Starting phenix.real_space_refine on Sat Apr 13 21:55:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soc_40653/04_2024/8soc_40653_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soc_40653/04_2024/8soc_40653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soc_40653/04_2024/8soc_40653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soc_40653/04_2024/8soc_40653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soc_40653/04_2024/8soc_40653_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soc_40653/04_2024/8soc_40653_neut_trim_updated.pdb" } resolution = 3.5 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= 0.023 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 P 2 5.49 5 S 85 5.16 5 C 9472 2.51 5 N 2564 2.21 5 O 2747 1.98 5 H 14881 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 15717 Classifications: {'peptide': 965} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 919} Chain breaks: 9 Chain: "B" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7877 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 466} Chain breaks: 8 Chain: "C" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.30, per 1000 atoms: 0.45 Number of scatterers: 29751 At special positions: 0 Unit cell: (98.28, 136.08, 145.8, 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) S 85 16.00 P 2 15.00 O 2747 8.00 N 2564 7.00 C 9472 6.00 H 14881 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 24.05 Conformation dependent library (CDL) restraints added in 3.3 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 19 sheets defined 37.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.767A pdb=" N LYS A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.566A pdb=" N ARG A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.603A pdb=" N LYS A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.585A pdb=" N THR A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.790A pdb=" N LYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.059A pdb=" N ARG A 542 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.537A pdb=" N ILE A 558 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'A' and resid 579 through 584 removed outlier: 4.943A pdb=" N LYS A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 592 removed outlier: 3.557A pdb=" N TYR A 589 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Proline residue: A 590 - end of helix No H-bonds generated for 'chain 'A' and resid 586 through 592' Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.816A pdb=" N GLN A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 624 through 631 removed outlier: 3.596A pdb=" N MET A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 624 through 631' Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.644A pdb=" N ALA A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 667 removed outlier: 4.749A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 666 " --> pdb=" O GLN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 687 removed outlier: 3.636A pdb=" N ARG A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 703 removed outlier: 3.749A pdb=" N SER A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 removed outlier: 3.626A pdb=" N ILE A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 751 Processing helix chain 'A' and resid 761 through 776 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 839 through 857 removed outlier: 3.579A pdb=" N GLU A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 853 " --> pdb=" O ARG A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 906 through 914 Processing helix chain 'A' and resid 918 through 942 Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 989 through 994 Processing helix chain 'A' and resid 1004 through 1037 removed outlier: 3.542A pdb=" N ARG A1021 " --> pdb=" O TYR A1017 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A1024 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASN A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A1026 " --> pdb=" O HIS A1022 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1053 removed outlier: 3.734A pdb=" N TYR A1050 " --> pdb=" O ASP A1047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A1053 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1076 removed outlier: 3.673A pdb=" N VAL A1074 " --> pdb=" O ASP A1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 52 through 72 removed outlier: 3.729A pdb=" N LEU B 58 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 59 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 67 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 70 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.562A pdb=" N ARG B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 135 removed outlier: 3.850A pdb=" N CYS B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.596A pdb=" N ALA B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 189 through 208 removed outlier: 6.885A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.599A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 299 through 306 removed outlier: 4.108A pdb=" N LEU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 542 removed outlier: 4.168A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 No H-bonds generated for 'chain 'B' and resid 546 through 549' Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 651 through 662 removed outlier: 3.505A pdb=" N TYR B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 23 removed outlier: 3.512A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'G' and resid 5 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.597A pdb=" N ILE A 38 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY A 133 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A 43 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 135 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 231 through 236 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 353 No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 412 through 415 removed outlier: 7.054A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 367 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.962A pdb=" N PHE A 382 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 434 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 386 through 388 Processing sheet with id= H, first strand: chain 'A' and resid 811 through 816 removed outlier: 3.768A pdb=" N PHE A 815 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 885 through 887 Processing sheet with id= J, first strand: chain 'B' and resid 288 through 292 removed outlier: 8.675A pdb=" N TYR B 289 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 162 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR B 291 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU B 164 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS B 551 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 517 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 553 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 519 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE B 555 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 684 through 688 removed outlier: 3.670A pdb=" N LYS B 801 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 691 through 694 removed outlier: 3.637A pdb=" N SER B 750 " --> pdb=" O THR B 775 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 754 " --> pdb=" O THR B 771 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 770 " --> pdb=" O VAL B 799 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.685A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.464A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.952A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.303A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.760A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.570A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.80 Time building geometry restraints manager: 24.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14830 1.03 - 1.22: 52 1.22 - 1.42: 6274 1.42 - 1.61: 8785 1.61 - 1.81: 119 Bond restraints: 30060 Sorted by residual: bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " ideal model delta sigma weight residual 1.458 1.440 0.018 1.40e-02 5.10e+03 1.57e+00 bond pdb=" CB TRP A 413 " pdb=" CG TRP A 413 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB PHE A 832 " pdb=" CG PHE A 832 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.79e-01 bond pdb=" CA VAL C 133 " pdb=" CB VAL C 133 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 8.74e-01 ... (remaining 30055 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.97: 582 106.97 - 114.24: 36828 114.24 - 121.51: 11133 121.51 - 128.78: 5673 128.78 - 136.05: 137 Bond angle restraints: 54353 Sorted by residual: angle pdb=" N ASN A 430 " pdb=" CA ASN A 430 " pdb=" C ASN A 430 " ideal model delta sigma weight residual 109.24 113.73 -4.49 1.63e+00 3.76e-01 7.57e+00 angle pdb=" N LEU A 429 " pdb=" CA LEU A 429 " pdb=" C LEU A 429 " ideal model delta sigma weight residual 109.15 106.01 3.14 1.44e+00 4.82e-01 4.77e+00 angle pdb=" C1' ADP A1201 " pdb=" C2' ADP A1201 " pdb=" C3' ADP A1201 " ideal model delta sigma weight residual 111.00 104.74 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" CA ILE A1029 " pdb=" CB ILE A1029 " pdb=" CG2 ILE A1029 " ideal model delta sigma weight residual 110.50 113.78 -3.28 1.70e+00 3.46e-01 3.72e+00 angle pdb=" O1B ADP A1201 " pdb=" PB ADP A1201 " pdb=" O2B ADP A1201 " ideal model delta sigma weight residual 119.90 114.19 5.71 3.00e+00 1.11e-01 3.62e+00 ... (remaining 54348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.02: 13757 32.02 - 64.05: 313 64.05 - 96.07: 19 96.07 - 128.10: 0 128.10 - 160.12: 1 Dihedral angle restraints: 14090 sinusoidal: 7700 harmonic: 6390 Sorted by residual: dihedral pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " pdb=" CZ ARG A 294 " pdb=" NH1 ARG A 294 " ideal model delta sinusoidal sigma weight residual 0.00 65.39 -65.39 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 100.12 -160.12 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" CD ARG A 712 " pdb=" NE ARG A 712 " pdb=" CZ ARG A 712 " pdb=" NH1 ARG A 712 " ideal model delta sinusoidal sigma weight residual 0.00 -40.24 40.24 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 14087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1528 0.032 - 0.065: 565 0.065 - 0.097: 152 0.097 - 0.130: 83 0.130 - 0.162: 14 Chirality restraints: 2342 Sorted by residual: chirality pdb=" CA ILE A 879 " pdb=" N ILE A 879 " pdb=" C ILE A 879 " pdb=" CB ILE A 879 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CB ILE A1029 " pdb=" CA ILE A1029 " pdb=" CG1 ILE A1029 " pdb=" CG2 ILE A1029 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE A 387 " pdb=" N ILE A 387 " pdb=" C ILE A 387 " pdb=" CB ILE A 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2339 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 294 " 0.901 9.50e-02 1.11e+02 3.01e-01 1.04e+02 pdb=" NE ARG A 294 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 294 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 294 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 294 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 294 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 294 " 0.015 2.00e-02 2.50e+03 pdb="HH21 ARG A 294 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 294 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 712 " 0.595 9.50e-02 1.11e+02 2.00e-01 5.04e+01 pdb=" NE ARG A 712 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 712 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 712 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 712 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 712 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 712 " 0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 712 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 712 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 184 " 0.564 9.50e-02 1.11e+02 1.89e-01 4.47e+01 pdb=" NE ARG A 184 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 184 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 184 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 184 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG A 184 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 184 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG A 184 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 184 " 0.017 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 431 2.05 - 2.69: 47713 2.69 - 3.33: 85244 3.33 - 3.96: 106731 3.96 - 4.60: 170461 Nonbonded interactions: 410580 Sorted by model distance: nonbonded pdb=" OD1 ASN A 688 " pdb=" H ILE A 691 " model vdw 1.418 1.850 nonbonded pdb=" HD1 HIS B 94 " pdb=" O ALA B 203 " model vdw 1.453 1.850 nonbonded pdb=" O LEU B 166 " pdb=" H TRP B 293 " model vdw 1.480 1.850 nonbonded pdb=" H LEU A 44 " pdb=" O GLU A 55 " model vdw 1.516 1.850 nonbonded pdb="HD21 ASN A 430 " pdb=" OD1 ASN A 465 " model vdw 1.534 1.850 ... (remaining 410575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.430 Extract box with map and model: 8.640 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 95.300 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.004 0.044 15179 Z= 0.247 Angle : 0.587 6.260 20569 Z= 0.307 Chirality : 0.041 0.162 2342 Planarity : 0.011 0.388 2612 Dihedral : 12.440 160.121 5609 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 2.13 % Allowed : 5.30 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.42 (0.20), residues: 1818 helix: -0.13 (0.20), residues: 676 sheet: -1.14 (0.28), residues: 339 loop : -1.47 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 413 HIS 0.006 0.001 HIS B 607 PHE 0.020 0.002 PHE B 129 TYR 0.024 0.002 TYR B 658 ARG 0.048 0.001 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 331 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 852 GLU cc_start: 0.8192 (tt0) cc_final: 0.7535 (tp30) REVERT: A 1050 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: C 155 ASN cc_start: 0.7549 (t0) cc_final: 0.7253 (t0) REVERT: C 186 ASP cc_start: 0.6397 (m-30) cc_final: 0.5789 (m-30) REVERT: G 11 GLN cc_start: 0.7513 (tt0) cc_final: 0.7256 (tp40) outliers start: 35 outliers final: 17 residues processed: 359 average time/residue: 0.7346 time to fit residues: 366.3247 Evaluate side-chains 203 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN A 554 GLN A 734 GLN A 776 ASN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 258 GLN C 230 ASN C 295 ASN G 4 ASN G 18 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15179 Z= 0.237 Angle : 0.628 7.095 20569 Z= 0.325 Chirality : 0.041 0.148 2342 Planarity : 0.005 0.056 2612 Dihedral : 7.753 166.830 2050 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.50 % Allowed : 10.55 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.35 (0.19), residues: 1818 helix: -0.05 (0.18), residues: 709 sheet: -1.16 (0.27), residues: 347 loop : -1.48 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.006 0.001 HIS B 190 PHE 0.023 0.002 PHE A1009 TYR 0.023 0.002 TYR A1067 ARG 0.009 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 852 GLU cc_start: 0.8061 (tt0) cc_final: 0.7489 (tp30) REVERT: A 1050 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: A 1074 VAL cc_start: 0.8492 (t) cc_final: 0.8262 (p) REVERT: B 741 TRP cc_start: 0.7576 (m100) cc_final: 0.6926 (m100) REVERT: G 11 GLN cc_start: 0.7007 (tt0) cc_final: 0.6721 (tp40) REVERT: G 40 TYR cc_start: 0.8171 (t80) cc_final: 0.7894 (t80) outliers start: 41 outliers final: 27 residues processed: 229 average time/residue: 0.7039 time to fit residues: 228.2858 Evaluate side-chains 196 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 chunk 149 optimal weight: 0.0470 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15179 Z= 0.162 Angle : 0.560 7.326 20569 Z= 0.282 Chirality : 0.040 0.144 2342 Planarity : 0.004 0.049 2612 Dihedral : 7.425 171.405 2042 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.95 % Allowed : 11.83 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1818 helix: 0.40 (0.19), residues: 705 sheet: -0.96 (0.27), residues: 343 loop : -1.29 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.006 0.001 HIS A 909 PHE 0.010 0.001 PHE C 199 TYR 0.020 0.001 TYR A1067 ARG 0.020 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8054 (tp30) cc_final: 0.7820 (tp30) REVERT: A 521 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: A 852 GLU cc_start: 0.7966 (tt0) cc_final: 0.7455 (tp30) REVERT: A 1050 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: G 11 GLN cc_start: 0.6937 (tt0) cc_final: 0.6678 (tp40) REVERT: G 40 TYR cc_start: 0.8201 (t80) cc_final: 0.7980 (t80) outliers start: 32 outliers final: 23 residues processed: 201 average time/residue: 0.6641 time to fit residues: 192.3025 Evaluate side-chains 185 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN C 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15179 Z= 0.276 Angle : 0.586 7.146 20569 Z= 0.301 Chirality : 0.040 0.253 2342 Planarity : 0.004 0.044 2612 Dihedral : 7.045 174.425 2031 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.44 % Allowed : 12.44 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.19 (0.19), residues: 1818 helix: 0.11 (0.18), residues: 703 sheet: -1.00 (0.27), residues: 348 loop : -1.45 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.005 0.001 HIS A 199 PHE 0.014 0.002 PHE B 129 TYR 0.019 0.002 TYR A1067 ARG 0.007 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8389 (mpt) cc_final: 0.8163 (mpt) REVERT: A 521 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: A 852 GLU cc_start: 0.7892 (tt0) cc_final: 0.7373 (tp30) REVERT: A 1050 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 161 VAL cc_start: 0.9208 (t) cc_final: 0.8910 (m) REVERT: G 11 GLN cc_start: 0.6842 (tt0) cc_final: 0.6598 (tp40) outliers start: 40 outliers final: 33 residues processed: 188 average time/residue: 0.7264 time to fit residues: 197.6249 Evaluate side-chains 186 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15179 Z= 0.305 Angle : 0.602 8.957 20569 Z= 0.310 Chirality : 0.040 0.151 2342 Planarity : 0.004 0.056 2612 Dihedral : 7.157 174.873 2031 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.05 % Allowed : 12.38 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.37 (0.19), residues: 1818 helix: -0.01 (0.19), residues: 703 sheet: -1.18 (0.27), residues: 347 loop : -1.54 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 697 HIS 0.005 0.001 HIS A 199 PHE 0.013 0.002 PHE B 129 TYR 0.016 0.002 TYR A1067 ARG 0.010 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 150 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8168 (tp30) cc_final: 0.7927 (tp30) REVERT: A 521 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: A 556 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: A 852 GLU cc_start: 0.7976 (tt0) cc_final: 0.7437 (tp30) REVERT: A 1050 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: B 161 VAL cc_start: 0.9217 (t) cc_final: 0.8916 (m) REVERT: C 188 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7317 (mpp) REVERT: G 11 GLN cc_start: 0.6893 (tt0) cc_final: 0.6646 (tp40) outliers start: 50 outliers final: 39 residues processed: 188 average time/residue: 0.6583 time to fit residues: 180.3184 Evaluate side-chains 189 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 188 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15179 Z= 0.176 Angle : 0.539 6.874 20569 Z= 0.271 Chirality : 0.039 0.147 2342 Planarity : 0.004 0.046 2612 Dihedral : 6.763 176.514 2026 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.32 % Allowed : 13.78 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1818 helix: 0.44 (0.19), residues: 703 sheet: -1.11 (0.27), residues: 334 loop : -1.30 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.004 0.001 HIS A 909 PHE 0.011 0.001 PHE A 473 TYR 0.013 0.001 TYR A1067 ARG 0.004 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8065 (tp30) cc_final: 0.7814 (tp30) REVERT: A 521 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: A 852 GLU cc_start: 0.7882 (tt0) cc_final: 0.7362 (tp30) REVERT: A 1050 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 161 VAL cc_start: 0.9210 (t) cc_final: 0.8903 (m) REVERT: C 186 ASP cc_start: 0.6565 (m-30) cc_final: 0.6125 (m-30) REVERT: C 188 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: G 11 GLN cc_start: 0.6892 (tt0) cc_final: 0.6631 (tp40) outliers start: 38 outliers final: 33 residues processed: 181 average time/residue: 0.7463 time to fit residues: 198.2831 Evaluate side-chains 185 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15179 Z= 0.183 Angle : 0.533 8.403 20569 Z= 0.267 Chirality : 0.039 0.147 2342 Planarity : 0.004 0.036 2612 Dihedral : 6.700 178.720 2026 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.26 % Allowed : 13.78 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1818 helix: 0.62 (0.19), residues: 703 sheet: -1.07 (0.28), residues: 336 loop : -1.27 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 PHE 0.009 0.001 PHE A 473 TYR 0.014 0.001 TYR A1067 ARG 0.004 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8116 (tp30) cc_final: 0.7876 (tp30) REVERT: A 521 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: A 852 GLU cc_start: 0.7866 (tt0) cc_final: 0.7360 (tp30) REVERT: A 990 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8588 (p0) REVERT: A 1050 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: B 161 VAL cc_start: 0.9250 (t) cc_final: 0.8937 (m) REVERT: C 186 ASP cc_start: 0.6588 (m-30) cc_final: 0.6176 (m-30) REVERT: C 188 MET cc_start: 0.7656 (tpt) cc_final: 0.7080 (mpp) REVERT: G 11 GLN cc_start: 0.6905 (tt0) cc_final: 0.6621 (tp40) outliers start: 37 outliers final: 32 residues processed: 181 average time/residue: 0.6992 time to fit residues: 183.6888 Evaluate side-chains 187 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15179 Z= 0.234 Angle : 0.556 9.911 20569 Z= 0.281 Chirality : 0.039 0.146 2342 Planarity : 0.004 0.047 2612 Dihedral : 6.769 179.499 2026 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.27 % Favored : 93.67 % Rotamer: Outliers : 2.68 % Allowed : 13.72 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1818 helix: 0.48 (0.19), residues: 710 sheet: -1.09 (0.27), residues: 342 loop : -1.37 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 PHE 0.009 0.001 PHE C 151 TYR 0.016 0.002 TYR A1067 ARG 0.008 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8124 (tp30) cc_final: 0.7911 (tp30) REVERT: A 521 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: A 852 GLU cc_start: 0.7897 (tt0) cc_final: 0.7682 (tm-30) REVERT: A 990 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8642 (p0) REVERT: A 1050 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: B 161 VAL cc_start: 0.9272 (t) cc_final: 0.8949 (m) REVERT: B 740 ARG cc_start: 0.5718 (OUTLIER) cc_final: 0.3187 (ptp-170) REVERT: C 186 ASP cc_start: 0.6632 (m-30) cc_final: 0.6205 (m-30) REVERT: C 188 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7036 (mpp) REVERT: G 11 GLN cc_start: 0.6904 (tt0) cc_final: 0.6611 (tp40) outliers start: 44 outliers final: 37 residues processed: 181 average time/residue: 0.6893 time to fit residues: 180.0336 Evaluate side-chains 190 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15179 Z= 0.184 Angle : 0.531 9.124 20569 Z= 0.266 Chirality : 0.039 0.145 2342 Planarity : 0.004 0.033 2612 Dihedral : 6.668 177.830 2026 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 2.62 % Allowed : 13.96 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1818 helix: 0.72 (0.19), residues: 704 sheet: -1.04 (0.28), residues: 339 loop : -1.26 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS A 199 PHE 0.010 0.001 PHE A 473 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8209 (tp30) cc_final: 0.8002 (tp30) REVERT: A 521 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: A 556 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: A 852 GLU cc_start: 0.7874 (tt0) cc_final: 0.7670 (tm-30) REVERT: A 990 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8612 (p0) REVERT: A 1050 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: B 161 VAL cc_start: 0.9269 (t) cc_final: 0.8941 (m) REVERT: B 740 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.3071 (ptp-170) REVERT: C 186 ASP cc_start: 0.6612 (m-30) cc_final: 0.6375 (m-30) REVERT: C 188 MET cc_start: 0.7638 (tpt) cc_final: 0.7062 (mpp) REVERT: G 11 GLN cc_start: 0.6903 (tt0) cc_final: 0.6612 (tp40) outliers start: 43 outliers final: 32 residues processed: 180 average time/residue: 0.7167 time to fit residues: 189.1741 Evaluate side-chains 184 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 112 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15179 Z= 0.142 Angle : 0.522 9.746 20569 Z= 0.257 Chirality : 0.039 0.148 2342 Planarity : 0.003 0.035 2612 Dihedral : 6.401 172.962 2026 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.07 % Allowed : 14.51 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1818 helix: 1.15 (0.20), residues: 704 sheet: -0.93 (0.27), residues: 341 loop : -1.07 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.000 HIS A 693 PHE 0.010 0.001 PHE A 732 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG B 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: A 990 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8527 (p0) REVERT: A 1050 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: B 161 VAL cc_start: 0.9266 (t) cc_final: 0.8930 (m) REVERT: B 740 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.2948 (ptp-170) REVERT: C 186 ASP cc_start: 0.6605 (m-30) cc_final: 0.6367 (m-30) REVERT: C 188 MET cc_start: 0.7639 (tpt) cc_final: 0.6984 (mpp) REVERT: G 11 GLN cc_start: 0.6903 (tt0) cc_final: 0.6612 (tp40) outliers start: 34 outliers final: 29 residues processed: 177 average time/residue: 0.6941 time to fit residues: 178.4509 Evaluate side-chains 180 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.116361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.081711 restraints weight = 121556.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.085550 restraints weight = 51331.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.087862 restraints weight = 31132.503| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15179 Z= 0.181 Angle : 0.528 9.457 20569 Z= 0.262 Chirality : 0.039 0.145 2342 Planarity : 0.003 0.034 2612 Dihedral : 6.377 169.973 2026 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 1.95 % Allowed : 14.76 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1818 helix: 1.10 (0.19), residues: 704 sheet: -0.89 (0.28), residues: 333 loop : -1.14 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS A 199 PHE 0.010 0.001 PHE A 249 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.27 seconds wall clock time: 115 minutes 38.08 seconds (6938.08 seconds total)