Starting phenix.real_space_refine on Fri Sep 27 00:49:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/09_2024/3jb7_6404.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/09_2024/3jb7_6404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/09_2024/3jb7_6404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/09_2024/3jb7_6404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/09_2024/3jb7_6404.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/09_2024/3jb7_6404.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.095 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 54 5.16 5 C 8939 2.51 5 N 2430 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1198, 9561 Classifications: {'peptide': 1198} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 35, 'TRANS': 1145} Chain breaks: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 170 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "t" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 138 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 6} Link IDs: {'rna3p': 5} Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna3p_pyr': 5} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CTP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.46, per 1000 atoms: 0.60 Number of scatterers: 14176 At special positions: 0 Unit cell: (103.36, 133.28, 108.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 20 15.00 O 2733 8.00 N 2430 7.00 C 8939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 16 sheets defined 53.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.553A pdb=" N GLU A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.599A pdb=" N HIS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.574A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.192A pdb=" N ILE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.605A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.552A pdb=" N LEU A 112 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 removed outlier: 3.571A pdb=" N HIS A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 165 through 175 removed outlier: 4.349A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.860A pdb=" N PHE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.716A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.876A pdb=" N LYS A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.584A pdb=" N ALA A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.739A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.669A pdb=" N SER A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.607A pdb=" N ALA A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 4.026A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.890A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 409 removed outlier: 3.619A pdb=" N ALA A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.619A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 4.035A pdb=" N ALA A 443 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.146A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 4.476A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.647A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 514 removed outlier: 3.581A pdb=" N ASN A 514 " --> pdb=" O TYR A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 514' Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.649A pdb=" N TYR A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 574 removed outlier: 4.063A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.545A pdb=" N GLN A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 666 removed outlier: 3.556A pdb=" N VAL A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.646A pdb=" N TYR A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.702A pdb=" N ALA A 756 " --> pdb=" O ARG A 752 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 762 " --> pdb=" O MET A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.930A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 783 " --> pdb=" O MET A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.821A pdb=" N THR A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 809 " --> pdb=" O TYR A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 800 through 809' Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 867 through 871 removed outlier: 4.109A pdb=" N TYR A 870 " --> pdb=" O ARG A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 4.042A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 removed outlier: 4.001A pdb=" N GLN A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.922A pdb=" N LEU A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 910 removed outlier: 3.832A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 925 removed outlier: 3.906A pdb=" N ASP A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.430A pdb=" N THR A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 3.726A pdb=" N ALA A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 969 through 971 No H-bonds generated for 'chain 'A' and resid 969 through 971' Processing helix chain 'A' and resid 972 through 978 removed outlier: 4.210A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 993 through 997 removed outlier: 3.557A pdb=" N ARG A 997 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.798A pdb=" N VAL A1003 " --> pdb=" O HIS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1021 removed outlier: 3.621A pdb=" N ALA A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1018 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A1019 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 removed outlier: 3.839A pdb=" N HIS A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 4.006A pdb=" N SER A1049 " --> pdb=" O TYR A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1062 removed outlier: 3.774A pdb=" N PHE A1058 " --> pdb=" O GLY A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1080 removed outlier: 3.797A pdb=" N ASN A1069 " --> pdb=" O ASP A1065 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1078 " --> pdb=" O ASP A1074 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1095 through 1101 removed outlier: 3.797A pdb=" N TYR A1099 " --> pdb=" O GLY A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1104 No H-bonds generated for 'chain 'A' and resid 1102 through 1104' Processing helix chain 'A' and resid 1105 through 1114 removed outlier: 3.621A pdb=" N THR A1111 " --> pdb=" O ASN A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1126 removed outlier: 3.643A pdb=" N LEU A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1159 removed outlier: 3.917A pdb=" N ARG A1159 " --> pdb=" O SER A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 removed outlier: 3.590A pdb=" N TYR A1167 " --> pdb=" O PRO A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'A' and resid 1176 through 1188 removed outlier: 3.755A pdb=" N HIS A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1186 " --> pdb=" O TYR A1182 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1188 " --> pdb=" O HIS A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1211 removed outlier: 3.619A pdb=" N ILE A1206 " --> pdb=" O HIS A1202 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A1207 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.650A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.634A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 132 through 147 removed outlier: 5.366A pdb=" N ALA B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.700A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.602A pdb=" N ASN B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.605A pdb=" N SER B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 244 through 248 removed outlier: 4.010A pdb=" N GLU B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.737A pdb=" N PHE B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.616A pdb=" N ALA B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.230A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.601A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.523A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 429 removed outlier: 3.776A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.658A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 461 removed outlier: 3.527A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.873A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 removed outlier: 3.614A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.534A pdb=" N ASP B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.705A pdb=" N MET B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.546A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.657A pdb=" N ARG A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.700A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.978A pdb=" N SER A 380 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 374 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.829A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 541 through 544 Processing sheet with id=G, first strand: chain 'A' and resid 547 through 548 removed outlier: 4.424A pdb=" N ASP A 547 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 712 " --> pdb=" O ASP A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=G Processing sheet with id=H, first strand: chain 'A' and resid 621 through 624 removed outlier: 3.665A pdb=" N GLY A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=J, first strand: chain 'A' and resid 795 through 797 removed outlier: 3.630A pdb=" N VAL A 796 " --> pdb=" O THR A 826 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 829 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 1022 through 1025 removed outlier: 3.578A pdb=" N GLU A1022 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A1199 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.833A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.827A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=M Processing sheet with id=N, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=O, first strand: chain 'B' and resid 266 through 267 removed outlier: 3.590A pdb=" N SER B 317 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N THR B 261 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 313 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'B' and resid 485 through 489 removed outlier: 6.385A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1389 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: 4.87 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 730 1.23 - 1.38: 4749 1.38 - 1.53: 8094 1.53 - 1.68: 832 1.68 - 1.83: 95 Bond restraints: 14500 Sorted by residual: bond pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta sigma weight residual 1.466 1.114 0.352 1.50e-02 4.44e+03 5.52e+02 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.233 1.087 0.146 1.13e-02 7.83e+03 1.67e+02 bond pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 1.540 1.401 0.138 1.10e-02 8.26e+03 1.59e+02 bond pdb=" CA PRO C 132 " pdb=" C PRO C 132 " ideal model delta sigma weight residual 1.522 1.383 0.139 1.16e-02 7.43e+03 1.43e+02 bond pdb=" N PRO D 111 " pdb=" CD PRO D 111 " ideal model delta sigma weight residual 1.473 1.638 -0.165 1.40e-02 5.10e+03 1.39e+02 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 19621 4.03 - 8.06: 76 8.06 - 12.09: 5 12.09 - 16.12: 2 16.12 - 20.15: 2 Bond angle restraints: 19706 Sorted by residual: angle pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" C LEU C 130 " ideal model delta sigma weight residual 113.61 133.76 -20.15 1.50e+00 4.44e-01 1.80e+02 angle pdb=" N THR C 118 " pdb=" CA THR C 118 " pdb=" C THR C 118 " ideal model delta sigma weight residual 111.14 121.30 -10.16 1.08e+00 8.57e-01 8.84e+01 angle pdb=" CG1 VAL C 120 " pdb=" CB VAL C 120 " pdb=" CG2 VAL C 120 " ideal model delta sigma weight residual 110.80 95.30 15.50 2.20e+00 2.07e-01 4.97e+01 angle pdb=" N PRO D 111 " pdb=" CD PRO D 111 " pdb=" CG PRO D 111 " ideal model delta sigma weight residual 103.20 93.05 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 112.00 102.63 9.37 1.40e+00 5.10e-01 4.48e+01 ... (remaining 19701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 8269 18.40 - 36.79: 346 36.79 - 55.19: 64 55.19 - 73.59: 26 73.59 - 91.98: 6 Dihedral angle restraints: 8711 sinusoidal: 3611 harmonic: 5100 Sorted by residual: dihedral pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual 122.80 145.09 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" C LEU C 130 " pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual -122.60 -144.35 21.75 0 2.50e+00 1.60e-01 7.57e+01 dihedral pdb=" CA TYR A 971 " pdb=" C TYR A 971 " pdb=" N GLY A 972 " pdb=" CA GLY A 972 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 8708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 2202 0.219 - 0.439: 4 0.439 - 0.658: 1 0.658 - 0.877: 1 0.877 - 1.096: 1 Chirality restraints: 2209 Sorted by residual: chirality pdb=" CA LEU C 130 " pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CB LEU C 130 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA PRO D 111 " pdb=" N PRO D 111 " pdb=" C PRO D 111 " pdb=" CB PRO D 111 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" C PRO C 132 " pdb=" CB PRO C 132 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 2206 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 117 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ARG C 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG C 117 " 0.024 2.00e-02 2.50e+03 pdb=" N THR C 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 125 " -0.015 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE C 125 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 125 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 125 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 125 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 125 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 116 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C SER C 116 " -0.027 2.00e-02 2.50e+03 pdb=" O SER C 116 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG C 117 " 0.009 2.00e-02 2.50e+03 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 4 1.61 - 2.44: 47 2.44 - 3.26: 15145 3.26 - 4.08: 34042 4.08 - 4.90: 62597 Warning: very small nonbonded interaction distances. Nonbonded interactions: 111835 Sorted by model distance: nonbonded pdb=" OD1 ASP A1053 " pdb=" NH1 ARG D 117 " model vdw 0.793 3.120 nonbonded pdb=" NH2 ARG A1193 " pdb=" CA VAL D 113 " model vdw 1.528 3.550 nonbonded pdb=" CE2 TYR B 264 " pdb=" N ARG C 117 " model vdw 1.529 3.420 nonbonded pdb=" OD1 ASP A1053 " pdb=" CZ ARG D 117 " model vdw 1.553 3.270 nonbonded pdb=" CE2 TYR B 264 " pdb=" C SER C 116 " model vdw 1.675 3.570 ... (remaining 111830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.110 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.007 0.352 14500 Z= 0.437 Angle : 0.761 20.148 19706 Z= 0.446 Chirality : 0.054 1.096 2209 Planarity : 0.004 0.038 2461 Dihedral : 11.597 91.984 5427 Min Nonbonded Distance : 0.793 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.90 % Favored : 95.87 % Rotamer: Outliers : 1.13 % Allowed : 3.05 % Favored : 95.82 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.19), residues: 1719 helix: -3.31 (0.11), residues: 727 sheet: -1.82 (0.35), residues: 155 loop : 0.78 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 742 HIS 0.013 0.001 HIS C 131 PHE 0.025 0.002 PHE C 125 TYR 0.017 0.001 TYR A1133 ARG 0.003 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 456 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.8916 (t70) cc_final: 0.8634 (t-170) REVERT: A 49 ILE cc_start: 0.9030 (mt) cc_final: 0.8783 (mt) REVERT: A 74 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8888 (mm-30) REVERT: A 91 ASP cc_start: 0.8768 (t0) cc_final: 0.8491 (m-30) REVERT: A 102 ASP cc_start: 0.9379 (m-30) cc_final: 0.8746 (t0) REVERT: A 106 THR cc_start: 0.9783 (m) cc_final: 0.9563 (p) REVERT: A 133 MET cc_start: 0.9243 (ptm) cc_final: 0.8981 (ptp) REVERT: A 137 GLN cc_start: 0.8964 (mt0) cc_final: 0.8594 (mt0) REVERT: A 150 CYS cc_start: 0.9696 (m) cc_final: 0.9440 (m) REVERT: A 172 LYS cc_start: 0.9497 (tttt) cc_final: 0.9224 (ttmm) REVERT: A 179 ASP cc_start: 0.9132 (t70) cc_final: 0.8304 (t0) REVERT: A 218 MET cc_start: 0.9682 (mmm) cc_final: 0.9237 (mmm) REVERT: A 310 GLU cc_start: 0.9330 (tt0) cc_final: 0.8998 (tp30) REVERT: A 349 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9173 (t) REVERT: A 372 LEU cc_start: 0.9562 (mt) cc_final: 0.9288 (mt) REVERT: A 373 MET cc_start: 0.9365 (ttm) cc_final: 0.9101 (ttm) REVERT: A 381 LEU cc_start: 0.9540 (mt) cc_final: 0.9123 (mt) REVERT: A 483 ASP cc_start: 0.9188 (p0) cc_final: 0.8956 (p0) REVERT: A 502 MET cc_start: 0.9789 (tpp) cc_final: 0.9513 (tpp) REVERT: A 542 LEU cc_start: 0.9583 (tp) cc_final: 0.9257 (tt) REVERT: A 547 ASP cc_start: 0.9229 (p0) cc_final: 0.8922 (m-30) REVERT: A 596 GLN cc_start: 0.8942 (mt0) cc_final: 0.8637 (pm20) REVERT: A 609 CYS cc_start: 0.9577 (m) cc_final: 0.9187 (m) REVERT: A 618 THR cc_start: 0.9005 (m) cc_final: 0.8606 (p) REVERT: A 623 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8945 (mm-30) REVERT: A 634 GLU cc_start: 0.8875 (tt0) cc_final: 0.8619 (tp30) REVERT: A 653 GLN cc_start: 0.9570 (pt0) cc_final: 0.9302 (tt0) REVERT: A 683 MET cc_start: 0.9279 (ttp) cc_final: 0.8877 (tmm) REVERT: A 685 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9385 (mp) REVERT: A 714 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8896 (mp0) REVERT: A 731 THR cc_start: 0.9401 (m) cc_final: 0.9009 (p) REVERT: A 759 GLU cc_start: 0.9327 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 784 CYS cc_start: 0.9728 (t) cc_final: 0.9147 (t) REVERT: A 788 CYS cc_start: 0.9546 (m) cc_final: 0.9241 (m) REVERT: A 799 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8771 (tptt) REVERT: A 834 LEU cc_start: 0.9795 (mt) cc_final: 0.9533 (mt) REVERT: A 844 GLU cc_start: 0.9513 (mt-10) cc_final: 0.8983 (mp0) REVERT: A 890 MET cc_start: 0.8724 (mtp) cc_final: 0.7981 (tmm) REVERT: A 899 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9183 (mp0) REVERT: A 918 ASP cc_start: 0.8822 (m-30) cc_final: 0.8589 (m-30) REVERT: A 937 LEU cc_start: 0.9185 (tp) cc_final: 0.8842 (tt) REVERT: A 939 GLN cc_start: 0.9460 (tp40) cc_final: 0.9013 (tp40) REVERT: A 961 HIS cc_start: 0.7988 (m90) cc_final: 0.7755 (m-70) REVERT: A 997 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.8155 (ttt180) REVERT: A 1000 ASP cc_start: 0.9196 (t0) cc_final: 0.8921 (m-30) REVERT: A 1007 ASP cc_start: 0.8741 (m-30) cc_final: 0.8510 (t0) REVERT: A 1009 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8470 (mmtt) REVERT: A 1033 LEU cc_start: 0.9187 (pp) cc_final: 0.8946 (pp) REVERT: A 1035 HIS cc_start: 0.9422 (m170) cc_final: 0.9219 (m170) REVERT: A 1170 SER cc_start: 0.3283 (OUTLIER) cc_final: 0.1337 (p) REVERT: A 1187 ARG cc_start: 0.9036 (ttp-170) cc_final: 0.8666 (ttm170) REVERT: B 73 TYR cc_start: 0.9223 (m-80) cc_final: 0.9004 (m-80) REVERT: B 162 GLU cc_start: 0.9461 (tt0) cc_final: 0.9160 (tm-30) REVERT: B 178 TYR cc_start: 0.9112 (m-80) cc_final: 0.8680 (m-10) REVERT: B 183 ILE cc_start: 0.9386 (mt) cc_final: 0.9148 (tp) REVERT: B 199 ARG cc_start: 0.8945 (ttt180) cc_final: 0.8535 (ttt-90) REVERT: B 212 ASN cc_start: 0.9221 (t0) cc_final: 0.8922 (t0) REVERT: B 267 VAL cc_start: 0.9279 (t) cc_final: 0.8873 (p) REVERT: B 289 GLU cc_start: 0.9559 (mm-30) cc_final: 0.8690 (mm-30) REVERT: B 337 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9118 (tp30) REVERT: B 354 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8780 (tt0) REVERT: B 398 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8794 (tm-30) REVERT: B 427 ILE cc_start: 0.9674 (mt) cc_final: 0.9470 (pt) REVERT: B 442 VAL cc_start: 0.9458 (t) cc_final: 0.9099 (p) REVERT: B 451 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9015 (tp30) REVERT: B 474 MET cc_start: 0.9444 (mmm) cc_final: 0.9240 (mmm) REVERT: B 501 THR cc_start: 0.9112 (p) cc_final: 0.8824 (t) REVERT: B 554 ILE cc_start: 0.9728 (mt) cc_final: 0.9506 (mt) REVERT: C 120 VAL cc_start: 0.7905 (t) cc_final: 0.7662 (t) REVERT: C 128 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5433 (mm-30) outliers start: 17 outliers final: 5 residues processed: 469 average time/residue: 0.3039 time to fit residues: 197.4050 Evaluate side-chains 268 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 259 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 1170 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 130 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 413 HIS A 519 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 436 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14500 Z= 0.314 Angle : 0.678 10.521 19706 Z= 0.352 Chirality : 0.043 0.158 2209 Planarity : 0.004 0.034 2461 Dihedral : 10.638 88.113 2156 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 3.38 % Allowed : 11.81 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: -0.96 (0.19), residues: 1719 helix: -1.19 (0.16), residues: 756 sheet: -1.57 (0.38), residues: 150 loop : 0.40 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 742 HIS 0.006 0.001 HIS A 999 PHE 0.021 0.002 PHE A 527 TYR 0.018 0.002 TYR A 805 ARG 0.009 0.001 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 279 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9011 (t0) cc_final: 0.8652 (p0) REVERT: A 74 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8858 (mm-30) REVERT: A 91 ASP cc_start: 0.8766 (t0) cc_final: 0.8120 (m-30) REVERT: A 102 ASP cc_start: 0.9148 (m-30) cc_final: 0.8841 (t0) REVERT: A 179 ASP cc_start: 0.8745 (t70) cc_final: 0.8264 (t0) REVERT: A 180 GLU cc_start: 0.8607 (mp0) cc_final: 0.8278 (mm-30) REVERT: A 218 MET cc_start: 0.9555 (mmm) cc_final: 0.9128 (tpp) REVERT: A 237 CYS cc_start: 0.9681 (OUTLIER) cc_final: 0.9408 (t) REVERT: A 240 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8196 (p0) REVERT: A 310 GLU cc_start: 0.9350 (tt0) cc_final: 0.9064 (tp30) REVERT: A 350 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9262 (mp0) REVERT: A 354 ASP cc_start: 0.9517 (t0) cc_final: 0.9293 (t0) REVERT: A 361 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9158 (mp) REVERT: A 362 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8544 (mp0) REVERT: A 381 LEU cc_start: 0.9518 (mt) cc_final: 0.9160 (mt) REVERT: A 539 ARG cc_start: 0.3488 (ptt90) cc_final: 0.3143 (ptt-90) REVERT: A 542 LEU cc_start: 0.9417 (tp) cc_final: 0.9097 (tt) REVERT: A 609 CYS cc_start: 0.9679 (m) cc_final: 0.9435 (m) REVERT: A 618 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 634 GLU cc_start: 0.9140 (tt0) cc_final: 0.8327 (tp30) REVERT: A 714 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8928 (mp0) REVERT: A 731 THR cc_start: 0.9420 (m) cc_final: 0.9202 (p) REVERT: A 759 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 779 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9128 (tpp) REVERT: A 788 CYS cc_start: 0.9476 (m) cc_final: 0.9215 (m) REVERT: A 799 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8728 (tptt) REVERT: A 844 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9066 (mp0) REVERT: A 877 ASP cc_start: 0.9444 (t0) cc_final: 0.8919 (t0) REVERT: A 890 MET cc_start: 0.8898 (mtp) cc_final: 0.8027 (tmm) REVERT: A 899 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8855 (mp0) REVERT: A 918 ASP cc_start: 0.8758 (m-30) cc_final: 0.8551 (m-30) REVERT: A 939 GLN cc_start: 0.9438 (tp40) cc_final: 0.9013 (tp40) REVERT: A 961 HIS cc_start: 0.8105 (m90) cc_final: 0.7782 (m-70) REVERT: A 997 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.8018 (ttt180) REVERT: A 1000 ASP cc_start: 0.9171 (t0) cc_final: 0.8968 (m-30) REVERT: A 1007 ASP cc_start: 0.8728 (m-30) cc_final: 0.8521 (t0) REVERT: A 1009 LYS cc_start: 0.9021 (mmtp) cc_final: 0.8624 (mmmm) REVERT: A 1072 ARG cc_start: 0.5992 (ttp80) cc_final: 0.5467 (tpt90) REVERT: A 1125 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8715 (ttp-110) REVERT: B 81 ASN cc_start: 0.8625 (p0) cc_final: 0.8379 (t0) REVERT: B 162 GLU cc_start: 0.9392 (tt0) cc_final: 0.8975 (tm-30) REVERT: B 183 ILE cc_start: 0.9404 (mt) cc_final: 0.9151 (pt) REVERT: B 199 ARG cc_start: 0.9059 (ttt180) cc_final: 0.8828 (ttt-90) REVERT: B 212 ASN cc_start: 0.9343 (t0) cc_final: 0.8996 (t0) REVERT: B 289 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8550 (mm-30) REVERT: B 321 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: B 322 MET cc_start: 0.8556 (mtm) cc_final: 0.6676 (mtp) REVERT: B 354 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8895 (tt0) REVERT: B 451 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8977 (tp30) REVERT: B 501 THR cc_start: 0.8905 (p) cc_final: 0.8586 (t) REVERT: B 522 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.7783 (ttm110) REVERT: B 549 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8912 (mm-30) REVERT: C 128 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5219 (mm-30) REVERT: D 121 PHE cc_start: 0.6503 (t80) cc_final: 0.5726 (t80) outliers start: 51 outliers final: 24 residues processed: 313 average time/residue: 0.3320 time to fit residues: 149.4475 Evaluate side-chains 265 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14500 Z= 0.231 Angle : 0.599 8.360 19706 Z= 0.308 Chirality : 0.041 0.162 2209 Planarity : 0.004 0.038 2461 Dihedral : 10.189 87.628 2145 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 3.85 % Allowed : 13.21 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: -0.48 (0.20), residues: 1719 helix: -0.37 (0.18), residues: 771 sheet: -1.21 (0.36), residues: 159 loop : 0.18 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 445 HIS 0.007 0.001 HIS A 28 PHE 0.014 0.001 PHE C 121 TYR 0.011 0.001 TYR B 178 ARG 0.007 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 253 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8983 (t0) cc_final: 0.8572 (p0) REVERT: A 91 ASP cc_start: 0.8755 (t0) cc_final: 0.8340 (m-30) REVERT: A 92 GLU cc_start: 0.9442 (mt-10) cc_final: 0.9208 (mp0) REVERT: A 102 ASP cc_start: 0.9127 (m-30) cc_final: 0.8873 (t0) REVERT: A 218 MET cc_start: 0.9522 (mmm) cc_final: 0.9058 (tpp) REVERT: A 240 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8147 (p0) REVERT: A 310 GLU cc_start: 0.9258 (tt0) cc_final: 0.8946 (tp30) REVERT: A 350 GLU cc_start: 0.9478 (OUTLIER) cc_final: 0.9242 (mp0) REVERT: A 354 ASP cc_start: 0.9489 (t0) cc_final: 0.9279 (t0) REVERT: A 361 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9147 (mp) REVERT: A 362 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8621 (mp0) REVERT: A 381 LEU cc_start: 0.9496 (mt) cc_final: 0.9134 (mt) REVERT: A 421 LEU cc_start: 0.9549 (mt) cc_final: 0.9100 (mp) REVERT: A 539 ARG cc_start: 0.2671 (ptt90) cc_final: 0.2293 (ptt-90) REVERT: A 542 LEU cc_start: 0.9350 (tp) cc_final: 0.8967 (tt) REVERT: A 609 CYS cc_start: 0.9628 (m) cc_final: 0.9402 (m) REVERT: A 618 THR cc_start: 0.9259 (m) cc_final: 0.8989 (p) REVERT: A 634 GLU cc_start: 0.8991 (tt0) cc_final: 0.8380 (tp30) REVERT: A 683 MET cc_start: 0.9209 (ttt) cc_final: 0.9007 (tmm) REVERT: A 731 THR cc_start: 0.9428 (m) cc_final: 0.9213 (p) REVERT: A 759 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 779 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9039 (tpp) REVERT: A 799 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8773 (tptt) REVERT: A 828 MET cc_start: 0.6299 (ppp) cc_final: 0.5834 (ppp) REVERT: A 877 ASP cc_start: 0.9537 (t0) cc_final: 0.9003 (t0) REVERT: A 890 MET cc_start: 0.8949 (mtp) cc_final: 0.8011 (tmm) REVERT: A 899 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8847 (mp0) REVERT: A 918 ASP cc_start: 0.8804 (m-30) cc_final: 0.8560 (m-30) REVERT: A 922 LYS cc_start: 0.8020 (tppt) cc_final: 0.7773 (mmmt) REVERT: A 961 HIS cc_start: 0.8018 (m90) cc_final: 0.7691 (m-70) REVERT: A 997 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.8027 (ttt180) REVERT: A 1007 ASP cc_start: 0.8743 (m-30) cc_final: 0.8517 (t0) REVERT: A 1009 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8821 (mmmm) REVERT: A 1072 ARG cc_start: 0.6019 (ttp80) cc_final: 0.5461 (tpt90) REVERT: A 1092 PHE cc_start: 0.7479 (t80) cc_final: 0.7075 (t80) REVERT: B 81 ASN cc_start: 0.8612 (p0) cc_final: 0.8388 (t0) REVERT: B 162 GLU cc_start: 0.9383 (tt0) cc_final: 0.8791 (tm-30) REVERT: B 165 GLN cc_start: 0.9561 (mt0) cc_final: 0.9073 (mp10) REVERT: B 199 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8641 (ttp80) REVERT: B 212 ASN cc_start: 0.9365 (t0) cc_final: 0.8994 (t0) REVERT: B 321 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8259 (mmm) REVERT: B 354 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8896 (tt0) REVERT: B 449 MET cc_start: 0.9180 (mtp) cc_final: 0.8653 (mmm) REVERT: B 451 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8961 (tp30) REVERT: B 487 VAL cc_start: 0.9781 (OUTLIER) cc_final: 0.9510 (m) REVERT: B 522 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.7897 (ttm110) REVERT: B 549 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8911 (mm-30) REVERT: B 552 GLU cc_start: 0.9439 (tp30) cc_final: 0.9154 (tp30) REVERT: C 125 PHE cc_start: 0.8327 (t80) cc_final: 0.8082 (t80) REVERT: C 128 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5477 (tm-30) outliers start: 58 outliers final: 30 residues processed: 288 average time/residue: 0.2713 time to fit residues: 113.5559 Evaluate side-chains 249 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 231 ASN C 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14500 Z= 0.180 Angle : 0.571 9.341 19706 Z= 0.289 Chirality : 0.040 0.184 2209 Planarity : 0.003 0.037 2461 Dihedral : 9.892 86.791 2145 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 3.78 % Allowed : 14.47 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: -0.06 (0.20), residues: 1719 helix: 0.16 (0.19), residues: 766 sheet: -0.73 (0.37), residues: 154 loop : 0.11 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 445 HIS 0.010 0.001 HIS A 28 PHE 0.019 0.001 PHE D 121 TYR 0.022 0.001 TYR A 805 ARG 0.009 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 243 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9014 (t0) cc_final: 0.8795 (t0) REVERT: A 91 ASP cc_start: 0.8737 (t0) cc_final: 0.8293 (m-30) REVERT: A 92 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9230 (mp0) REVERT: A 156 LEU cc_start: 0.9671 (mt) cc_final: 0.9233 (tt) REVERT: A 237 CYS cc_start: 0.9652 (OUTLIER) cc_final: 0.9413 (t) REVERT: A 338 MET cc_start: 0.9095 (mmm) cc_final: 0.8846 (mmt) REVERT: A 350 GLU cc_start: 0.9428 (OUTLIER) cc_final: 0.9200 (mp0) REVERT: A 361 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9174 (mp) REVERT: A 362 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8571 (mp0) REVERT: A 381 LEU cc_start: 0.9519 (mt) cc_final: 0.9165 (mt) REVERT: A 539 ARG cc_start: 0.2455 (ptt90) cc_final: 0.2240 (ptt90) REVERT: A 542 LEU cc_start: 0.9394 (tp) cc_final: 0.9071 (tt) REVERT: A 551 MET cc_start: 0.9161 (mmm) cc_final: 0.8586 (mmm) REVERT: A 609 CYS cc_start: 0.9600 (m) cc_final: 0.9390 (m) REVERT: A 731 THR cc_start: 0.9428 (m) cc_final: 0.9213 (p) REVERT: A 759 GLU cc_start: 0.9357 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 779 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8907 (tpp) REVERT: A 828 MET cc_start: 0.6158 (ppp) cc_final: 0.5528 (ppp) REVERT: A 877 ASP cc_start: 0.9490 (t0) cc_final: 0.9035 (t0) REVERT: A 890 MET cc_start: 0.8993 (mtp) cc_final: 0.7929 (tmm) REVERT: A 899 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8814 (mp0) REVERT: A 918 ASP cc_start: 0.8820 (m-30) cc_final: 0.8591 (m-30) REVERT: A 938 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8048 (pp20) REVERT: A 961 HIS cc_start: 0.8028 (m90) cc_final: 0.7686 (m-70) REVERT: A 997 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7888 (ttt180) REVERT: A 1007 ASP cc_start: 0.8689 (m-30) cc_final: 0.8473 (t0) REVERT: A 1009 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8846 (mmmm) REVERT: A 1048 MET cc_start: 0.9564 (mtp) cc_final: 0.9234 (tpp) REVERT: A 1072 ARG cc_start: 0.6114 (ttp80) cc_final: 0.5521 (tpt90) REVERT: A 1182 TYR cc_start: 0.9493 (t80) cc_final: 0.9286 (t80) REVERT: B 81 ASN cc_start: 0.8613 (p0) cc_final: 0.8391 (t0) REVERT: B 162 GLU cc_start: 0.9373 (tt0) cc_final: 0.8852 (tm-30) REVERT: B 188 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8342 (mm-40) REVERT: B 199 ARG cc_start: 0.8859 (ttt180) cc_final: 0.8190 (ptt-90) REVERT: B 212 ASN cc_start: 0.9465 (t0) cc_final: 0.9169 (t0) REVERT: B 321 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: B 354 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8740 (tt0) REVERT: B 433 GLU cc_start: 0.9039 (mp0) cc_final: 0.8833 (mp0) REVERT: B 449 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: B 451 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8953 (tp30) REVERT: B 522 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.7878 (ttm110) REVERT: C 125 PHE cc_start: 0.8135 (t80) cc_final: 0.7910 (t80) REVERT: C 128 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5494 (tm-30) outliers start: 57 outliers final: 26 residues processed: 272 average time/residue: 0.2717 time to fit residues: 106.7450 Evaluate side-chains 250 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14500 Z= 0.172 Angle : 0.571 11.590 19706 Z= 0.284 Chirality : 0.040 0.203 2209 Planarity : 0.003 0.043 2461 Dihedral : 9.734 86.426 2145 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 3.12 % Allowed : 16.19 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 0.10 (0.20), residues: 1719 helix: 0.37 (0.19), residues: 775 sheet: -0.50 (0.38), residues: 156 loop : 0.07 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 260 HIS 0.008 0.001 HIS A 28 PHE 0.020 0.001 PHE C 121 TYR 0.011 0.001 TYR A1182 ARG 0.010 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8748 (t0) cc_final: 0.8240 (m-30) REVERT: A 156 LEU cc_start: 0.9458 (mt) cc_final: 0.9086 (tt) REVERT: A 237 CYS cc_start: 0.9642 (OUTLIER) cc_final: 0.9399 (t) REVERT: A 350 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9053 (mp0) REVERT: A 361 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9072 (mp) REVERT: A 362 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8551 (mp0) REVERT: A 381 LEU cc_start: 0.9506 (mt) cc_final: 0.9135 (mt) REVERT: A 403 GLU cc_start: 0.9515 (tp30) cc_final: 0.9307 (tp30) REVERT: A 499 LEU cc_start: 0.9732 (OUTLIER) cc_final: 0.9484 (tt) REVERT: A 527 PHE cc_start: 0.8983 (t80) cc_final: 0.8774 (t80) REVERT: A 539 ARG cc_start: 0.2467 (ptt90) cc_final: 0.1842 (ptt-90) REVERT: A 542 LEU cc_start: 0.9387 (tp) cc_final: 0.9077 (tt) REVERT: A 551 MET cc_start: 0.9133 (mmm) cc_final: 0.8491 (mmm) REVERT: A 563 TYR cc_start: 0.9182 (t80) cc_final: 0.8908 (t80) REVERT: A 591 GLU cc_start: 0.9089 (tp30) cc_final: 0.8875 (tp30) REVERT: A 731 THR cc_start: 0.9425 (m) cc_final: 0.9217 (p) REVERT: A 759 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 778 LYS cc_start: 0.9310 (ttpt) cc_final: 0.9095 (ttpp) REVERT: A 779 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8887 (tpp) REVERT: A 828 MET cc_start: 0.5976 (ppp) cc_final: 0.5244 (ppp) REVERT: A 877 ASP cc_start: 0.9501 (t0) cc_final: 0.9066 (t0) REVERT: A 890 MET cc_start: 0.9001 (mtp) cc_final: 0.7874 (tmm) REVERT: A 899 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8841 (mp0) REVERT: A 918 ASP cc_start: 0.8780 (m-30) cc_final: 0.8557 (m-30) REVERT: A 961 HIS cc_start: 0.8017 (m90) cc_final: 0.7701 (m-70) REVERT: A 997 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.7856 (ttt180) REVERT: A 1009 LYS cc_start: 0.9202 (mmtp) cc_final: 0.8951 (mmmm) REVERT: A 1072 ARG cc_start: 0.6066 (ttp80) cc_final: 0.5409 (tpt90) REVERT: A 1125 ARG cc_start: 0.8568 (ptm-80) cc_final: 0.8297 (ptp90) REVERT: A 1182 TYR cc_start: 0.9476 (t80) cc_final: 0.9196 (t80) REVERT: B 56 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9236 (mm) REVERT: B 162 GLU cc_start: 0.9371 (tt0) cc_final: 0.8776 (tm-30) REVERT: B 165 GLN cc_start: 0.9571 (mt0) cc_final: 0.9074 (mp10) REVERT: B 195 ASP cc_start: 0.9251 (t70) cc_final: 0.9019 (t70) REVERT: B 199 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8143 (ptt-90) REVERT: B 212 ASN cc_start: 0.9503 (t0) cc_final: 0.9187 (t0) REVERT: B 321 MET cc_start: 0.8431 (mmm) cc_final: 0.8228 (mmm) REVERT: B 354 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8709 (tt0) REVERT: B 449 MET cc_start: 0.9235 (mtp) cc_final: 0.8789 (mmm) REVERT: B 451 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8957 (tp30) REVERT: B 522 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.7815 (ttm110) REVERT: C 125 PHE cc_start: 0.8095 (t80) cc_final: 0.7782 (t80) REVERT: C 128 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5556 (tm-30) outliers start: 47 outliers final: 25 residues processed: 263 average time/residue: 0.2757 time to fit residues: 104.6795 Evaluate side-chains 245 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 81 ASN B 515 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14500 Z= 0.177 Angle : 0.571 9.849 19706 Z= 0.288 Chirality : 0.040 0.174 2209 Planarity : 0.003 0.048 2461 Dihedral : 9.638 86.094 2145 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 3.58 % Allowed : 16.39 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 0.27 (0.20), residues: 1719 helix: 0.60 (0.19), residues: 765 sheet: -0.65 (0.36), residues: 176 loop : 0.13 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 445 HIS 0.011 0.001 HIS A 28 PHE 0.022 0.001 PHE C 121 TYR 0.024 0.001 TYR A 805 ARG 0.010 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 233 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9477 (mt) cc_final: 0.9029 (tt) REVERT: A 237 CYS cc_start: 0.9637 (OUTLIER) cc_final: 0.9379 (t) REVERT: A 350 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: A 361 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9032 (mp) REVERT: A 362 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8540 (mp0) REVERT: A 381 LEU cc_start: 0.9495 (mt) cc_final: 0.9185 (mt) REVERT: A 403 GLU cc_start: 0.9547 (tp30) cc_final: 0.9311 (tp30) REVERT: A 539 ARG cc_start: 0.2350 (ptt90) cc_final: 0.2075 (ptt90) REVERT: A 542 LEU cc_start: 0.9373 (tp) cc_final: 0.9095 (tt) REVERT: A 551 MET cc_start: 0.9118 (mmm) cc_final: 0.8343 (mmm) REVERT: A 563 TYR cc_start: 0.9200 (t80) cc_final: 0.8922 (t80) REVERT: A 591 GLU cc_start: 0.8989 (tp30) cc_final: 0.8786 (tp30) REVERT: A 731 THR cc_start: 0.9416 (m) cc_final: 0.9207 (p) REVERT: A 759 GLU cc_start: 0.9404 (tm-30) cc_final: 0.8217 (tm-30) REVERT: A 779 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8915 (tpp) REVERT: A 828 MET cc_start: 0.6102 (ppp) cc_final: 0.5340 (ppp) REVERT: A 845 TYR cc_start: 0.9193 (t80) cc_final: 0.8927 (t80) REVERT: A 877 ASP cc_start: 0.9506 (t0) cc_final: 0.9070 (t0) REVERT: A 890 MET cc_start: 0.8994 (mtp) cc_final: 0.8753 (mpp) REVERT: A 899 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8844 (mp0) REVERT: A 918 ASP cc_start: 0.8799 (m-30) cc_final: 0.8578 (m-30) REVERT: A 939 GLN cc_start: 0.9507 (mm-40) cc_final: 0.9051 (tp40) REVERT: A 961 HIS cc_start: 0.8033 (m90) cc_final: 0.7716 (m-70) REVERT: A 997 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7775 (ttt180) REVERT: A 1048 MET cc_start: 0.9549 (mtp) cc_final: 0.9300 (tpp) REVERT: A 1108 ASP cc_start: 0.8482 (m-30) cc_final: 0.8128 (t0) REVERT: A 1125 ARG cc_start: 0.8244 (ptm-80) cc_final: 0.7998 (ptp90) REVERT: A 1147 LEU cc_start: 0.8624 (tp) cc_final: 0.8390 (mt) REVERT: B 7 LEU cc_start: 0.9514 (mt) cc_final: 0.9280 (mt) REVERT: B 56 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9224 (mm) REVERT: B 162 GLU cc_start: 0.9287 (tt0) cc_final: 0.8781 (tm-30) REVERT: B 165 GLN cc_start: 0.9577 (mt0) cc_final: 0.9079 (mp10) REVERT: B 195 ASP cc_start: 0.9300 (t70) cc_final: 0.9099 (t70) REVERT: B 199 ARG cc_start: 0.8804 (ttt180) cc_final: 0.8137 (ptt-90) REVERT: B 212 ASN cc_start: 0.9517 (t0) cc_final: 0.9200 (t0) REVERT: B 321 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8174 (mmm) REVERT: B 354 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8697 (tt0) REVERT: B 433 GLU cc_start: 0.9037 (mp0) cc_final: 0.8820 (mp0) REVERT: B 449 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8642 (mmm) REVERT: B 451 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8963 (tp30) REVERT: B 487 VAL cc_start: 0.9813 (OUTLIER) cc_final: 0.9486 (m) REVERT: B 488 GLU cc_start: 0.9629 (OUTLIER) cc_final: 0.9234 (tt0) REVERT: B 522 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.7862 (ttm110) REVERT: B 532 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.8959 (t70) REVERT: C 125 PHE cc_start: 0.8076 (t80) cc_final: 0.7703 (t80) REVERT: C 128 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5510 (tm-30) outliers start: 54 outliers final: 28 residues processed: 262 average time/residue: 0.2697 time to fit residues: 102.8991 Evaluate side-chains 260 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 164 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN A 617 GLN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14500 Z= 0.166 Angle : 0.564 10.139 19706 Z= 0.284 Chirality : 0.040 0.178 2209 Planarity : 0.003 0.049 2461 Dihedral : 9.546 85.358 2145 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 3.38 % Allowed : 17.78 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 0.32 (0.20), residues: 1719 helix: 0.66 (0.19), residues: 773 sheet: -0.54 (0.37), residues: 174 loop : 0.10 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 445 HIS 0.010 0.001 HIS A 28 PHE 0.043 0.001 PHE A1056 TYR 0.020 0.001 TYR A1182 ARG 0.011 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: A 119 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8831 (tmmt) REVERT: A 156 LEU cc_start: 0.9498 (mt) cc_final: 0.9031 (tt) REVERT: A 202 ILE cc_start: 0.9584 (tp) cc_final: 0.9354 (tp) REVERT: A 237 CYS cc_start: 0.9627 (OUTLIER) cc_final: 0.9363 (t) REVERT: A 350 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.9018 (mp0) REVERT: A 361 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9035 (mp) REVERT: A 362 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8752 (mp0) REVERT: A 381 LEU cc_start: 0.9541 (mt) cc_final: 0.9205 (mt) REVERT: A 403 GLU cc_start: 0.9560 (tp30) cc_final: 0.9312 (tp30) REVERT: A 539 ARG cc_start: 0.2653 (ptt90) cc_final: 0.2386 (ptt90) REVERT: A 542 LEU cc_start: 0.9363 (tp) cc_final: 0.9101 (tt) REVERT: A 551 MET cc_start: 0.9114 (mmm) cc_final: 0.8266 (tmm) REVERT: A 563 TYR cc_start: 0.9206 (t80) cc_final: 0.8919 (t80) REVERT: A 591 GLU cc_start: 0.8960 (tp30) cc_final: 0.8756 (tp30) REVERT: A 731 THR cc_start: 0.9404 (m) cc_final: 0.9186 (p) REVERT: A 758 MET cc_start: 0.9041 (tmm) cc_final: 0.8579 (tmm) REVERT: A 759 GLU cc_start: 0.9407 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 779 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8915 (tpp) REVERT: A 828 MET cc_start: 0.6037 (ppp) cc_final: 0.5155 (ppp) REVERT: A 845 TYR cc_start: 0.9157 (t80) cc_final: 0.8906 (t80) REVERT: A 877 ASP cc_start: 0.9509 (t0) cc_final: 0.8958 (t0) REVERT: A 890 MET cc_start: 0.9044 (mtp) cc_final: 0.7792 (tmm) REVERT: A 899 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8917 (mm-30) REVERT: A 961 HIS cc_start: 0.7911 (m90) cc_final: 0.7627 (m-70) REVERT: A 997 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7820 (ttt180) REVERT: A 1048 MET cc_start: 0.9568 (mtp) cc_final: 0.9304 (tpp) REVERT: A 1108 ASP cc_start: 0.8468 (m-30) cc_final: 0.8139 (t0) REVERT: B 56 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9206 (mm) REVERT: B 162 GLU cc_start: 0.9286 (tt0) cc_final: 0.8799 (tm-30) REVERT: B 165 GLN cc_start: 0.9582 (mt0) cc_final: 0.9078 (mp10) REVERT: B 212 ASN cc_start: 0.9506 (t0) cc_final: 0.9205 (t0) REVERT: B 276 ARG cc_start: 0.9312 (ptt180) cc_final: 0.9064 (ptt90) REVERT: B 321 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: B 354 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8740 (tt0) REVERT: B 368 GLU cc_start: 0.9667 (mt-10) cc_final: 0.9276 (mp0) REVERT: B 433 GLU cc_start: 0.9037 (mp0) cc_final: 0.8812 (mp0) REVERT: B 449 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8590 (mmm) REVERT: B 451 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8963 (tp30) REVERT: B 488 GLU cc_start: 0.9642 (OUTLIER) cc_final: 0.9289 (tt0) REVERT: B 522 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.7757 (ttm110) REVERT: B 532 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.8991 (t70) REVERT: C 125 PHE cc_start: 0.8080 (t80) cc_final: 0.7667 (t80) REVERT: C 128 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5495 (tm-30) REVERT: D 121 PHE cc_start: 0.7130 (t80) cc_final: 0.6868 (t80) outliers start: 51 outliers final: 29 residues processed: 258 average time/residue: 0.2602 time to fit residues: 99.1262 Evaluate side-chains 256 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14500 Z= 0.216 Angle : 0.590 10.244 19706 Z= 0.297 Chirality : 0.041 0.176 2209 Planarity : 0.004 0.062 2461 Dihedral : 9.503 85.253 2143 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 3.25 % Allowed : 18.25 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 1719 helix: 0.65 (0.19), residues: 780 sheet: -0.51 (0.37), residues: 174 loop : 0.07 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.012 0.001 HIS A 28 PHE 0.020 0.001 PHE C 121 TYR 0.025 0.001 TYR A 805 ARG 0.012 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8881 (tp30) REVERT: A 91 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: A 156 LEU cc_start: 0.9539 (mt) cc_final: 0.9077 (tt) REVERT: A 180 GLU cc_start: 0.9083 (tt0) cc_final: 0.8714 (tm-30) REVERT: A 202 ILE cc_start: 0.9642 (tp) cc_final: 0.9412 (tp) REVERT: A 350 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8978 (mp0) REVERT: A 361 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9059 (mp) REVERT: A 362 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8729 (mp0) REVERT: A 381 LEU cc_start: 0.9533 (mt) cc_final: 0.9281 (mt) REVERT: A 468 LYS cc_start: 0.9561 (tppt) cc_final: 0.9271 (tptp) REVERT: A 502 MET cc_start: 0.9307 (tpp) cc_final: 0.8474 (tmm) REVERT: A 539 ARG cc_start: 0.2553 (ptt90) cc_final: 0.2237 (ptt90) REVERT: A 542 LEU cc_start: 0.9350 (tp) cc_final: 0.9101 (tt) REVERT: A 551 MET cc_start: 0.9145 (mmm) cc_final: 0.8719 (mmm) REVERT: A 563 TYR cc_start: 0.9239 (t80) cc_final: 0.8915 (t80) REVERT: A 625 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8763 (tp30) REVERT: A 758 MET cc_start: 0.9028 (tmm) cc_final: 0.8578 (tmm) REVERT: A 759 GLU cc_start: 0.9444 (tm-30) cc_final: 0.8417 (tm-30) REVERT: A 779 MET cc_start: 0.9156 (tpp) cc_final: 0.8790 (tpp) REVERT: A 828 MET cc_start: 0.6096 (ppp) cc_final: 0.5061 (ppp) REVERT: A 845 TYR cc_start: 0.9195 (t80) cc_final: 0.8938 (t80) REVERT: A 877 ASP cc_start: 0.9527 (t0) cc_final: 0.8983 (t0) REVERT: A 890 MET cc_start: 0.8986 (mtp) cc_final: 0.7755 (tmm) REVERT: A 899 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8867 (mp0) REVERT: A 961 HIS cc_start: 0.7970 (m90) cc_final: 0.7719 (m-70) REVERT: A 1041 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8556 (p90) REVERT: A 1048 MET cc_start: 0.9581 (mtp) cc_final: 0.9307 (tpp) REVERT: A 1108 ASP cc_start: 0.8476 (m-30) cc_final: 0.8155 (t0) REVERT: A 1125 ARG cc_start: 0.8578 (ptm-80) cc_final: 0.8254 (ptp90) REVERT: B 56 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9256 (mm) REVERT: B 162 GLU cc_start: 0.9270 (tt0) cc_final: 0.8852 (tm-30) REVERT: B 199 ARG cc_start: 0.8756 (ttt180) cc_final: 0.8084 (ptt-90) REVERT: B 212 ASN cc_start: 0.9510 (t0) cc_final: 0.9218 (t0) REVERT: B 276 ARG cc_start: 0.9321 (ptt180) cc_final: 0.9071 (ptt90) REVERT: B 321 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: B 354 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8776 (tt0) REVERT: B 368 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9271 (mp0) REVERT: B 433 GLU cc_start: 0.9029 (mp0) cc_final: 0.8794 (mp0) REVERT: B 449 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8589 (mmm) REVERT: B 451 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8939 (tp30) REVERT: B 488 GLU cc_start: 0.9640 (OUTLIER) cc_final: 0.9290 (tt0) REVERT: B 522 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.7754 (ttm110) REVERT: B 532 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.9037 (t70) REVERT: C 125 PHE cc_start: 0.8251 (t80) cc_final: 0.7804 (t80) REVERT: C 128 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: D 121 PHE cc_start: 0.7222 (t80) cc_final: 0.6936 (t80) outliers start: 49 outliers final: 34 residues processed: 246 average time/residue: 0.2636 time to fit residues: 94.8989 Evaluate side-chains 253 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14500 Z= 0.197 Angle : 0.590 11.117 19706 Z= 0.295 Chirality : 0.040 0.177 2209 Planarity : 0.004 0.063 2461 Dihedral : 9.471 85.078 2143 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.38 % Allowed : 18.31 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 1719 helix: 0.66 (0.19), residues: 784 sheet: -0.40 (0.38), residues: 174 loop : 0.13 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.011 0.001 HIS A 28 PHE 0.017 0.001 PHE C 121 TYR 0.020 0.001 TYR A1182 ARG 0.013 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 1.703 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: A 27 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8889 (tp30) REVERT: A 91 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: A 119 LYS cc_start: 0.9257 (mmtt) cc_final: 0.8978 (tmmt) REVERT: A 156 LEU cc_start: 0.9541 (mt) cc_final: 0.9080 (tt) REVERT: A 180 GLU cc_start: 0.9058 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 202 ILE cc_start: 0.9629 (tp) cc_final: 0.9381 (tp) REVERT: A 350 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8962 (mp0) REVERT: A 361 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9026 (mp) REVERT: A 362 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8728 (mp0) REVERT: A 381 LEU cc_start: 0.9548 (mt) cc_final: 0.9283 (mt) REVERT: A 468 LYS cc_start: 0.9572 (tppt) cc_final: 0.9293 (tptp) REVERT: A 502 MET cc_start: 0.9313 (tpp) cc_final: 0.8487 (tmm) REVERT: A 539 ARG cc_start: 0.2334 (ptt90) cc_final: 0.2042 (ptt90) REVERT: A 542 LEU cc_start: 0.9278 (tp) cc_final: 0.9037 (tt) REVERT: A 563 TYR cc_start: 0.9235 (t80) cc_final: 0.8908 (t80) REVERT: A 625 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8769 (tp30) REVERT: A 758 MET cc_start: 0.8977 (tmm) cc_final: 0.8541 (tmm) REVERT: A 779 MET cc_start: 0.9154 (tpp) cc_final: 0.8790 (tpp) REVERT: A 828 MET cc_start: 0.6098 (ppp) cc_final: 0.5050 (ppp) REVERT: A 845 TYR cc_start: 0.9188 (t80) cc_final: 0.8928 (t80) REVERT: A 877 ASP cc_start: 0.9527 (t0) cc_final: 0.8980 (t0) REVERT: A 890 MET cc_start: 0.9071 (mtp) cc_final: 0.8716 (mpp) REVERT: A 899 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8948 (mm-30) REVERT: A 961 HIS cc_start: 0.8015 (m90) cc_final: 0.7773 (m-70) REVERT: A 997 ARG cc_start: 0.8226 (mmt180) cc_final: 0.7449 (ttt180) REVERT: A 1041 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8570 (p90) REVERT: A 1043 SER cc_start: 0.9335 (p) cc_final: 0.9048 (t) REVERT: A 1048 MET cc_start: 0.9568 (mtp) cc_final: 0.9197 (tpp) REVERT: A 1108 ASP cc_start: 0.8473 (m-30) cc_final: 0.8152 (t0) REVERT: A 1125 ARG cc_start: 0.8452 (ptm-80) cc_final: 0.8140 (ptp90) REVERT: B 56 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9212 (mm) REVERT: B 162 GLU cc_start: 0.9270 (tt0) cc_final: 0.8850 (tm-30) REVERT: B 199 ARG cc_start: 0.8736 (ttt180) cc_final: 0.8076 (ptt-90) REVERT: B 212 ASN cc_start: 0.9505 (t0) cc_final: 0.9219 (t0) REVERT: B 276 ARG cc_start: 0.9317 (ptt180) cc_final: 0.9066 (ptt90) REVERT: B 321 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: B 368 GLU cc_start: 0.9665 (mt-10) cc_final: 0.9270 (mp0) REVERT: B 433 GLU cc_start: 0.9033 (mp0) cc_final: 0.8791 (mp0) REVERT: B 449 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8602 (mmm) REVERT: B 522 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.7758 (ttm110) REVERT: B 532 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.9038 (t70) REVERT: C 125 PHE cc_start: 0.8226 (t80) cc_final: 0.7770 (t80) REVERT: C 128 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5441 (tm-30) REVERT: D 121 PHE cc_start: 0.7572 (t80) cc_final: 0.7352 (t80) outliers start: 51 outliers final: 35 residues processed: 245 average time/residue: 0.2840 time to fit residues: 103.5252 Evaluate side-chains 250 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14500 Z= 0.182 Angle : 0.595 11.340 19706 Z= 0.295 Chirality : 0.040 0.178 2209 Planarity : 0.003 0.065 2461 Dihedral : 9.429 84.918 2143 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 3.12 % Allowed : 18.98 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 0.40 (0.20), residues: 1719 helix: 0.68 (0.19), residues: 784 sheet: -0.34 (0.38), residues: 174 loop : 0.16 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.012 0.001 HIS A 28 PHE 0.016 0.001 PHE C 121 TYR 0.026 0.001 TYR A 805 ARG 0.014 0.000 ARG B 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 207 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8928 (tp30) REVERT: A 91 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: A 156 LEU cc_start: 0.9518 (mt) cc_final: 0.9048 (tt) REVERT: A 180 GLU cc_start: 0.8973 (tt0) cc_final: 0.8587 (tm-30) REVERT: A 202 ILE cc_start: 0.9603 (tp) cc_final: 0.9340 (tp) REVERT: A 266 GLN cc_start: 0.9110 (pp30) cc_final: 0.8856 (pp30) REVERT: A 350 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8982 (mp0) REVERT: A 361 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9034 (mp) REVERT: A 362 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8748 (mp0) REVERT: A 381 LEU cc_start: 0.9543 (mt) cc_final: 0.9277 (mt) REVERT: A 468 LYS cc_start: 0.9563 (tppt) cc_final: 0.9293 (tptp) REVERT: A 502 MET cc_start: 0.9406 (tpp) cc_final: 0.8457 (tmm) REVERT: A 539 ARG cc_start: 0.1876 (ptt90) cc_final: 0.1624 (ptt90) REVERT: A 542 LEU cc_start: 0.9275 (tp) cc_final: 0.9054 (tt) REVERT: A 563 TYR cc_start: 0.9221 (t80) cc_final: 0.8885 (t80) REVERT: A 758 MET cc_start: 0.8963 (tmm) cc_final: 0.8533 (tmm) REVERT: A 779 MET cc_start: 0.9163 (tpp) cc_final: 0.8799 (tpp) REVERT: A 828 MET cc_start: 0.6118 (ppp) cc_final: 0.5070 (ppp) REVERT: A 845 TYR cc_start: 0.9171 (t80) cc_final: 0.8915 (t80) REVERT: A 877 ASP cc_start: 0.9526 (t0) cc_final: 0.8978 (t0) REVERT: A 884 MET cc_start: 0.9511 (mtp) cc_final: 0.9204 (ttt) REVERT: A 899 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8943 (mm-30) REVERT: A 961 HIS cc_start: 0.8011 (m90) cc_final: 0.7771 (m-70) REVERT: A 997 ARG cc_start: 0.8254 (mmt180) cc_final: 0.7484 (ttt180) REVERT: A 1041 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8460 (p90) REVERT: A 1043 SER cc_start: 0.9321 (p) cc_final: 0.9036 (t) REVERT: A 1048 MET cc_start: 0.9564 (mtp) cc_final: 0.9186 (tpp) REVERT: A 1108 ASP cc_start: 0.8472 (m-30) cc_final: 0.8157 (t0) REVERT: A 1125 ARG cc_start: 0.8458 (ptm-80) cc_final: 0.8139 (ptp90) REVERT: B 56 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9211 (mm) REVERT: B 162 GLU cc_start: 0.9268 (tt0) cc_final: 0.8849 (tm-30) REVERT: B 212 ASN cc_start: 0.9509 (t0) cc_final: 0.9238 (t0) REVERT: B 276 ARG cc_start: 0.9313 (ptt180) cc_final: 0.9063 (ptt90) REVERT: B 321 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7946 (mmm) REVERT: B 368 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9303 (mp0) REVERT: B 433 GLU cc_start: 0.9023 (mp0) cc_final: 0.8782 (mp0) REVERT: B 449 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8609 (mmm) REVERT: B 488 GLU cc_start: 0.9649 (tt0) cc_final: 0.9194 (tt0) REVERT: B 522 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.7926 (ttm110) REVERT: B 532 ASP cc_start: 0.9340 (OUTLIER) cc_final: 0.9035 (t70) REVERT: C 125 PHE cc_start: 0.8210 (t80) cc_final: 0.7752 (t80) REVERT: C 128 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5405 (tm-30) REVERT: D 121 PHE cc_start: 0.7558 (t80) cc_final: 0.7325 (t80) outliers start: 47 outliers final: 35 residues processed: 237 average time/residue: 0.2686 time to fit residues: 93.5709 Evaluate side-chains 253 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 119 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085347 restraints weight = 33961.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088106 restraints weight = 18216.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089834 restraints weight = 11858.314| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14500 Z= 0.161 Angle : 0.597 11.843 19706 Z= 0.294 Chirality : 0.040 0.178 2209 Planarity : 0.003 0.064 2461 Dihedral : 9.373 84.398 2143 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 2.99 % Allowed : 19.44 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: 0.46 (0.20), residues: 1719 helix: 0.74 (0.19), residues: 788 sheet: -0.29 (0.39), residues: 172 loop : 0.17 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 445 HIS 0.013 0.001 HIS A 28 PHE 0.015 0.001 PHE C 121 TYR 0.024 0.001 TYR A1182 ARG 0.014 0.000 ARG B 252 =============================================================================== Job complete usr+sys time: 3037.13 seconds wall clock time: 55 minutes 16.19 seconds (3316.19 seconds total)