc_start: 0.6929 (p0) cc_final: 0.6487 (p0) REVERT: B 713 MET cc_start: 0.4377 (tpp) cc_final: 0.2772 (ttp) REVERT: C 225 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8760 (t) REVERT: D 1328 TYR cc_start: 0.1311 (OUTLIER) cc_final: 0.0520 (t80) outliers start: 97 outliers final: 68 residues processed: 198 average time/residue: 0.3472 time to fit residues: 112.4590 Evaluate side-chains 174 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 104 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 366 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 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 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 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 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 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 252 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 HIS 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 31 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 300 ASN 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 1224 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25428 Z= 0.258 Angle : 0.633 12.208 34768 Z= 0.326 Chirality : 0.043 0.228 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.567 167.922 4369 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.12 % Favored : 90.70 % Rotamer: Outliers : 4.24 % Allowed : 27.14 % Favored : 68.63 % 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: -1.93 (0.15), residues: 2883 helix: 0.15 (0.18), residues: 807 sheet: -1.24 (0.20), residues: 705 loop : -2.19 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 308 HIS 0.008 0.001 HIS C 110 PHE 0.024 0.002 PHE D1296 TYR 0.017 0.001 TYR C 136 ARG 0.006 0.000 ARG A 282 *********************** 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 206 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 98 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7735 (p0) cc_final: 0.7266 (p0) REVERT: A 252 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 588 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8524 (tt) REVERT: B 713 MET cc_start: 0.4386 (tpp) cc_final: 0.2764 (ttp) REVERT: C 131 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.6195 (p90) REVERT: C 225 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8845 (t) REVERT: D 1288 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7134 (tp40) REVERT: D 1328 TYR cc_start: 0.1428 (OUTLIER) cc_final: 0.0508 (t80) outliers start: 108 outliers final: 85 residues processed: 197 average time/residue: 0.3195 time to fit residues: 106.8366 Evaluate side-chains 189 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 98 time to evaluate : 3.001 ------------------------------------------------------------------------------- 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 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 606 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 802 LEU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 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 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 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 252 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 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 C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 chunk 159 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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** A1031 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25428 Z= 0.186 Angle : 0.605 11.167 34768 Z= 0.310 Chirality : 0.042 0.227 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.477 167.235 4367 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.46 % Favored : 91.36 % Rotamer: Outliers : 3.88 % Allowed : 27.49 % Favored : 68.63 % 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: -1.82 (0.16), residues: 2883 helix: 0.21 (0.18), residues: 803 sheet: -1.11 (0.20), residues: 687 loop : -2.14 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 PHE 0.027 0.001 PHE D1296 TYR 0.015 0.001 TYR C 136 ARG 0.005 0.000 ARG A 282 *********************** 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 201 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 102 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7738 (p0) cc_final: 0.7264 (p0) REVERT: A 252 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 588 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 713 MET cc_start: 0.4357 (tpp) cc_final: 0.2761 (ttp) REVERT: C 225 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8779 (t) REVERT: D 1328 TYR cc_start: 0.1410 (OUTLIER) cc_final: 0.0543 (t80) outliers start: 99 outliers final: 86 residues processed: 189 average time/residue: 0.3045 time to fit residues: 99.3182 Evaluate side-chains 191 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 101 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 252 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU 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 802 LEU 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 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 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 252 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 185 optimal weight: 0.2980 chunk 249 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A1031 HIS ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25428 Z= 0.171 Angle : 0.601 11.579 34768 Z= 0.307 Chirality : 0.042 0.230 3941 Planarity : 0.003 0.049 4195 Dihedral : 15.387 165.240 4367 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 3.45 % Allowed : 27.84 % Favored : 68.71 % 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: -1.76 (0.16), residues: 2883 helix: 0.27 (0.18), residues: 803 sheet: -1.06 (0.20), residues: 685 loop : -2.11 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 PHE 0.019 0.001 PHE D1296 TYR 0.014 0.001 TYR C 136 ARG 0.006 0.000 ARG B 781 ********************** 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 fitting. rotamer outliers: 88 poor density : 104 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7742 (p0) cc_final: 0.7284 (p0) REVERT: A 252 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (p) REVERT: A 588 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8525 (tt) REVERT: B 713 MET cc_start: 0.4332 (tpp) cc_final: 0.2789 (ttp) REVERT: C 225 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8759 (t) REVERT: D 1328 TYR cc_start: 0.1497 (OUTLIER) cc_final: 0.0420 (t80) outliers start: 88 outliers final: 77 residues processed: 182 average time/residue: 0.3136 time to fit residues: 98.2493 Evaluate side-chains 180 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 99 time to evaluate : 2.878 ------------------------------------------------------------------------------- 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 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 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 653 LEU 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 802 LEU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1014 TYR Chi-restraints excluded: chain A residue 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 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 252 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 328 SER 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 701 THR Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 234 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** A1031 HIS ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.086549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067945 restraints weight = 108343.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.067914 restraints weight = 77188.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068137 restraints weight = 59261.089| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25428 Z= 0.146 Angle : 0.590 11.680 34768 Z= 0.301 Chirality : 0.042 0.234 3941 Planarity : 0.003 0.049 4195 Dihedral : 15.266 162.536 4367 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.53 % Favored : 92.30 % Rotamer: Outliers : 3.06 % Allowed : 28.43 % Favored : 68.51 % 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: -1.62 (0.16), residues: 2883 helix: 0.41 (0.19), residues: 794 sheet: -0.95 (0.20), residues: 675 loop : -2.04 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 661 HIS 0.006 0.001 HIS A1290 PHE 0.017 0.001 PHE D1296 TYR 0.012 0.001 TYR C 136 ARG 0.004 0.000 ARG A 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.77 seconds wall clock time: 72 minutes 33.82 seconds (4353.82 seconds total)